Gut microbe-targeted choline trimethylamine lyase inhibition improves obesity via rewiring of host circadian rhythms

  1. Rebecca C Schugar
  2. Christy M Gliniak
  3. Lucas J Osborn
  4. William Massey
  5. Naseer Sangwan
  6. Anthony Horak
  7. Rakhee Banerjee
  8. Danny Orabi
  9. Robert N Helsley
  10. Amanda L Brown
  11. Amy Burrows
  12. Chelsea Finney
  13. Kevin K Fung
  14. Frederick M Allen
  15. Daniel Ferguson
  16. Anthony D Gromovsky
  17. Chase Neumann
  18. Kendall Cook
  19. Amy McMillan
  20. Jennifer A Buffa
  21. James T Anderson
  22. Margarete Mehrabian
  23. Maryam Goudarzi
  24. Belinda Willard
  25. Tytus D Mak
  26. Andrew R Armstrong
  27. Garth Swanson
  28. Ali Keshavarzian
  29. Jose Carlos Garcia-Garcia
  30. Zeneng Wang
  31. Aldons J Lusis
  32. Stanley L Hazen
  33. Jonathan Mark Brown  Is a corresponding author
  1. Cleveland Clinic Lerner College of Medicine, United States
  2. University of Texas Southwestern Medical Center, United States
  3. University of California, Los Angeles, United States
  4. National Institute of Standards and Technology (NIST), United States
  5. Rush University Medical Center, United States
  6. Procter and Gamble, United States

Abstract

Obesity has repeatedly been linked to reorganization of the gut microbiome, yet to this point obesity therapeutics have been targeted exclusively toward the human host. Here we show that gut microbe-targeted inhibition of the trimethylamine N-oxide (TMAO) pathway protects mice against the metabolic disturbances associated with diet-induced obesity (DIO) or leptin deficiency (Lepob/ob). Small molecule inhibition of the gut microbial enzyme choline TMA-lyase (CutC) does not reduce food intake but is instead associated with alterations in the gut microbiome, improvement in glucose tolerance, and enhanced energy expenditure. We also show that gut microbial CutC inhibition is associated with reorganization of host circadian control of both phosphatidylcholine and energy metabolism. This study underscores the relationship between microbe and host metabolism and provides evidence that gut microbe-derived trimethylamine (TMA) is a key regulator of the host circadian clock. This work also demonstrates that gut microbe-targeted enzyme inhibitors have potential as anti-obesity therapeutics.

Data availability

RNA sequencing data has been deposited in GEO under accession code GSE157925Microbiome data were submitted to the European Nucleotide Archive under accession code PRJEB48232

Article and author information

Author details

  1. Rebecca C Schugar

    Department of Cardiovascular and Metabolic Sciences, Cleveland Clinic Lerner College of Medicine, Cleveland, United States
    Competing interests
    No competing interests declared.
  2. Christy M Gliniak

    Internal Medicine, University of Texas Southwestern Medical Center, Dallas, United States
    Competing interests
    No competing interests declared.
  3. Lucas J Osborn

    Department of Cardiovascular and Metabolic Sciences, Cleveland Clinic Lerner College of Medicine, Cleveland, United States
    Competing interests
    No competing interests declared.
  4. William Massey

    Department of Cardiovascular and Metabolic Sciences, Cleveland Clinic Lerner College of Medicine, Cleveland, United States
    Competing interests
    No competing interests declared.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-2087-6048
  5. Naseer Sangwan

    Department of Cardiovascular and Metabolic Sciences, Cleveland Clinic Lerner College of Medicine, Cleveland, United States
    Competing interests
    No competing interests declared.
  6. Anthony Horak

    Department of Cardiovascular and Metabolic Sciences, Cleveland Clinic Lerner College of Medicine, Cleveland, United States
    Competing interests
    No competing interests declared.
  7. Rakhee Banerjee

    Department of Cardiovascular and Metabolic Sciences, Cleveland Clinic Lerner College of Medicine, Cleveland, United States
    Competing interests
    No competing interests declared.
  8. Danny Orabi

