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Single-cell dissection of obesity-exercise axis in adipose-muscle tissues

Jiekun Yang, Maria Vamvini, Pasquale Nigro, Li-Lun Ho, Kiki Galani, Marcus Alvarez, View ORCID ProfileYosuke Tanigawa, Markku Laakso, View ORCID ProfileLeandro Agudelo, Päivi Pajukanta, Roeland J. W. Middelbeek, Kevin Grove, Laurie J. Goodyear, View ORCID ProfileManolis Kellis
doi: https://doi.org/10.1101/2021.11.22.469622
Jiekun Yang
1Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, MA, USA.
2Broad Institute of MIT and Harvard, Cambridge, MA, USA.
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Maria Vamvini
3Section on Integrative Physiology and Metabolism, Joslin Diabetes Center, Harvard Medical School, Boston, MA, USA.
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Pasquale Nigro
3Section on Integrative Physiology and Metabolism, Joslin Diabetes Center, Harvard Medical School, Boston, MA, USA.
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Li-Lun Ho
1Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, MA, USA.
2Broad Institute of MIT and Harvard, Cambridge, MA, USA.
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Kiki Galani
1Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, MA, USA.
2Broad Institute of MIT and Harvard, Cambridge, MA, USA.
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Marcus Alvarez
4Department of Human Genetics, David Geffen School of Medicine at UCLA, University of California, Los Angeles, Los Angeles, CA, USA.
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Yosuke Tanigawa
1Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, MA, USA.
2Broad Institute of MIT and Harvard, Cambridge, MA, USA.
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  • ORCID record for Yosuke Tanigawa
Markku Laakso
6Institute of Clinical Medicine, Internal Medicine, University of Eastern Finland, Kuopio, Finland.
7Department of Medicine, Kuopio University Hospital, Kuopio, Finland.
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Leandro Agudelo
1Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, MA, USA.
2Broad Institute of MIT and Harvard, Cambridge, MA, USA.
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  • ORCID record for Leandro Agudelo
Päivi Pajukanta
4Department of Human Genetics, David Geffen School of Medicine at UCLA, University of California, Los Angeles, Los Angeles, CA, USA.
5Institute for Precision Health, David Geffen School of Medicine at UCLA, University of California, Los Angeles, Los Angeles, CA, USA.
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Roeland J. W. Middelbeek
3Section on Integrative Physiology and Metabolism, Joslin Diabetes Center, Harvard Medical School, Boston, MA, USA.
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Kevin Grove
8Novo Nordisk Research Center, Seattle, WA, USA.
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Laurie J. Goodyear
3Section on Integrative Physiology and Metabolism, Joslin Diabetes Center, Harvard Medical School, Boston, MA, USA.
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  • For correspondence: Laurie.Goodyear@joslin.har-vard.edu manoli@mit.edu
Manolis Kellis
1Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, MA, USA.
2Broad Institute of MIT and Harvard, Cambridge, MA, USA.
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  • ORCID record for Manolis Kellis
  • For correspondence: Laurie.Goodyear@joslin.har-vard.edu manoli@mit.edu
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Abstract

Regular physical exercise has long been recognized to reverse the effects of diet-induced obesity, but the molecular mechanisms mediating these multi-tissue beneficial effects remain uncharacterized. Here, we address this challenge by studying the opposing effects of exercise training and high-fat diet at single-cell, deconvolution and tissue-level resolutions across 3 metabolic tissues. We profile scRNA-seq in 204,883 cells, grouped into 53 distinct cell subtypes/states in 22 major cell types, from subcuta-neous and visceral white adipose tissue (WAT), and skeletal muscle (SkM) in mice with diet and exercise training interventions. With a great number of mesenchymal stem cells (MSCs) profiled, we compared depot-specific adipose stem cell (ASC) states, and defined 7 distinct fibro-adipogenic progenitor (FAP) states in SkM including discovering and validating a novel CD140+/CD34+/SCA1-FAP population. Exercise- and obesity-regulated proportion, transcriptional and cell-cell interaction changes were most strongly pronounced in and centered around ASCs, FAPs, macrophages and T-cells. These changes reflected thermogenesis-vs-lipogenesis and hyperplasia-vs-hypertrophy shifts, clustered in pathways including extracellular matrix remodeling and circadian rhythm, and implicated complex single- and multi-tissue communication including training-associated shift of a cytokine from binding to its decoy receptor on ASCs to true receptor on M2 macrophages in vWAT. Overall, our work provides new insights on the metabolic protective effects of exercise training, uncovers a previously-underappreciated role of MSCs in mediating tissue-specific and multi-tissue effects, and serves as a model for multitissue single-cell analyses in physiologically complex and multifactorial traits exemplified by obesity and exercise training.

Competing Interest Statement

The authors have declared no competing interest.

Copyright 
The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-NC-ND 4.0 International license.
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Posted November 23, 2021.
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Single-cell dissection of obesity-exercise axis in adipose-muscle tissues
Jiekun Yang, Maria Vamvini, Pasquale Nigro, Li-Lun Ho, Kiki Galani, Marcus Alvarez, Yosuke Tanigawa, Markku Laakso, Leandro Agudelo, Päivi Pajukanta, Roeland J. W. Middelbeek, Kevin Grove, Laurie J. Goodyear, Manolis Kellis
bioRxiv 2021.11.22.469622; doi: https://doi.org/10.1101/2021.11.22.469622
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Single-cell dissection of obesity-exercise axis in adipose-muscle tissues
Jiekun Yang, Maria Vamvini, Pasquale Nigro, Li-Lun Ho, Kiki Galani, Marcus Alvarez, Yosuke Tanigawa, Markku Laakso, Leandro Agudelo, Päivi Pajukanta, Roeland J. W. Middelbeek, Kevin Grove, Laurie J. Goodyear, Manolis Kellis
bioRxiv 2021.11.22.469622; doi: https://doi.org/10.1101/2021.11.22.469622

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