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Single-cell RNA sequencing reveals that lung mesenchymal progenitor cells in IPF exhibit pathological features early in their differentiation trajectory.

ABSTRACT: In Idiopathic Pulmonary Fibrosis (IPF), there is unrelenting scarring of the lung mediated by pathological mesenchymal progenitor cells (MPCs) that manifest autonomous fibrogenicity in xenograft models. To determine where along their differentiation trajectory IPF MPCs acquire fibrogenic properties, we analyzed the transcriptome of 335 MPCs isolated from the lungs of 3 control and 3 IPF patients at the single-cell level. Using transcriptional entropy as a metric for differentiated state, we found that the least differentiated IPF MPCs displayed the largest differences in their transcriptional profile compared to control MPCs. To validate entropy as a surrogate for differentiated state functionally, we identified increased CD44 as a characteristic of the most entropic IPF MPCs. Using FACS to stratify IPF MPCs based on CD44 expression, we determined that CD44^hi IPF MPCs manifested an increased capacity for anchorage-independent colony formation compared to CD44^lo IPF MPCs. To validate our analysis morphologically, we used two differentially expressed genes distinguishing IPF MPCs from control (CD44, cell surface; and MARCKS, intracellular). In IPF lung tissue, pathological MPCs resided in the highly cellular perimeter region of the fibroblastic focus. Our data support the concept that IPF fibroblasts acquire a cell-autonomous pathological phenotype early in their differentiation trajectory.

SUBMITTER: Beisang DJ

PROVIDER: S-EPMC7341888 | biostudies-literature | 2020 Jul

REPOSITORIES: biostudies-literature

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Single-cell RNA sequencing reveals that lung mesenchymal progenitor cells in IPF exhibit pathological features early in their differentiation trajectory.

Beisang Daniel J DJ Smith Karen K Yang Libang L Benyumov Alexey A Gilbertsen Adam A Herrera Jeremy J Lock Eric E Racila Emilian E Forster Colleen C Sandri Brian J BJ Henke Craig A CA Bitterman Peter B PB

Scientific reports 20200707 1

In Idiopathic Pulmonary Fibrosis (IPF), there is unrelenting scarring of the lung mediated by pathological mesenchymal progenitor cells (MPCs) that manifest autonomous fibrogenicity in xenograft models. To determine where along their differentiation trajectory IPF MPCs acquire fibrogenic properties, we analyzed the transcriptome of 335 MPCs isolated from the lungs of 3 control and 3 IPF patients at the single-cell level. Using transcriptional entropy as a metric for differentiated state, we foun ...[more]

PMID: 32636398

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Project description:BackgroundDiabetic foot ulcer (DFU) is one of the most common and complex complications of diabetes, but the underlying pathophysiology remains unclear. Single-cell RNA sequencing (scRNA-seq) has been conducted to explore novel cell types or molecular profiles of DFU from various perspectives. This study aimed to comprehensively analyze the potential mechanisms underlying impaired re-epithelization of DFU in a single-cell perspective.MethodsWe conducted scRNA-seq on tissues from human normal skin, acute wound, and DFU to investigate the potential mechanisms underlying impaired epidermal differentiation and the pathological microenvironment. Pseudo-time and lineage inference analyses revealed the distinct states and transition trajectories of epidermal cells under different conditions. Transcription factor analysis revealed the potential regulatory mechanism of key subtypes of keratinocytes. Cell-cell interaction analysis revealed the regulatory network between the proinflammatory microenvironment and epidermal cells. Laser-capture microscopy coupled with RNA sequencing (LCM-seq) and multiplex immunohistochemistry were used to validate the expression and location of key subtypes of keratinocytes.ResultsOur research provided a comprehensive map of the phenotypic and dynamic changes that occur during epidermal differentiation, alongside the corresponding regulatory networks in DFU. Importantly, we identified two subtypes of keratinocytes: basal cells (BC-2) and diabetes-associated keratinocytes (DAK) that might play crucial roles in the impairment of epidermal homeostasis. BC-2 and DAK showed a marked increase in DFU, with an inactive state and insufficient motivation for epidermal differentiation. BC-2 was involved in the cellular response and apoptosis processes, with high expression of TXNIP, IFITM1, and IL1R2. Additionally, the pro-differentiation transcription factors were downregulated in BC-2 in DFU, indicating that the differentiation process might be inhibited in BC-2 in DFU. DAK was associated with cellular glucose homeostasis. Furthermore, increased CCL2 + CXCL2+ fibroblasts, VWA1+ vascular endothelial cells, and GZMA+CD8+ T cells were detected in DFU. These changes in the wound microenvironment could regulate the fate of epidermal cells through the TNFSF12-TNFRSF12A, IFNG-IFNGR1/2, and IL-1B-IL1R2 pathways, which might result in persistent inflammation and impaired epidermal differentiation in DFU.ConclusionsOur findings offer novel insights into the pathophysiology of DFU and present potential therapeutic targets that could improve wound care and treatment outcomes for DFU patients.

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Single-cell RNA sequencing reveals that lung mesenchymal progenitor cells in IPF exhibit pathological features early in their differentiation trajectory.

Publications

Single-cell RNA sequencing reveals that lung mesenchymal progenitor cells in IPF exhibit pathological features early in their differentiation trajectory.

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