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Justynski O, Bridges K, Krause W, Forni MF, Phan QM, Sandoval-Schaefer T, Carter K, King DE, Hsia HC, Gazes MI, Vyce SD, Driskell RR, Miller-Jensen K, Horsley V. Apoptosis recognition receptors regulate skin tissue repair in mice. eLife 2023; 12:e86269. [PMID: 38127424 PMCID: PMC10735221 DOI: 10.7554/elife.86269] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2023] [Accepted: 11/17/2023] [Indexed: 12/23/2023] Open
Abstract
Apoptosis and clearance of apoptotic cells via efferocytosis are evolutionarily conserved processes that drive tissue repair. However, the mechanisms by which recognition and clearance of apoptotic cells regulate repair are not fully understood. Here, we use single-cell RNA sequencing to provide a map of the cellular dynamics during early inflammation in mouse skin wounds. We find that apoptotic pathways and efferocytosis receptors are elevated in fibroblasts and immune cells, including resident Lyve1+ macrophages, during inflammation. Interestingly, human diabetic foot wounds upregulate mRNAs for efferocytosis pathway genes and display altered efferocytosis signaling via the receptor Axl and its ligand Gas6. During early inflammation in mouse wounds, we detect upregulation of Axl in dendritic cells and fibroblasts via TLR3-independent mechanisms. Inhibition studies in vivo in mice reveal that Axl signaling is required for wound repair but is dispensable for efferocytosis. By contrast, inhibition of another efferocytosis receptor, Timd4, in mouse wounds decreases efferocytosis and abrogates wound repair. These data highlight the distinct mechanisms by which apoptotic cell detection coordinates tissue repair and provides potential therapeutic targets for chronic wounds in diabetic patients.
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Affiliation(s)
- Olivia Justynski
- Dept. of Molecular Cellular and Developmental Biology, Yale University, New Haven, United States
| | - Kate Bridges
- Dept. of Biomedical Engineering, Yale University, New Haven, United States
| | - Will Krause
- Dept. of Molecular Cellular and Developmental Biology, Yale University, New Haven, United States
| | - Maria Fernanda Forni
- Dept. of Molecular Cellular and Developmental Biology, Yale University, New Haven, United States
| | - Quan M Phan
- Washington State University, SMB, Pullman, United States
| | - Teresa Sandoval-Schaefer
- Dept. of Molecular Cellular and Developmental Biology, Yale University, New Haven, United States
| | - Kristyn Carter
- Dept. of Molecular Cellular and Developmental Biology, Yale University, New Haven, United States
| | - Diane E King
- Sunnycrest Bioinformatics, Flemington, United States
| | - Henry C Hsia
- Dept. of Surgery (Plastic), Yale School of Medicine, New Haven, United States
| | - Michael I Gazes
- Dept of Podiatric Surgery, Yale New Haven Hospital, New Haven, United States
| | - Steven D Vyce
- Dept of Podiatric Surgery, Yale New Haven Hospital, New Haven, United States
| | | | - Kathryn Miller-Jensen
- Dept. of Molecular Cellular and Developmental Biology, Yale University, New Haven, United States
- Dept. of Biomedical Engineering, Yale University, New Haven, United States
| | - Valerie Horsley
- Dept. of Molecular Cellular and Developmental Biology, Yale University, New Haven, United States
- Dept. of Dermatology, Yale School of Medicine, New Haven, United States
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Phan QM, Salz L, Kindl SS, Lopez JS, Thompson SM, Makkar J, Driskell IM, Driskell RR. Lineage commitment of dermal fibroblast progenitors is controlled by Kdm6b-mediated chromatin demethylation. EMBO J 2023; 42:e113880. [PMID: 37602956 PMCID: PMC10548174 DOI: 10.15252/embj.2023113880] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2023] [Revised: 07/26/2023] [Accepted: 08/01/2023] [Indexed: 08/22/2023] Open
Abstract
Dermal Fibroblast Progenitors (DFPs) differentiate into distinct fibroblast lineages during skin development. However, the epigenetic mechanisms that regulate DFP differentiation are not known. Our objective was to use multimodal single-cell approaches, epigenetic assays, and allografting techniques to define a DFP state and the mechanism that governs its differentiation potential. Our initial results indicated that the overall transcription profile of DFPs is repressed by H3K27me3 and has inaccessible chromatin at lineage-specific genes. Surprisingly, the repressive chromatin profile of DFPs renders them unable to reform the skin in allograft assays despite their multipotent potential. We hypothesized that chromatin derepression was modulated by the H3K27me3 demethylase, Kdm6b/Jmjd3. Dermal fibroblast-specific deletion of Kdm6b/Jmjd3 in mice resulted in adipocyte compartment ablation and inhibition of mature dermal papilla functions, confirmed by additional single-cell RNA-seq, ChIP-seq, and allografting assays. We conclude that DFPs are functionally derepressed during murine skin development by Kdm6b/Jmjd3. Our studies therefore reveal a multimodal understanding of how DFPs differentiate into distinct fibroblast lineages and provide a novel publicly available multiomics search tool.
