Single-cell RNA-seq reveals fibroblast heterogeneity and increased mesenchymal fibroblasts in human fibrotic skin diseases

Pathogenesis, attenuation, and treatment strategies for keloid management

Keloid is an outcome of abnormal cellular response in the wound healing process with excessive fibroblast and collagen deposition in the dermal layer of the skin. It is characterized by a scar showing fibrous outgrowth that grows beyond the original boundaries of the wound. Thus, it is cosmetically and functionally disturbing to the patient. Keloidal development depends on various patient and environmental factors, possibly initiating abnormal wound healing. Due to abnormal wound healing, various aberrant cellular responses are observed during keloid development, like delayed inflammatory response, increased growth factors, varied cytokine level, decreased apoptosis, increased angiogenesis, and imbalanced proteinases. Bacteria and the immune system also play a role in keloid development. Advancements like single-cell RNA sequencing and transcriptomics studies have led to a better understanding of pathogenesis. In line with the complex pathogenesis, the later part of the review covers a detailed analysis of various treatment options employed for keloid, which includes silicone-based topical therapy, drug-based therapy, invasive approach (surgery), and minimally invasive therapies (radiation, laser therapy, and cryotherapy). The advantages and limitations of individual and combination therapies are also discussed. Keloids tend to re-occur after treatment; hence, follow-up is very important, making keloid treatment a complex procedure. Novel therapeutics in keloid have advantages like better efficacy of drugs, less pain, self-administration, and fewer side effects. A few nanotherapeutics advancements, such as microneedles, nanoparticles, liposomes, and exosomes, are discussed in the review.

Keloid vasculature reacts to intralesional injection therapies but does not predict the response to treatment: Biopsies from double-blinded, randomized, controlled trial

Keloids are benign fibroproliferative skin scars that expand beyond the original wound site. Hypoxia and angiogenesis are thought to drive pathological scar formation in keloids. We utilized biopsies collected before, during and after the double-blinded randomized controlled trial (RCT) comparing the intralesional treatments of 5-fluorouracil and triamcinolone injections in 48 human keloids. We could not detect any cells expressing the hypoxia markers (carbonic anhydrase 9 and hypoxia-inducible factor 1α) in the three distinct regions of keloid dermis. The amount of epidermal hypoxia could not predict the response to treatment. The middle dermis of the patients obtaining a clinical response to the intralesional injections showed significant increase in mature blood vessels and in lymphatics after the treatment. Our study does not support hypoxia being the driver behind keloid formation but demonstrates that the patients obtaining a response to intralesional therapies develop more blood vessels and lymphatics in the middle dermis of the keloids during the treatment.

Characterization of a pathogenic nonmigratory fibroblast population in systemic sclerosis skin

Fibroblasts are central to pathogenesis of systemic sclerosis (SSc). However, studies of conventional explant fibroblast cultures incompletely reflect disease biology and treatment response. We isolated a second nonmigratory "resident" population of fibroblasts from skin biopsies after outgrowth of explant "migratory" cells. These nonmotile resident fibroblasts were compared with migratory cells from the same biopsy, using functional studies, bulk and single-cell RNA-seq, and localized in situ by multichannel immunofluorescence. Migratory and resident fibroblast populations in SSc showed distinct profibrotic characteristics and gene expression for pathogenic pathways differing by stage and autoantibody subgroup. TGF-β signaling was highly active in migratory fibroblasts in early-stage diffuse cutaneous SSc (dcSSc). Conversely, resident fibroblasts had less upregulated TGF-β signaling, especially in late-stage dcSSc. Increased chemokine expression was a hallmark of resident fibroblasts at all stages. In vitro studies confirmed differential response to TGF-β1 and CCL2 between migratory and resident cells. We suggest that migratory fibroblasts are especially important in early skin disease, whereas nonmigratory fibroblasts may have a regulatory role and contribute more to fibrosis in later-stage disease. Thus, we have identified a pathogenic fibroblast population in SSc, not isolated by conventional explant culture, that could play an important role in fibrosis and be targeted therapeutically.

