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Transfer learning in a biomaterial fibrosis model identifies in vivo senescence heterogeneity and contributions to vascularization and matrix production across species and diverse pathologies

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Abstract

Cellular senescence is a state of permanent growth arrest that plays an important role in wound healing, tissue fibrosis, and tumor suppression. Despite senescent cells’ (SnCs) pathological role and therapeutic interest, their phenotype in vivo remains poorly defined. Here, we developed an in vivo–derived senescence signature (SenSig) using a foreign body response–driven fibrosis model in a p16-CreERT2;Ai14 reporter mouse. We identified pericytes and “cartilage-like” fibroblasts as senescent and defined cell type–specific senescence-associated secretory phenotypes (SASPs). Transfer learning and senescence scoring identified these two SnC populations along with endothelial and epithelial SnCs in new and publicly available murine and human data single-cell RNA sequencing (scRNAseq) datasets from diverse pathologies. Signaling analysis uncovered crosstalk between SnCs and myeloid cells via an IL34–CSF1R–TGFβR signaling axis, contributing to tissue balance of vascularization and matrix production. Overall, our study provides a senescence signature and a computational approach that may be broadly applied to identify SnC transcriptional profiles and SASP factors in wound healing, aging, and other pathologies.

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Data availability

The newly generated and publicly available data presented in this manuscript are available from GEO using accession numbers GSE199864 (SnC bulkRNAseq), GSE175890 (VML scRNAseq), GSE135893 (Adams et al. IPF), GSE136831 (Habermann et al. IPF), and GSE123814 (BCC scRNAseq).

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Acknowledgements

Biorender was used to create some of the figures presented in this manuscript. The authors thank David R. Maestas Jr. for experimental insight and advice.

Funding

This research was supported by the Department of Defense (W81XWH-17–1-0627 and W81XWH-14–1-0285), National Institutes of Health Pioneer Award DP1AR076959 (J.H.E.), Bloomberg ~ Kimmel Institute (J.H.E., D.M.P.), Morton Goldberg Professorship (J.H.E.), Bristol Myers Squib (J.H.E., D.M.P.), National Science Foundation Graduate Research Fellowship Program DGE-1746891 (A.R. and A.N.P.), NCI U01CA253403 (E.J.F.), National Institutes of Health R01 AG057493 (J.M.v.D.), and NIH T32 Training Grants 1T32AG058527-01 and 5T32CA153952-08 (J.I.A.).

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Authors and Affiliations

  1. Translational Tissue Engineering Center, Wilmer Eye Institute and the Department of Biomedical Engineering, Johns Hopkins University School of Medicine, Baltimore, MD, USA

    Christopher Cherry, James I. Andorko, Kavita Krishnan, Joscelyn C. Mejías, Helen Hieu Nguyen, Katlin B. Stivers, Elise F. Gray-Gaillard, Anna Ruta, Jin Han, John H. Michel, Locke Davenport Huyer, Alexis N. Peña & Jennifer H. Elisseeff

  2. Department of Pediatric and Adolescent Medicine, Mayo Clinic, Rochester, MN, USA

    Naomi Hamada, Masakazu Hamada, Ines Sturmlechner, Shawn Trewartha, Darren J. Baker & Jan M. van Deursen

  3. Department of Pediatrics, Molecular Genetics Section, University of Groningen, University Medical Center Groningen, Antonius Deusinglaan 1, 9713 AV, Groningen, Netherlands