    Department of Cardiovascular and Metabolic Sciences, Cleveland Clinic Lerner College of Medicine, Cleveland, United States
    Competing interests
    No competing interests declared.
  9. Robert N Helsley

    Department of Cardiovascular and Metabolic Sciences, Cleveland Clinic Lerner College of Medicine, Cleveland, United States
    Competing interests
    No competing interests declared.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0001-5000-3187
  10. Amanda L Brown

    Department of Cardiovascular and Metabolic Sciences, Cleveland Clinic Lerner College of Medicine, Cleveland, United States
    Competing interests
    No competing interests declared.
  11. Amy Burrows

    Department of Cardiovascular and Metabolic Sciences, Cleveland Clinic Lerner College of Medicine, Cleveland, United States
    Competing interests
    No competing interests declared.
  12. Chelsea Finney

    Department of Cardiovascular and Metabolic Sciences, Cleveland Clinic Lerner College of Medicine, Cleveland, United States
    Competing interests
    No competing interests declared.
  13. Kevin K Fung

    Department of Cardiovascular and Metabolic Sciences, Cleveland Clinic Lerner College of Medicine, Cleveland, United States
    Competing interests
    No competing interests declared.
  14. Frederick M Allen

    Department of Cardiovascular and Metabolic Sciences, Cleveland Clinic Lerner College of Medicine, Cleveland, United States
    Competing interests
    No competing interests declared.
  15. Daniel Ferguson

    Department of Cardiovascular and Metabolic Sciences, Cleveland Clinic Lerner College of Medicine, Cleveland, United States
    Competing interests
    No competing interests declared.
  16. Anthony D Gromovsky

    Department of Cardiovascular and Metabolic Sciences, Cleveland Clinic Lerner College of Medicine, Cleveland, United States
    Competing interests
    No competing interests declared.
  17. Chase Neumann

    Department of Cardiovascular and Metabolic Sciences, Cleveland Clinic Lerner College of Medicine, Cleveland, United States
    Competing interests
    No competing interests declared.
  18. Kendall Cook

    Department of Cardiovascular and Metabolic Sciences, Cleveland Clinic Lerner College of Medicine, Cleveland, United States
    Competing interests
    No competing interests declared.
  19. Amy McMillan

    Department of Cardiovascular and Metabolic Sciences, Cleveland Clinic Lerner College of Medicine, Cleveland, United States
    Competing interests
    No competing interests declared.
  20. Jennifer A Buffa

    Department of Cardiovascular and Metabolic Sciences, Cleveland Clinic Lerner College of Medicine, Cleveland, United States
    Competing interests
    Jennifer A Buffa, reports being eligible to receive royalty payments for inventions or discoveries related to cardiovascular therapeutics from the Proctor & Gamble Co..
  21. James T Anderson

    Department of Cardiovascular and Metabolic Sciences, Cleveland Clinic Lerner College of Medicine, Cleveland, United States
    Competing interests
    No competing interests declared.
  22. Margarete Mehrabian

    Department of Medicine, University of California, Los Angeles, Los Angeles, United States
    Competing interests
    No competing interests declared.
  23. Maryam Goudarzi

    Department of Cardiovascular and Metabolic Sciences, Cleveland Clinic Lerner College of Medicine, Cleveland, United States
    Competing interests
    No competing interests declared.
  24. Belinda Willard

    Research Core Services, Cleveland Clinic Lerner College of Medicine, Cleveland, United States
    Competing interests
    No competing interests declared.
  25. Tytus D Mak

    Mass Spectromety Data Center, National Institute of Standards and Technology (NIST), Gaithersburg, United States
    Competing interests
    No competing interests declared.
  26. Andrew R Armstrong

    Department of Internal Medicine, Rush University Medical Center, Chicago, United States
    Competing interests
    No competing interests declared.
  27. Garth Swanson

    Department of Internal Medicine, Rush University Medical Center, Chicago, United States
    Competing interests
    No competing interests declared.
  28. Ali Keshavarzian