Apoptotic Bodies Restore NAD and Mitochondrial Homeostasis in Fibroblasts

Fibrotic skin diseases are characterized by excessive fibroblast proliferation and pathological extracellular matrix deposition. As a pivotal coenzyme in cellular energetics, NAD homeostasis perturbation is implicated in fibrosis. Multiple studies have demonstrated the therapeutic potential of mesenchymal stem cells (MSCs) against cutaneous fibrosis, while the specific mechanism remains elusive. Herein, this work finds that although almost all MSCs undergo in situ apoptosis within 24 h post-subcutaneous administration, MSC-derived apoptotic bodies (ABs) mediated potent anti-fibrotic effects. Mechanistically, ABs can restore NAD and mitochondrial homeostasis through NAMPT transfer, FOXO1 deacetylation enhancement, and PINK1/PARKIN-dependent mitophagy activation. To achieve penetration into the hard matrix of fibrotic skin, permeable apoptotic bodies (pABs) are constructed via metabolic glycoengineering and copper-free click chemistry techniques. In both keloid xenograft and scleroderma murine models, pABs can significantly penetrate collagen matrix and reduce skin fibrosis. In summary, this research establishes a highly promising strategy for reversing skin fibrosis with hard fibrotic matrix.

Single-cell RNA-seq uncovers lineage-specific regulatory alterations of fibroblasts and endothelial cells in ligamentum flavum hypertrophy

Background

Lumbar spinal stenosis (LSS) represents a major global healthcare burden resulting in back pain and disorders of the limbs among the elderly population. The hypertrophy of ligamentum flavum (HLF), marked by fibrosis and inflammation, significantly contributes to LSS. Fibroblasts and endothelial cells are two important cells in the pathological process of ligamentum flavum (LF) fibrosis and inflammation. These two cells exhibit heterogeneity in various fibrotic diseases, yet their heterogeneity in LF fibrosis remains poorly defined.

Methods

Using single-cell RNA-seq, we examined the alterations of fibroblasts, endothelial cells, and key genes in the hypertrophic LF, aiming to establish a comprehensive single-cell atlas of LF to identify high-priority targets for pharmaceutical treatment of LSS.

Results

Here, we find there are five distinct subpopulations of LF fibroblasts: secretory-papillary, secretory-reticular, mesenchymal, pro-inflammatory, and unknown. Importantly, in HLF, the proportion of mesenchymal fibroblast subpopulations increases significantly compared to normal LF (NLF), reflecting their close association with the pathogenesis of HLF. Furthermore, critical target genes that might be involved in HLF and fibrosis, such as MGP, ASPN, OGN, LUM, and CTSK, are identified. In addition, we also investigate the heterogeneity of endothelial cells and highlight the critical role of AECs subpopulation in LF fibrosis.

Conclusion

This study will contribute to our understanding of the pathogenesis of HLF and offer possible targets for the treatment of fibrotic diseases.

Schwann cells secrete IGFBP5 to facilitate the growth of keloids

Keloids (KD) are noncancerous fibroproliferative tumors exhibiting cancer-like traits, encompass aggressive unregulated growth, absence of natural regression, and a significantly high rate of recurrence. The precise molecular mechanisms underlying KD pathology remain poorly understood. In this study, we employed single-cell sequencing to examine the characteristics of cells in KD and normal scar (NS) tissue. We evaluated Schwann cells and their secretory protein IGFBP5 function in KD. Then, the recombinant IGFBP5 protein was employed to elucidate the regulatory roles of IGFBP5 in the proliferation, migration, invasion, angiogenesis, and cell cycle of keloids fibroblasts (KF). The rabbit ear scar model was utilized to ascertain the function of IGFBP5 in vivo. We demonstrated that in KD, the proportion of Schwann cells was 4.13 times that of NS. Besides, the IGFBP5 gene exhibited an expression level that was 8.02 times higher in KD Schwann cells compared to those in NS Schwann cells. High IGFBP5 expression was positively associated with the cell proliferation, migration, invasion, angiogenesis, and cell cycle of KF. Additionally, the p53/p21/Cyclin D1 pathway regulated cell cycle and promoted cell proliferation, which was suppressed after rIGFBP5 administration. These findings suggest that Schwann cells infiltrate in KD and secrete IGFBP5 protein to promote KD growth, and targeting IGFBP5 or Schwann cell infiltration could offer novel therapeutic strategies for KD.