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Affiliation(s)
- Quan M Phan
- School of Molecular BiosciencesWashington State UniversityPullmanWAUSA
| | - Lucia Salz
- North Rhine‐Westphalia Technical University of AachenAachenGermany
| | - Sam S Kindl
- School of Molecular BiosciencesWashington State UniversityPullmanWAUSA
| | - Jayden S Lopez
- School of Molecular BiosciencesWashington State UniversityPullmanWAUSA
| | - Sean M Thompson
- School of Molecular BiosciencesWashington State UniversityPullmanWAUSA
| | - Jasson Makkar
- School of Molecular BiosciencesWashington State UniversityPullmanWAUSA
| | - Iwona M Driskell
- School of Molecular BiosciencesWashington State UniversityPullmanWAUSA
| | - Ryan R Driskell
- School of Molecular BiosciencesWashington State UniversityPullmanWAUSA
- Center for Reproductive BiologyWashington State UniversityPullmanWAUSA
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3
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Phan QM, Salz L, Kindl SS, Lopez JS, Thompson SM, Makkar J, Driskell IM, Driskell RR. Lineage Commitment of Dermal Fibroblast Progenitors is Mediated by Chromatin De-repression. bioRxiv 2023:2023.03.07.531478. [PMID: 36945417 PMCID: PMC10028926 DOI: 10.1101/2023.03.07.531478] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
Dermal Fibroblast Progenitors (DFPs) differentiate into distinct fibroblast lineages during skin development. However, the mechanisms that regulate lineage commitment of naive dermal progenitors to form niches around the hair follicle, dermis, and hypodermis, are unknown. In our study, we used multimodal single-cell approaches, epigenetic assays, and allografting techniques to define a DFP state and the mechanisms that govern its differentiation potential. Our results indicate that the overall chromatin profile of DFPs is repressed by H3K27me3 and has inaccessible chromatin at lineage specific genes. Surprisingly, the repressed chromatin profile of DFPs renders them unable to reform skin in allograft assays despite their multipotent potential. Distinct fibroblast lineages, such as the dermal papilla and adipocytes contained specific chromatin profiles that were de-repressed during late embryogenesis by the H3K27-me3 demethylase, Kdm6b/Jmjd3. Tissue-specific deletion of Kdm6b/Jmjd3 resulted in ablating the adipocyte compartment and inhibiting mature dermal papilla functions in single-cell-RNA-seq, ChIPseq, and allografting assays. Altogether our studies reveal a mechanistic multimodal understanding of how DFPs differentiate into distinct fibroblast lineages, and we provide a novel multiomic search-tool within skinregeneration.org.