    Department of Internal Medicine, Rush University Medical Center, Chicago, United States
    Competing interests
    No competing interests declared.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-7969-3369
  29. Jose Carlos Garcia-Garcia

    Life Sciences Transformative Platform Technologies, Procter and Gamble, Cincinatti, United States
    Competing interests
    Jose Carlos Garcia-Garcia, Employee of Procter & Gamble Company.
  30. Zeneng Wang

    Department of Cardiovascular and Metabolic Sciences, Cleveland Clinic Lerner College of Medicine, Cleveland, United States
    Competing interests
    Zeneng Wang, reports being named as co-inventor on pending and issued patents 20200121615 held by the Cleveland Clinic relating to cardiovascular diagnostics and therapeutics.Reports being a paid consultant for Procter & Gamble, having received research funds from Procter & Gamble, Roche Diagnostics, and being eligible to receive royalty payments for inventions or discoveries related to cardiovascular diagnostics or therapeutics from Cleveland Heart Lab and Procter & Gamble..
  31. Aldons J Lusis

    Department of Medicine, University of California, Los Angeles, Los Angeles, United States
    Competing interests
    No competing interests declared.
  32. Stanley L Hazen

    Department of Cellular and Molecular Medicine, Cleveland Clinic Lerner College of Medicine, Cleveland, United States
    Competing interests
    Stanley L Hazen, reports being named as co-inventor on pending and issued patents 20200121615 held by the Cleveland Clinic relating to cardiovascular diagnostics and therapeutics.Reports being a paid consultant for Procter & Gamble, having received research funds from Procter & Gamble, Roche Diagnostics, and being eligible to receive royalty payments for inventions or discoveries related to cardiovascular diagnostics or therapeutics from Cleveland Heart Lab and Procter & Gamble..
  33. Jonathan Mark Brown

    Department of Cardiovascular and Metabolic Sciences, Cleveland Clinic Lerner College of Medicine, Cleveland, United States
    For correspondence
    brownm5@ccf.org
    Competing interests
    No competing interests declared.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0003-2708-7487

Funding

National Institute of Diabetes and Digestive and Kidney Diseases (R01 DK120679)

  • Jonathan Mark Brown

National Heart, Lung, and Blood Institute (R01 HL130819)

  • Zeneng Wang

National Institute of Diabetes and Digestive and Kidney Diseases (F32 DK122623)

  • Christy M Gliniak

National Institute of Diabetes and Digestive and Kidney Diseases (T32 DK007307)

  • Christy M Gliniak

Leducq Transatlantic Network of Excellence awar (No grant number)

  • Stanley L Hazen

American Heart Association (17POST3285000)

  • Robert N Helsley

American Heart Association (15POST2535000)

  • Rebecca C Schugar

Clinical and Translational Science Collaborative of Cleveland, School of Medicine, Case Western Reserve University (4UL1TR000439)

  • Belinda Willard

Case Comprehensive Cancer Center, Case Western Reserve University (P30 CA043703)

  • Jonathan Mark Brown

National Heart, Lung, and Blood Institute (P01 HL146823)

  • Stanley L Hazen

National Institute on Alcohol Abuse and Alcoholism (P50 AA024333)

  • Jonathan Mark Brown

National Institute on Alcohol Abuse and Alcoholism (U01 AA026938)

  • Jonathan Mark Brown

National Institute of Diabetes and Digestive and Kidney Diseases (R01 DK130227)

  • Jonathan Mark Brown

National Cancer Institute (P50 CA150964)

  • Jonathan Mark Brown

National Heart, Lung, and Blood Institute (R01 HL103866)

  • Stanley L Hazen

National Heart, Lung, and Blood Institute (R01 HL147883)

  • Aldons J Lusis

National Heart, Lung, and Blood Institute (R01 HL144651)

  • Aldons J Lusis

The funders had no role in study design, data collection and interpretation, or the decision to submit the work for publication.