Should We Do Postoperative Radiotherapy After Keloid Excision as Soon as Possible? A Systematic Review and Meta-Analysis

BACKGROUND

There is no consensus on the timing of postoperative radiotherapy for keloid.

OBJECTIVE

We conducted this meta-analysis to investigate the appropriate time of radiotherapy for keloid in the first 24 hours after operation and identify the potential risk factors.

MATERIALS AND METHOD

A systematic review and meta-analysis were conducted on observational studies by searching PubMed, Embase, and the Cochrane Library. The pooled estimate of the keloid recurrence rate was calculated using a random-effects model. Subgroup analyses were conducted based on time, overtime, BED, length, and location of keloid.

RESULTS

Eight observational studies with 507 keloids met the inclusion criteria, and 7 studies were finally included in this study after sensitivity analysis. The recurrence rate was lower in the 2 hours postoperative radiotherapy group (7% CI 2-14%) than in the 6 hours postoperative radiotherapy group (16%, CI 3-36%) (P<0.01). In HDR subgroup analysis, the 2 hours group was better than the 6 hours group ((5%, CI 1-14%) versus (16%, CI 3-36.1%) (P<0.01). Subgroup analysis based on BED indicated that the BED 30 group (5%, CI 1-14%) had a lower recurrence rate than the BED 20 group (6%, CI 0-21%) and the BED 15 group (26%, CI 19-33%) (P<0.01). The keloid length >5 cm subgroup (10.4%, CI 0.4-29%) showed a higher recurrence rate than the keloid length <5 cm group (9.9%, CI 0-41%) (P=0.011).

CONCLUSION

Immediate postoperative radiotherapy within 2 hours significantly decreased recurrence rate than postoperative radiotherapy within 6 hours.

LEVEL OF EVIDENCE I

This journal requires that authors assign a level of evidence to each article. For a full description of these Evidence-Based Medicine ratings, please refer to the Table of Contents or the online Instructions to Authors   www.springer.com/00266 .

From castaways to discoveries: unveiling treasures in skin RNAseq using a novel multidimensional data processing workflow including infection-host dynamics

Defining physiology and methods to measure biological mechanisms is essential. Extensive datasets such as RNA sequencing are used with little analysis of the knowledge gained from the various methodologies. Within this work, we have processed publicly available NCBI RNAseq datasets using a combination of bioinformatics tools for the largest physiological organ, the skin. In many datasets, we identify the quality of the sample, human transcript mapping, the sex of each sample, foreign RNA from bacteria/viruses/protists, and the presence of B/T-cell immune repertoire. Processing 8,274 samples from 132 different experiments for skin samples identifies common flora of skin with elevation of protists (such as Leishmania), bacteria (Staphylococcus, Cutibacterium acnes), and viruses [Human alphaherpesvirus (HSV), Human papillomavirus (HPV)] that may be involved in physiological differences. We observed samples with the Heilongjiang tick virus, human T-cell leukemia virus type I, and equine infectious anemia virus that likely play pathological roles in physiology. Integrating the various biomarkers identified five ideal datasets for skin pathologies that elucidated a novel correlation between the normal skin flora bacterium Bacillus megaterium with major histocompatibility complex (MHC) regulation and the immune repertoire clonal expansion, particularly in patients with hidradenitis suppurativa. Finally, we show that in multiple independent experiments, biological sex is associated with multiple sex chromosome gene differences, highlighting the importance of future work in studying sex differences in skin. Data integrations and multidimensional data mapping are critical for physiological omics advancements, and this work highlights the exciting ability to apply these tools to skin physiology.NEW & NOTEWORTHY Complex bioinformatics mapping to skin RNA sequencing datasets can simultaneously map biological sex, skin-specific genes, bacteria, viruses, protists, and the acquired immune response. The integration of these datasets elucidated bacterial signatures from common skin flora while identifying novel insights on Bacillus megaterium in the acquired immune response and novel viral signatures for Heilongjiang tick virus and equine infectious anemia virus.