    Ines Sturmlechner

  4. Laboratory of Cancer Immunometabolism, Center for Cancer Research, National Cancer Institute, Frederick, MD, USA

    Matthew T. Wolf

  5. Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD, USA

    Ada J. Tam

  6. Bloomberg~Kimmel Institute for Cancer Immunotherapy and Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD, USA

    Ada J. Tam, Franck Housseau, Drew M. Pardoll & Jennifer H. Elisseeff

  7. Tumor Microenvironment Thematic Research Center, Bristol Myers Squibb, San Francisco, CA, USA

    Shilpa Keerthivasan

  8. Department of Medicine, University of California, San Francisco, San Francisco, CA, USA

    Claude Jordan Le Saux

  9. Department of Biomedical Engineering and Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, MD, USA

    Elana J. Fertig

  10. Department of Applied Mathematics and Statistics, Johns Hopkins University, Baltimore, MD, USA

    Elana J. Fertig

  11. Convergence Institute, Johns Hopkins University School of Medicine, Baltimore, MD, USA

    Elana J. Fertig

  12. Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, MN, USA

    Darren J. Baker & Jan M. van Deursen

  13. Paul F. Glenn Center for the Biology of Aging Research at Mayo Clinic, Rochester, MN, USA

    Darren J. Baker

Authors
  1. Christopher Cherry
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  2. James I. Andorko
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  3. Kavita Krishnan
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  4. Joscelyn C. Mejías
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  7. Elise F. Gray-Gaillard
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  26. Jennifer H. Elisseeff
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Contributions

C.C., J.I.A., and J.H.E. conceptualized and drafted figures and manuscript. C.C., K.K., J.H.E, and E.J.F. formulated, performed, and interpreted computational analysis of bulk and single-cell RNA sequencing data sets. C.C., J.C.M., K.K., and J.H. performed Drop-Seq single-cell RNA sequencing. J.I.A., J.H., and L.D.H. performed the volumetric muscle loss surgeries. J.I.A., J.C.M., K.B.S., F.H., and D.M.P. performed and analyzed flow cytometry. H.H.N., A.N.P., and M.T.W. performed, imaged, and analyzed immunofluorescent staining and imaging including sectioning and sample processing. E.F.G-G. performed and analyzed in vitro co-culture experiments. A.R. performed, imaged, and analyzed fluorescence in situ hybridization staining and imaging. H.M. and J.M.v.D. designed and generated the p16-EF/CreERT2 strain, and N.H., I.S., S.T., and D.J.B. contributed to various validation experiments for this model. J.I.A. and J.H.M. performed cryosectioning and imaging of native fluorescence of the fluorescent reporter. A.J.T. and J.I.A. performed fluorescence-activated cytometric sorting. C.J.L.S. performed and analyzed Ingenuity Pathway Analysis. S.K. provided key insights to fibroblast biology that contributed to manuscript preparation and critical review. All authors participated in the construction of the manuscript and figures.

Corresponding author

Correspondence to Jennifer H. Elisseeff.

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Conflict of interest

J.H.E. holds equity in Unity Biotechnology and Aegeria Soft Tissue and is an advisor for Tessera Therapeutics, HapInScience, and Font Bio. D.M.P. is consultant at Aduro Biotech, Amgen, Astra Zeneca, Bayer, Compugen, DNAtrix, Dynavax Technologies Corporation, Ervaxx, FLX Bio, Immunomic, Janssen, Merck, and Rock Springs Capital. D.M.P. holds equity in Aduro Biotech, DNAtrix, Ervaxx, Five Prime therapeutics, Immunomic, Potenza, and Trieza Therapeutics. D.M.P. is a member of the scientific advisory board for Bristol Myers Squibb, Camden Nexus II, Five Prime Therapeutics, and WindMil. D.M.P. is a member of the board of directors in Dracen Pharmaceuticals. C.C. is the founder and owner of C M Cherry Consulting, LLC. E.J.F. is a member of the scientific advisory board for Resistance Bio and is a consultant for Merck and Mestag Therapeutics. J.M.v.D. is a co-founder of and holds equity in Unity Biotechnology and Cavalry Biosciences. D.J.B. is a shareholder and co-inventor on patent applications licensed to or filed by Unity Biotechnology, a company developing senolytic medicines, including small molecules that selectively eliminate senescent cells. Research in his laboratory has been reviewed by the Mayo Clinic Conflict of Interest Review Board and is being conducted in compliance with Mayo Clinic Conflict of Interest policies.

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Cherry, C., Andorko, J.I., Krishnan, K. et al. Transfer learning in a biomaterial fibrosis model identifies in vivo senescence heterogeneity and contributions to vascularization and matrix production across species and diverse pathologies. GeroScience 45, 2559–2587 (2023). https://doi.org/10.1007/s11357-023-00785-7

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