Ethics

Animal experimentation: All mice were maintained in an Association for the Assessment and Accreditation of Laboratory Animal Care, International-approved animal facility, and all experimental protocols were approved by the Institutional Animal Care and use Committee of the Cleveland Clinic. (Approved IACUC protocol numbers 2015-1381, 2018-1941, and 00002499).

Reviewing Editor

  1. Peter J Turnbaugh, University of California, San Francisco, United States

Publication history

  1. Received: October 13, 2020
  2. Preprint posted: December 6, 2020 (view preprint)
  3. Accepted: January 20, 2022
  4. Accepted Manuscript published: January 24, 2022 (version 1)
  5. Version of Record published: February 3, 2022 (version 2)

Copyright

© 2022, Schugar et al.

This article is distributed under the terms of the Creative Commons Attribution License permitting unrestricted use and redistribution provided that the original author and source are credited.

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  1. Rebecca C Schugar
  2. Christy M Gliniak
  3. Lucas J Osborn
  4. William Massey
  5. Naseer Sangwan
  6. Anthony Horak
  7. Rakhee Banerjee
  8. Danny Orabi
  9. Robert N Helsley
  10. Amanda L Brown
  11. Amy Burrows
  12. Chelsea Finney
  13. Kevin K Fung
  14. Frederick M Allen
  15. Daniel Ferguson
  16. Anthony D Gromovsky
  17. Chase Neumann
  18. Kendall Cook
  19. Amy McMillan
  20. Jennifer A Buffa
  21. James T Anderson
  22. Margarete Mehrabian
  23. Maryam Goudarzi
  24. Belinda Willard
  25. Tytus D Mak
  26. Andrew R Armstrong
  27. Garth Swanson
  28. Ali Keshavarzian
  29. Jose Carlos Garcia-Garcia
  30. Zeneng Wang
  31. Aldons J Lusis
  32. Stanley L Hazen
  33. Jonathan Mark Brown
(2022)
Gut microbe-targeted choline trimethylamine lyase inhibition improves obesity via rewiring of host circadian rhythms
eLife 11:e63998.
https://doi.org/10.7554/eLife.63998

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    MicroRNAs (miRNA) and other components contained in extracellular vesicles may reflect the presence of a disease. Lung tissue, sputum, and sera of individuals with idiopathic pulmonary fibrosis (IPF) show alterations in miRNA expression. We designed this study to test whether urine and/or tissue derived exosomal miRNAs from individuals with IPF carry cargo that can promote fibrosis.

    Methods:

    Exosomes were isolated from urine (U-IPFexo), lung tissue myofibroblasts (MF-IPFexo), serum from individuals with IPF (n=16) and age/sex-matched controls without lung disease (n=10). We analyzed microRNA expression of isolated exosomes and their in vivo bio-distribution. We investigated the effect on ex vivo skin wound healing and in in vivo mouse lung models.

    Results:

    U-IPFexo or MF-IPFexo expressed miR-let-7d, miR-29a-5p, miR-181b-3p and miR-199a-3p consistent with previous reports of miRNA expression obtained from lung tissue/sera from patients with IPF. In vivo bio-distribution experiments detected bioluminescent exosomes in the lung of normal C57Bl6 mice within 5 min after intravenous infusion, followed by distribution to other organs irrespective of exosome source. Exosomes labeled with gold nanoparticles and imaged by transmission electron microscopy were visualized in alveolar epithelial type I and type II cells. Treatment of human and mouse lung punches obtained from control, non-fibrotic lungs with either U-IPFexo or MF-IPFexo produced a fibrotic phenotype. A fibrotic phenotype was also induced in a human ex vivo skin model and in in vivo lung models.

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    Our results provide evidence of a systemic feature of IPF whereby exosomes contain pro-fibrotic miRNAs when obtained from a fibrotic source and interfere with response to tissue injury as measured in skin and lung models.

    Funding:

    This work was supported in part by Lester and Sue Smith Foundation and The Samrick Family Foundation and NIH grants R21 AG060338 (SE and MKG), U01 DK119085 (IP, RS, MTC).