Hidradenitis Suppurativa Tunnels: Unveiling a Unique Disease Entity

Hidradenitis suppurativa tunnel structures lined with epithelium within the dermis are unique features of advanced disease stages that significantly impair patients' QOL. The presence of hidradenitis suppurativa tunnels is associated with a decreased likelihood of achieving a clinical response, even when receiving biological therapy. The cellular and molecular mechanisms underlying tunnel formation and pathology are only partially understood, which hampers the development of more effective targeted therapies. Tunnels create a unique microenvironment that drives a vicious cycle of hidradenitis suppurativa inflammation, with tunnel keratinocytes exhibiting an activated phenotype characterized by distinct gene expression signatures. In this review, we summarize the current literature and discuss aspects of the pathophysiology of tunnels, including the role of hair follicle epidermal stem cells in tunnel formation, potential role of fibroblast-mediated epithelial-mesenchymal transition, role of dermal papilla fibroblasts, and aberrant proinflammatory repair response contributing to the observed fibrosis and scarring. Finally, tunnel structures are characterized by unique microbial dysbiosis and an overabundance of Gram-negative anaerobes that are not targeted by current therapeutics. In addition to outlining the possible mechanisms of tunnel formation, we provide perspectives on the translation of current knowledge into more effective treatment approaches for patients with hidradenitis suppurativa tunnels.

Single-cell RNA sequencing highlights the role of proinflammatory fibroblasts, vascular endothelial cells, and immune cells in the keloid immune microenvironment

BACKGROUND

Keloids, characterized by an aberrant wound-healing process and a highly complex immune microenvironment, pose significant challenges for clinical management. Fibroblasts and vascular endothelial cells (VEC) were identified as the leading cells of keloid development. However, their roles in the keloid immune landscape have yet to be thoroughly elucidated.

METHODS

To explore the functional state of cells in the immune landscape of keloids, we conducted a single-cell RNA sequencing analysis on the tissue from three keloid lesions and two specimens of healthy skin. We simultaneously utilized available keloid data from the public database for external validation.

RESULTS

Specific subsets, such as proinflammatory fibroblasts (piF) and VEC, were markedly elevated in lesional skin compared to normal skin. Subsequent differential gene expression and Gene Ontology analyses indicated that these subsets may be involved in shaping the microenvironment. In keloids, there is an increased expression of immune-associated genes (P < 0.05), including TNFRSF6B, HGF, and TGFB3, alongside a decreased expression of inflammatory chemokines in the piF. Moreover, the significant upregulation of immune suppressive genes (P < 0.05), including CD39, CD73, and HIF1A, suggested the potential involvement of VEC as a conditional immune subpopulation in the keloid microenvironment. Immune cell communication analysis revealed preferential enrichment of macrophages and Tregs, highlighting intensified macrophage-centered interactions within the keloid microenvironment.

CONCLUSION

Our study highlighted the role of piF and VEC in the immune microenvironment of keloids for the first time, providing potential targets for therapeutic development.

Effects of embryonic origin, tissue cues and pathological signals on fibroblast diversity in humans

Fibroblasts, once perceived as a uniform cell type, are now recognized as a mosaic of distinct populations with specialized roles in tissue homeostasis and pathology. Here we provide a global overview of the expanding compendium of fibroblast cell types and states, their diverse lineage origins and multifaceted functions across various human organs. By integrating insights from developmental biology, lineage tracing and single-cell technologies, we highlight the complex nature of fibroblasts. We delve into their origination from embryonic mesenchyme and tissue-resident populations, elucidating lineage-specific behaviours in response to physiological cues. Furthermore, we highlight the pivotal role of fibroblasts in orchestrating tissue repair, connective tissue remodelling and immune modulation across diverse pathologies. This knowledge is essential to develop novel fibroblast-targeted therapies to restore steady-state fibroblast function and advance regenerative medicine strategies across multiple diseases.

