A single-cell atlas of E. faecalis wound infection reveals novel bacterial-host immunomodulatory mechanisms
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Curated by eLife
eLife assessment
Wound infections are very common and can lead to delayed wound healing or poor wound healing which significantly impacts morbidity and overall quality of life for patients. This manuscript uses scRNA-Seq to try to understand the impact of infection on various cell types during wound healing in a mouse model. The methodology is solid and the results provide a valuable 'atlas' of the cellular changes associated with infected and uninfected wounds which will of interest to the field.
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- Microbiology and Infectious Disease (eLife)
Abstract
Wound infections are highly prevalent, and can lead to delayed or failed healing, causing significant morbidity and adverse economic impacts. These infections occur in various contexts, including diabetic foot ulcers, burns, and surgical sites. Enterococcus faecalis is often found in persistent non-healing wounds, but its contribution to chronic wounds remains understudied. To address this, we employed single-cell RNA sequencing (scRNA-seq) on infected wounds in comparison to uninfected wounds in a mouse model. Examining over 23,000 cells, we created a comprehensive single-cell atlas that captures the cellular and transcriptomic landscape of these wounds. Our analysis revealed unique transcriptional and metabolic alterations in infected wounds, elucidating the distinct molecular changes associated with bacterial infection compared to the normal wound healing process. We identified dysregulated keratinocyte and fibroblast transcriptomes in response to infection, jointly contributing to an anti-inflammatory environment. Notably, E. faecalis infection prompted a premature, incomplete epithelial-to-mesenchymal transition in keratinocytes. Additionally, E. faecalis infection modulated M2-like macrophage polarization by inhibiting pro-inflammatory resolution in vitro , in vivo, and in our scRNA-seq atlas. Furthermore, we discovered macrophage crosstalk with neutrophils, which regulates chemokine signaling pathways, while promoting anti-inflammatory interactions with endothelial cells. Overall, our findings offer new insights into the immunosuppressive role of E. faecalis in wound infections. Wound infections, including diabetic foot ulcers, burns, or surgical sites, often lead to prolonged healing and significant health and economic burdens. Among the bacteria implicated in these persistent wounds, Enterococcus faecalis remains a relatively enigmatic player. To unravel its role in non-healing wounds, we used single-cell RNA sequencing in a mouse model, scrutinizing over 23,000 cells to construct a comprehensive single-cell map of infected wounds compared to uninfected wounds. Our investigation revealed distinct genetic and metabolic alterations in infected wounds, in which infection resulted in a perturbed inflammatory environment delayed wound healing signatures. Specifically, E. faecalis infection induces a premature and incomplete transition in keratinocytes, impeding their healing function. Furthermore, infection influences the behavior of immune cells like macrophages, affecting the body’s response to the infection. These findings not only shed light on E. faecalis ’s role in delayed wound healing but also offer potential avenues for future treatments, providing valuable insights into the challenging realm of wound infections.
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eLife assessment
Wound infections are very common and can lead to delayed wound healing or poor wound healing which significantly impacts morbidity and overall quality of life for patients. This manuscript uses scRNA-Seq to try to understand the impact of infection on various cell types during wound healing in a mouse model. The methodology is solid and the results provide a valuable 'atlas' of the cellular changes associated with infected and uninfected wounds which will of interest to the field.
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Reviewer #1 (Public Review):
Summary:
This is an interesting study that performs scRNA-Seq on infected and uninfected wounds. The authors sought to understand how infection with E. faecalis influences the transcriptional profile of healing wounds. The analysis demonstrated that there is a unique transcriptional profile in infected wounds with specific changes in macrophages, keratinocytes, and fibroblasts. They also speculated on potential crosstalk between macrophages and neutrophils and macrophages and endothelial cells using NicheNet analysis and CellChat. Overall the data suggest that infection causes keratinocytes to not fully transition which may impede their function in wound healing and that the infection greatly influenced the transcriptional profile of macrophages and how they interact with other cells.
Strengths:
It is a …
Reviewer #1 (Public Review):
Summary:
This is an interesting study that performs scRNA-Seq on infected and uninfected wounds. The authors sought to understand how infection with E. faecalis influences the transcriptional profile of healing wounds. The analysis demonstrated that there is a unique transcriptional profile in infected wounds with specific changes in macrophages, keratinocytes, and fibroblasts. They also speculated on potential crosstalk between macrophages and neutrophils and macrophages and endothelial cells using NicheNet analysis and CellChat. Overall the data suggest that infection causes keratinocytes to not fully transition which may impede their function in wound healing and that the infection greatly influenced the transcriptional profile of macrophages and how they interact with other cells.
Strengths:
It is a useful dataset to help understand the impact of wound infection on the transcription of specific cell types. The analysis is very thorough in terms of transcriptional analysis and uses a variety of techniques and metrics.
Weaknesses:
Some drawbacks of the study are the following. First, the fact that it only has two mice per group, and only looks at one time point after wounding decreases the impact of the study. Wound healing is a dynamic and variable process so understanding the full course of the wound healing response would be very important to understand the impact of infection on the healing wound. Including unwounded skin in the scRNA-Seq would also lend a lot more significance to this study. Another drawback of the study is that mouse punch biopsies are very different than human wounds as they heal primarily by contraction instead of re-epithelialization like human wounds. So while the conclusions are generally supported the scope of the work is limited.
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Reviewer #2 (Public Review):
Summary:
The authors have performed a detailed analysis of the complex transcriptional status of numerous cell types present in wounded tissue, including keratinocytes, fibroblasts, macrophages, neutrophils, and endothelial cells. The comparison between infected and uninfected wounds is interesting and the analysis suggests possible explanations for why infected wounds are delayed in their healing response.
Strengths:
The paper presents a thorough and detailed analysis of the scRNAseq data. The paper is clearly written and the conclusions drawn from the analysis are appropriately cautious. The results provide an important foundation for future work on the healing of infected and uninfected wounds.
Weaknesses:
The analysis is purely descriptive and no attempt is made to validate whether any of the factors …
Reviewer #2 (Public Review):
Summary:
The authors have performed a detailed analysis of the complex transcriptional status of numerous cell types present in wounded tissue, including keratinocytes, fibroblasts, macrophages, neutrophils, and endothelial cells. The comparison between infected and uninfected wounds is interesting and the analysis suggests possible explanations for why infected wounds are delayed in their healing response.
Strengths:
The paper presents a thorough and detailed analysis of the scRNAseq data. The paper is clearly written and the conclusions drawn from the analysis are appropriately cautious. The results provide an important foundation for future work on the healing of infected and uninfected wounds.
Weaknesses:
The analysis is purely descriptive and no attempt is made to validate whether any of the factors identified are playing functional roles in wound healing. The experimental setup is analyzing a single time point and does not include a comparison to unwounded skin.
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