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Affiliation(s)
- Quan M. Phan
- School of Molecular Biosciences, Washington State University, Pullman, WA
| | - Lucia Salz
- North Rhine-Westphalia Technical University of Aachen, Aachen, Germany
| | - Sam S. Kindl
- School of Molecular Biosciences, Washington State University, Pullman, WA
| | - Jayden S. Lopez
- School of Molecular Biosciences, Washington State University, Pullman, WA
| | - Sean M. Thompson
- School of Molecular Biosciences, Washington State University, Pullman, WA
| | - Jasson Makkar
- School of Molecular Biosciences, Washington State University, Pullman, WA
| | - Iwona M. Driskell
- School of Molecular Biosciences, Washington State University, Pullman, WA
| | - Ryan R. Driskell
- School of Molecular Biosciences, Washington State University, Pullman, WA
- Center for Reproductive Biology, Washington State University, Pullman, WA
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4
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Thompson SM, Phan QM, Winuthayanon S, Driskell IM, Driskell RR. Parallel single cell multi-omics analysis of neonatal skin reveals transitional fibroblast states that restricts differentiation into distinct fates. J Invest Dermatol 2021; 142:1812-1823.e3. [PMID: 34922949 DOI: 10.1016/j.jid.2021.11.032] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2021] [Revised: 11/26/2021] [Accepted: 11/30/2021] [Indexed: 12/18/2022]
Abstract
One of the keys to achieving skin regeneration lies within understanding the heterogeneity of neonatal fibroblasts, which support skin regeneration. However, the molecular underpinnings regulating the cellular states and fates of these cells are not fully understood. To investigate this, we performed a parallel multi-omics analysis by processing neonatal murine skin for single-cell ATAC-sequencing (scATAC-seq) and single-cell RNA-sequencing (scRNA-seq) separately. Our approach revealed that fibroblast clusters could be sorted into papillary and reticular lineages based on transcriptome profiling, as previously published. However, scATAC-seq analysis of neonatal fibroblast lineage markers, such as, Dpp4/CD26, Corin, and Dlk1 along with markers of myofibroblasts, revealed accessible chromatin in all fibroblast populations despite their lineage-specific transcriptome profiles. These results suggests that accessible chromatin does not always translate to gene expression and that many fibroblast lineage markers reflect a fibroblast state, which includes neonatal papillary, reticular, and myofibroblasts. This analysis also provides a possible explanation as to why these marker genes can be promiscuously expressed in different fibroblast populations under different conditions. Our scATAC-seq analysis also revealed that the functional lineage restriction between dermal papilla and adipocyte fates are regulated by distinct chromatin landscapes. Finally, we have developed a webtool for our multi-omics analysis: https://skinregeneration.org/scatacseq-and-scrnaseq-data-from-thompson-et-al-2021-2/.
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Affiliation(s)
- Sean M Thompson
- School of Molecular Biosciences, Washington State University, Pullman, WA
| | - Quan M Phan
- School of Molecular Biosciences, Washington State University, Pullman, WA
| | - Sarayut Winuthayanon
- School of Molecular Biosciences, Washington State University, Pullman, WA; Center for Reproductive Biology, Washington State University, Pullman, WA
| | - Iwona M Driskell
- School of Molecular Biosciences, Washington State University, Pullman, WA
| | - Ryan R Driskell
- School of Molecular Biosciences, Washington State University, Pullman, WA; Center for Reproductive Biology, Washington State University, Pullman, WA. https://twitter.com/Driskellab
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Phan QM, Sinha S, Biernaskie J, Driskell RR. Single-cell transcriptomic analysis of small and large wounds reveals the distinct spatial organization of regenerative fibroblasts. Exp Dermatol 2021; 30:92-101. [PMID: 33237598 PMCID: PMC7839523 DOI: 10.1111/exd.14244] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2020] [Revised: 11/19/2020] [Accepted: 11/19/2020] [Indexed: 12/30/2022]
Abstract
Wound-induced hair follicle neogenesis (WIHN) has been an important model to study hair follicle regeneration during wound repair. However, the cellular and molecular components of the dermis that make large wounds more regenerative are not fully understood. Here, we compare and contrast recently published scRNA-seq data of small scarring wounds to wounds that regenerate in hope to elucidate the role of fibroblasts lineages in WIHN. Our analysis revealed an over-representation of the newly identified upper wound fibroblasts in regenerative wound conditions, which express the retinoic acid binding protein Crabp1. This regenerative cell type shares a similar gene signature to the murine papillary fibroblast lineage, which are necessary to support hair follicle morphogenesis and homeostasis. RNA velocity analysis comparing scarring and regenerating wounds revealed the divergent trajectories towards upper and lower wound fibroblasts and that the upper populations were closely associated with the specialized dermal papilla. We also provide analyses and explanation reconciling the inconsistency between the histological lineage tracing and the scRNA-seq data from recent reports investigating large wounds. Finally, we performed a computational test to map the spatial location of upper wound fibroblasts in large wounds which revealed that upper peripheral fibroblasts might harbour equivalent regenerative competence as those in the centre. Overall, our scRNA-seq reanalysis combining multiple samples suggests that upper wound fibroblasts are required for hair follicle regeneration and that papillary fibroblasts may migrate from the wound periphery to the centre during wound re-epithelialization. Moreover, data from this publication are made available on our searchable web resource: https://skinregeneration.org/.