Temporal evolution of fibroblast responses following salivary gland ductal ligation injury

Extracellular matrix remodeling is a natural response to injury but, excessive extracellular matrix accumulation, or fibrosis, is a causative factor in hundreds of diseases that limit organ function, regenerative responses, and can interfere with regenerative therapies. Fibrosis is closely related to inflammation, both of which occur in the salivary glands of patients treated with radiation for head and neck cancers and in patients suffering from autoimmune conditions, such as Sjögren's Disease. Despite the known involvement of fibrosis in disease and the inhibitory effects of fibrosis on tissue regeneration, the mechanisms through which extracellular matrix is elaborated in the salivary gland are poorly understood. Stromal fibroblasts are the primary matrix-producing cells and are known to drive both fibrosis and inflammation. To define the temporal responses of fibroblasts to injury, we induced a temporary obstructive injury though ligation of the primary submandibular and sublingual salivary gland ducts and then performed single-cell RNA sequencing and pathway analysis at timepoints immediately following the injury. Using bioinformatic approaches, we identified three unique fibroblast groups that dynamically respond to the injury. We characterized the changes in matrisomal and inflammatory gene expression over a 7-day time course and identified one group of fibroblasts to be the primary injury-responsive fibrogenic cell type. Understanding how fibroblasts respond at the early and later injury timepoints, along with defining signaling pathways regulated by fibroblasts, could lead to a better understanding of the contribution of fibroblast to acute injury responses to facilitate the development of therapeutics that minimize fibrosis and promote regenerative gland responses in chronic disease states.

Advances and applications in single-cell and spatial genomics

The applications of single-cell and spatial technologies in recent times have revolutionized the present understanding of cellular states and the cellular heterogeneity inherent in complex biological systems. These advancements offer unprecedented resolution in the examination of the functional genomics of individual cells and their spatial context within tissues. In this review, we have comprehensively discussed the historical development and recent progress in the field of single-cell and spatial genomics. We have reviewed the breakthroughs in single-cell multi-omics technologies, spatial genomics methods, and the computational strategies employed toward the analyses of single-cell atlas data. Furthermore, we have highlighted the advances made in constructing cellular atlases and their clinical applications, particularly in the context of disease. Finally, we have discussed the emerging trends, challenges, and opportunities in this rapidly evolving field.

Collagen fiber and cellular dynamics of axolotl skin with aging

As skin ages, its structure and function undergo significant transformations driven by complex cellular and molecular processes. In this study, we explore these changes using the axolotl, an amphibian model known for its transparent skin, allowing detailed observation of both epidermal and dermal layers. We found that axolotl skin, composed of an epidermis and a collagen-rich dermis with three distinct layers (stratum baladachinum, spongiosum, and compactum), shows clear age-related alterations. These changes include reduced fibroblast numbers, altered lattice-patterned cell morphology, disruption of the lattice patterned collagen fiber pattern, thickening the stratum spongiosum, and thinning of the stratum compactum. Notably, fibroblasts, which play a crucial role in collagen braiding, displayed diminished functionality in older axolotls. This study highlights how aging affects both the structural integrity of dermal collagen and cellular dynamics. Given the similarity between axolotl and mammalian skin, these findings may provide valuable insights into the mechanisms of skin aging and potential avenues for anti-aging therapies. This research offers a foundation for future studies aimed at understanding skin aging and regeneration.

