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Parallel single cell multi-omics analysis of neonatal skin reveals transitional fibroblast states that restrict differentiation into distinct fates

ABSTRACT: Parallel single cell multi-omics analysis of neonatal skin reveals transitional fibroblast states that restrict differentiation into distinct fates

PROVIDER: PRJNA781969 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR16988117_1.fastq.gz	Fastqsanger.gz
	SRR16988117_2.fastq.gz	Fastqsanger.gz
	SRR16988118_1.fastq.gz	Fastqsanger.gz
	SRR16988118_2.fastq.gz	Fastqsanger.gz

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Parallel single cell multi-omics analysis of neonatal skin reveals transitional fibroblast states that restrict differentiation into distinct fates

Project description: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 adipocytes 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/.

2021-11-24 | GSE189210 | GEO

Parallel Single-Cell Multiomics Analysis of Neonatal Skin Reveals the Transitional Fibroblast States that Restrict Differentiation into Distinct Fates.

Project description: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 multiomics analysis by processing neonatal murine skin for single-cell Assay for Transposase-Accessible Chromatin sequencing and single-cell RNA sequencing separately. Our approach revealed that fibroblast clusters could be sorted into papillary and reticular lineages on the basis of transcriptome profiling, as previously reported. However, single-cell Assay for Transposase-Accessible Chromatin sequencing 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 suggest that accessible chromatin does not always translate to gene expression and that many fibroblast lineage markers reflect a fibroblast state, which includes neonatal papillary fibroblasts, reticular fibroblasts, 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 single-cell Assay for Transposase-Accessible Chromatin sequencing analysis also revealed that the functional lineage restriction between dermal papilla and adipocyte fates is regulated by distinct chromatin landscapes. Finally, we have developed a webtool for our multiomics analysis: https://skinregeneration.org/scatacseq-and-scrnaseq-data-from-thompson-et-al-2021-2/.

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BRG1 establishes the neuroectodermal chromatin landscape to restrict dorsal cell fates

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Project description:Fibroblast to myofibroblast conversion is a major driver of tissue remodeling in organ fibrosis. Here, we combined spatial transcriptomics, longitudinal single-cell RNA-seq and genetic lineage tracing to study fibroblast fates during mouse lung regeneration. We discovered a transitional fibroblast state characterized by high Sfrp1 expression, derived from both Tcf21-Cre lineage positive and negative cells. Sfrp1+ cells appeared early after injury in peribronchiolar, adventitial and alveolar locations and preceded the emergence of myofibroblasts. We identified lineage specific paracrine signals and inferred converging transcriptional trajectories towards Sfrp1+ transitional fibroblasts and Cthrc1+ myofibroblasts. Tgfβ1 downregulated Sfrp1 in non-invasive transitional cells and induced their switch to an invasive Cthrc1+ myofibroblast identity. Our study reveals the convergence of spatially and transcriptionally distinct fibroblast lineages into transcriptionally uniform myofibroblasts and identifies Sfrp1 as an autocrine inhibitor of fibroblast invasion during early stages of fibrogenesis.

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Autocrine Sfrp1 inhibits fibroblast invasion during transition to injury induced myofibroblasts - daily profiling of mouse lungs after Bleomycin injury

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Regulation of the Alveolar Epithelial Transitional State in Murine and Human Pulmonary Fibrosis

Project description:Idiopathic Pulmonary Fibrosis (IPF) is a progressive scarring disease arising from impaired regeneration of the alveolar epithelium after injury. During regeneration, type 2 alveolar epithelial cells (AEC2s) differentiate into AEC1s via a transitional state that upregulates keratin 8. In IPF, transitional AECs persist with ineffectual AEC1 differentiation. However, whether keratin 8 regulates transitional state persistence and fibrosis is unclear. Here, we isolated AEC2s from WT or keratin 8 KO mice and harvested RNA from freshly isolated cells or from cells cultured for 1, 3, or 7 days. RNAseq was performed.

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