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Affiliation(s)
- Quan M. Phan
- School of Molecular BiosciencesWashington State UniversityPullmanWAUSA
| | - Sarthak Sinha
- Department of Comparative Biology and Experimental MedicineFaculty of Veterinary MedicineUniversity of CalgaryCalgaryABCanada
| | - Jeff Biernaskie
- Department of Surgery, Cumming School of MedicineAlberta Children's Hospital Research InstituteHotchkiss Brain Institute University of CalgaryCalgaryABCanada
| | - Ryan R. Driskell
- School of Molecular BiosciencesWashington State UniversityPullmanWAUSA
- Center for Reproductive BiologyWashington State UniversityPullmanWAUSA
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Phan QM, Fine GM, Salz L, Herrera GG, Wildman B, Driskell IM, Driskell RR. Lef1 expression in fibroblasts maintains developmental potential in adult skin to regenerate wounds. eLife 2020; 9:e60066. [PMID: 32990218 PMCID: PMC7524549 DOI: 10.7554/elife.60066] [Citation(s) in RCA: 88] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2020] [Accepted: 09/09/2020] [Indexed: 12/28/2022] Open
Abstract
Scars are a serious health concern for burn victims and individuals with skin conditions associated with wound healing. Here, we identify regenerative factors in neonatal murine skin that transforms adult skin to regenerate instead of only repairing wounds with a scar, without perturbing development and homeostasis. Using scRNA-seq to probe unsorted cells from regenerating, scarring, homeostatic, and developing skin, we identified neonatal papillary fibroblasts that form a transient regenerative cell type that promotes healthy skin regeneration in young skin. These fibroblasts are defined by the expression of a canonical Wnt transcription factor Lef1 and using gain- and loss of function genetic mouse models, we demonstrate that Lef1 expression in fibroblasts primes the adult skin macroenvironment to enhance skin repair, including regeneration of hair follicles with arrector pili muscles in healed wounds. Finally, we share our genomic data in an interactive, searchable companion website (https://skinregeneration.org/). Together, these data and resources provide a platform to leverage the regenerative abilities of neonatal skin to develop clinically tractable solutions that promote the regeneration of adult tissue.
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Affiliation(s)
- Quan M Phan
- School of Molecular Biosciences, Washington State UniversityPullmanUnited States
| | - Gracelyn M Fine
- School of Molecular Biosciences, Washington State UniversityPullmanUnited States
| | - Lucia Salz
- School of Molecular Biosciences, Washington State UniversityPullmanUnited States
| | - Gerardo G Herrera
- School of Molecular Biosciences, Washington State UniversityPullmanUnited States
| | - Ben Wildman
- School of Molecular Biosciences, Washington State UniversityPullmanUnited States
| | - Iwona M Driskell
- School of Molecular Biosciences, Washington State UniversityPullmanUnited States
| | - Ryan R Driskell
- School of Molecular Biosciences, Washington State UniversityPullmanUnited States
- Center for Reproductive Biology, Washington State UniversityPullmanUnited States
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