Identifying the Pattern Characteristics of Anoikis-Related Genes in Keloid

Objective: Anoikis is a kind of programmed cell death that is triggered when cells lose contact with each other or with the matrix. However, the potential value of anoikis-related genes (ARGs) in keloid (KD) has not been investigated. Approach: We downloaded three keloid fibroblast (KF) RNA sequencing (RNA-seq) datasets from the Gene Expression Omnibus (GEO) and obtained 338 ARGs from a search of the GeneCards database and PubMed articles. Weighted correlation network analysis was used to construct the coexpression network and obtain the KF-related ARGs. The LASSO-Cox method was used to screen the hub ARGs and construct the best prediction model. Then, GEO single-cell sequencing datasets were used to verify the expression of hub genes. We used whole RNA-seq for gene-level validation and the correlation between KD immune infiltration and anoikis. Results: Our study comprehensively analyzed the role of ARGs in KD for the first time. The least absolute shrinkage and selection operator (LASSO) regression analysis identified six hub ARGs (HIF1A, SEMA7A, SESN1, CASP3, LAMA3, and SIK2). A large number of miRNAs participate in the regulation of hub ARGs. In addition, correlation analysis revealed that ARGs were significantly correlated with the infiltration levels of multiple immune cells in patients with KD. Innovation: We explored the expression characteristics of ARGs in KD, which is extremely important for determining the molecular pathways and mechanisms underlying KD. Conclusions: This study provides a useful reference for revealing the characteristics of ARGs in the pathogenesis of KD. The identified hub genes may provide potential therapeutic targets for patients. This study provides new ideas for individualized therapy and immunotherapy.

Fibroproliferative conditions: the 3R approach bridging fibrosis and tumors

Soft-tissue fibroproliferative conditions (FPCs) affect many organs. All demonstrate the accumulation of (myo)fibroblasts and extracellular matrix. Currently, FPCs are classified according to the affected body site/organ. To promote research into the etiological mechanisms that drive pathological FPCs, we propose a new, more clinically grounded, FPC classification that is based on the intent and severity of the fibroproliferation. There are three categories: responsive, replacement, and reconstructive FPCs. Reconstructive FPCs (e.g., keloids) have quasi-neoplastic behaviors, including local invasiveness, and serve as a bridge between fibrosis and cancers. Comparisons of reconstructive FPCs to both cancers and the other FPC categories may help elucidate their pathogenic cellular properties, microenvironmental components, and intracellular-signaling mechanisms. Thus, the new FPC classification may promote research in the fibrosis field.

Pronounced expression of extracellular matrix proteoglycans regulated by Wnt pathway underlies the parallel evolution of lip hypertrophy in East African cichlids

Cichlid fishes inhabiting the East African Great Lakes, Victoria, Malawi, and Tanganyika, are textbook examples of parallel evolution, as they have acquired similar traits independently in each of the three lakes during the process of adaptive radiation. In particular, 'hypertrophied lip' has been highlighted as a prominent example of parallel evolution. However, the underlying molecular mechanisms remain poorly understood. In this study, we conducted an integrated comparative analysis between the hypertrophied and normal lips of cichlids across three lakes based on histology, proteomics, and transcriptomics. Histological and proteomic analyses revealed that the hypertrophied lips were characterized by enlargement of the proteoglycan-rich layer, in which versican and periostin proteins were abundant. Transcriptome analysis revealed that the expression of extracellular matrix-related genes, including collagens, glycoproteins, and proteoglycans, was higher in hypertrophied lips, regardless of their phylogenetic relationships. In addition, the genes in Wnt signaling pathway, which is involved in promoting proteoglycan expression, was highly expressed in both the juvenile and adult stages of hypertrophied lips. Our comprehensive analyses showed that hypertrophied lips of the three different phylogenetic origins can be explained by similar proteomic and transcriptomic profiles, which may provide important clues into the molecular mechanisms underlying phenotypic parallelisms in East African cichlids.

