Reverse metabolomics for the discovery of chemical structures from humans

Emily C Gentry; Stephanie L Collins; Morgan Panitchpakdi; Pedro Belda-Ferre; Allison K Stewart; Marvic Carrillo Terrazas; Hsueh-Han Lu; Simone Zuffa; Tingting Yan; Julian Avila-Pacheco; Damian R Plichta; Allegra T Aron; Mingxun Wang; Alan K Jarmusch; Fuhua Hao; Mashette Syrkin-Nikolau; Hera Vlamakis; Ashwin N Ananthakrishnan; Brigid S Boland; Amy Hemperly; Niels Vande Casteele; Frank J Gonzalez; Clary B Clish; Ramnik J Xavier; Hiutung Chu; Erin S Baker; Andrew D Patterson; Rob Knight; Dionicio Siegel; Pieter C Dorrestein

doi:10.1038/s41586-023-06906-8

Reverse metabolomics for the discovery of chemical structures from humans

Nature. 2024 Feb;626(7998):419-426. doi: 10.1038/s41586-023-06906-8. Epub 2023 Dec 5.

Authors

Emily C Gentry^{1

2

3}, Stephanie L Collins⁴, Morgan Panitchpakdi^{1

2}, Pedro Belda-Ferre^{5

6}, Allison K Stewart⁷, Marvic Carrillo Terrazas⁸, Hsueh-Han Lu⁸, Simone Zuffa^{1

2}, Tingting Yan⁹, Julian Avila-Pacheco¹⁰, Damian R Plichta¹⁰, Allegra T Aron^{1

2}, Mingxun Wang^{1

2}, Alan K Jarmusch^{1

2

11}, Fuhua Hao¹², Mashette Syrkin-Nikolau¹³, Hera Vlamakis^{10

14}, Ashwin N Ananthakrishnan¹⁵, Brigid S Boland¹⁶, Amy Hemperly¹³, Niels Vande Casteele¹⁶, Frank J Gonzalez⁹, Clary B Clish¹⁰, Ramnik J Xavier^{10

14

17

18}, Hiutung Chu^{8

19}, Erin S Baker^{7

20}, Andrew D Patterson¹², Rob Knight^{5

6

21

22}, Dionicio Siegel¹, Pieter C Dorrestein^{23

24}

Affiliations

¹ Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, USA.
² Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, USA.
³ Department of Chemistry, Virginia Tech, Blacksburg, VA, USA.
⁴ Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA, USA.
⁵ Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA.
⁶ Department of Computer Science and Engineering, Jacobs School of Engineering, University of California, San Diego, San Diego, CA, USA.
⁷ Department of Chemistry, North Carolina State University, Raleigh, NC, USA.
⁸ Department of Pathology, University of California, San Diego, La Jolla, CA, USA.
⁹ Laboratory of Metabolism, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA.
¹⁰ Broad Institute of MIT and Harvard, Cambridge, MA, USA.
¹¹ Immunity, Inflammation, and Disease Laboratory, Division of Intramural Research, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC, USA.
¹² Center for Molecular Toxicology and Carcinogenesis, Department of Veterinary and Biomedical Sciences, The Pennsylvania State University, University Park, PA, USA.
¹³ Division of Gastroenterology, Department of Pediatrics, Rady Children's Hospital University of California San Diego, La Jolla, CA, USA.
¹⁴ Center for Microbiome Informatics and Therapeutics, Massachusetts Institute of Technology, Cambridge, MA, USA.
¹⁵ Division of Gastroenterology, Massachusetts General Hospital, Boston, MA, USA.
¹⁶ Division of Gastroenterology, University of California, San Diego, La Jolla, CA, USA.
¹⁷ Center for Computational and Integrative Biology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA.
¹⁸ Department of Molecular Biology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA.
¹⁹ CU-UCSD, Center for Mucosal Immunology, Allergy and Vaccine Development, University of California, San Diego, La Jolla, California, USA.
²⁰ Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
²¹ Center for Microbiome Innovation, Jacobs School of Engineering, University of California, San Diego, San Diego, CA, USA.
²² Department of Bioengineering, University of California, San Diego, San Diego, California, USA.
²³ Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, USA. pdorrestein@health.ucsd.edu.
²⁴ Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, USA. pdorrestein@health.ucsd.edu.

Abstract

Determining the structure and phenotypic context of molecules detected in untargeted metabolomics experiments remains challenging. Here we present reverse metabolomics as a discovery strategy, whereby tandem mass spectrometry spectra acquired from newly synthesized compounds are searched for in public metabolomics datasets to uncover phenotypic associations. To demonstrate the concept, we broadly synthesized and explored multiple classes of metabolites in humans, including N-acyl amides, fatty acid esters of hydroxy fatty acids, bile acid esters and conjugated bile acids. Using repository-scale analysis^1,2, we discovered that some conjugated bile acids are associated with inflammatory bowel disease (IBD). Validation using four distinct human IBD cohorts showed that cholic acids conjugated to Glu, Ile/Leu, Phe, Thr, Trp or Tyr are increased in Crohn's disease. Several of these compounds and related structures affected pathways associated with IBD, such as interferon-γ production in CD4⁺ T cells³ and agonism of the pregnane X receptor⁴. Culture of bacteria belonging to the Bifidobacterium, Clostridium and Enterococcus genera produced these bile amidates. Because searching repositories with tandem mass spectrometry spectra has only recently become possible, this reverse metabolomics approach can now be used as a general strategy to discover other molecules from human and animal ecosystems.

MeSH terms

Amides* / chemistry
Amides* / metabolism
Animals
Bifidobacterium / metabolism
Bile Acids and Salts* / chemistry
Bile Acids and Salts* / metabolism
CD4-Positive T-Lymphocytes / immunology
CD4-Positive T-Lymphocytes / metabolism
Clostridium / metabolism
Cohort Studies
Crohn Disease / metabolism
Enterococcus / metabolism
Esters* / chemistry
Esters* / metabolism
Fatty Acids* / chemistry
Fatty Acids* / metabolism
Humans
Inflammatory Bowel Diseases / metabolism
Metabolomics* / methods
Phenotype
Pregnane X Receptor / metabolism
Reproducibility of Results
Tandem Mass Spectrometry

Substances

Bile Acids and Salts
Esters
Fatty Acids
IFNG protein, human
Pregnane X Receptor
Amides

Abstract

MeSH terms

Substances

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