Single-cell mapping of regenerative and fibrotic healing responses after musculoskeletal injury

Distinct impacts of aging on the immune responses to extracellular matrix-based versus synthetic biomaterials

All implanted materials inevitably trigger an acute inflammatory response. The long-term outcome, however, is dependent on the trajectory of this response. This study investigates the effects of aging on the immune response to two commercially available biomaterials. Extracellular matrix-based urinary bladder matrix (UBM) and synthetic polypropylene mesh (PPM) were implanted in young (4 months) and aged (18 months) C57BL/6J mice. Overall, PPM led to a sustained inflammatory response regardless of the age of the mice. In contrast, UBM induced an initial inflammatory response that matured into a pro-regenerative/remodeling response with time, though aged mice exhibited a delayed resolution of inflammation. The PPM-induced response was predominantly pro-inflammatory with consistently higher M1-like macrophage phenotype, whereas the response to UBM was characterized by an anti-inflammatory M2-like phenotype, especially in young mice. RNA sequencing revealed marked age-related differences in gene transcription. At day 7 post-implantation, the young mice with UBM showed a robust upregulation of both pro- and anti-inflammatory pathways as compared to young mice implanted with PPM, however, by day 14, the gene expression profile transitioned into an anti-inflammatory profile. Intriguingly, in aged mice, the response to UBM was distinct with consistent downregulation of inflammatory genes compared to PPM, while the response to PPM in both young and aged animals was largely consistent. Upstream analysis identified cytokines as key drivers of the host response, with IL-4 and IL-13 in young mice, and TNF-α and IL-1β driving chronic inflammation in aged mice. These findings highlight the importance of host age in biomaterial outcome, and the potential of ECM-based materials to mount a favorable response even in the presence of age-related immune dysregulation.

Single-Cell Multiomics Analysis of Early Wound Response Programs in the Mouse Corneal Epithelium

Purpose

Wound healing is crucial for restoring homeostasis in living organisms. Although wound response mechanisms have been studied extensively, the gene regulatory programs involved remain to be elucidated. Here, we used single-cell RNA sequencing (RNA-seq) and ATAC sequencing (ATAC-seq) analysis to profile the regulatory landscape of mouse corneal epithelium in early wound response.

Methods

We used our previously published single-cell data sets of homeostatic adult mouse corneal epithelium as the unwounded group. The wounded group data sets were obtained by sequencing the epithelium after an annular epithelial wound. Following the integration of the relevant data sets, the Seurat and ArchR packages were employed for single-cell RNA-seq and single-cell ATAC-seq data processing and downstream analysis, respectively. The Monocle 2 was used for pseudo-time analysis, CellChat for intercellular communication analysis, and pySCENIC for analyzing transcription factors. The expression of key genes was validated via immunofluorescence staining and quantitative real-time PCR.

Results

Our data show that the number of cell type-specific genes decreases and the number of common transcriptional responses increases in early wound response. Concurrently, we find that the chromatin accessibility landscape undergoes significant changes across all epithelial cell types and that the wound-induced open regions are similarly distributed across the genome. Motif enrichment analysis shows that Fosl1/AP-1 binding site is highly enriched among the opened regions. However, by assessing the correlation between changes in chromatin accessibility and gene expression, we observe that only a small subset of wound-induced genes shows a high correlation with the accessibility of nearby chromatin.

Conclusions

Our study provides a detailed single-cell landscape for transcriptomic and epigenetic changes in mouse corneal epithelium during early wound response, which improved our understanding of the mechanisms of wound healing.

Making a new limb out of old cells: exploring endogenous cell reprogramming and its role during limb regeneration

Cellular reprogramming is characterized by the induced dedifferentiation of mature cells into a more plastic and potent state. This process can occur through artificial reprogramming manipulations in the laboratory such as nuclear reprogramming and induced pluripotent stem cell (iPSC) generation, and endogenously in vivo during amphibian limb regeneration. In amphibians such as the Mexican axolotl, a regeneration permissive environment is formed by nerve-dependent signaling in the wounded limb tissue. When exposed to these signals, limb connective tissue cells dedifferentiate into a limb progenitor-like state. This state allows the cells to acquire new pattern information, a property called positional plasticity. Here, we review our current understanding of endogenous reprogramming and why it is important for successful regeneration. We will also explore how naturally induced dedifferentiation and plasticity were leveraged to study how the missing pattern is established in the regenerating limb tissue.