Inhibiting the Histone Demethylase Kdm4a Restrains Cardiac Fibrosis After Myocardial Infarction by Promoting Autophagy in Premature Senescent Fibroblasts

Premature senescent fibroblasts (PSFs) play an important role in regulating the fibrotic process after myocardial infarction (MI), but their effect on cardiac fibrosis remains unknown. Here, the investigation is aimed to determine whether PSFs contribute to cardiac fibrosis and the underlying mechanisms involved. It is observed that premature senescence of fibroblasts is strongly activated in the injured myocardium at 7 days after MI and identified that Kdm4a is located in PSFs by the analysis of scRNA-seq data and immunostaining staining. Moreover, fibroblast specific gain- and loss-of-function assays showed that Kdm4a promoted the premature senescence of fibroblasts and cardiac interstitial fibrosis, contributing to cardiac remodeling in the advanced stage after MI, without influencing early cardiac rupture. ChIP-seq and ChIP-PCR revealed that Kdm4a deficiency promoted autophagy in PSFs by reducing Trim44 expression through increased levels of the H3K9me3 modification in the Trim44 promoter region. Furthermore, a coculture system revealed that Kdm4a overexpression increased the accumulation of PSFs and the secretion of senescence-associated secretory phenotype (SASP) factors, subsequently inducing cardiac fibrosis, which could be reversed by Trim44 interference. Kdm4a induces the premature senescence of fibroblasts through Trim44-mediated autophagy and then facilitates interstitial fibrosis after MI, ultimately resulting in cardiac remodeling, but not affecting ventricular rupture.

RNA-sequencing demonstrates transcriptional differences between human vocal fold fibroblasts and myofibroblasts

BACKGROUND

Differentiation of fibroblasts into myofibroblasts is necessary for wound healing, but excessive myofibroblast presence and persistence can result in scarring. Treatment for scarring is limited largely due to a lack of comprehensive understanding of how fibroblasts and myofibroblasts differ at the transcript level. The purpose of this study was to characterize transcriptional profiles of injured fibroblasts relative to normal fibroblasts, utilizing fibroblasts from the vocal fold as a model.

RESULTS

Utilizing bulk RNA sequencing technology, we identified differentially expressed genes between four cell lines of normal fibroblasts (cVFF), one line of scarred fibroblasts (sVFF), and four lines of fibroblasts treated with transforming growth factor-beta 1 (TGF-β1), representing an induced-scar phenotype (tVFF). Principal component analysis revealed clustering of normal fibroblasts separate from the clustering of fibroblasts treated with TGF-β1; scarred fibroblasts were more similar to normal fibroblasts than fibroblasts treated with TGF-β1. Enrichment analyses revealed pathways related to cell signaling, receptor-ligand activity, and regulation of cell functions in scarred fibroblasts, pathways related to cell adhesion in normal fibroblasts, and pathways related to ECM binding in fibroblasts treated with TGF-β1. Although transcriptomic profiles between scarred fibroblasts and fibroblasts treated with TGF-β1 were relatively dissimilar, the most highly co-expressed genes were enriched in pathways related to actin cytoskeleton binding, which supports the use of fibroblasts treated with TGF-β1 to represent a scarred cell phenotype.

CONCLUSIONS

Transcriptomics of normal fibroblasts differ from myofibroblasts, including from those retrieved from scar and those treated with TGF-β1. Despite large differences in transcriptomics between tVFF and sVFF, tVFF serve as a useful in vitro model of myofibroblasts and highlight key similarities to myofibroblasts extracted from scar pathology, as well as expected differences related to normal fibroblasts from healthy vocal folds.

Impact of pentoxifylline on efficacy, safety, tolerability, and treatment satisfaction of fractional carbon dioxide laser in patients with burn scars: a pilot blinded randomized controlled trial

Burn scars are significant consequence of thermal burn injuries, causing cosmetic concerns and potentially leading to symptomatic discomfort or functional limitations; therefore, continuous adoption of novel methods is warranted to improve outcomes. This study aims to assess and compare the effectiveness, safety, and satisfaction of fractional CO2 laser treatment alone versus its combination with oral pentoxifylline at a dosage of 400 mg twice daily for four months in patients with hypertrophic/keloid burn scars. In a assessor and analyst blinded randomized controlled trial, patients with hypertrophic/keloidal thermal burn scars were allocated into two intervention groups. Both groups underwent treatment with a fractional CO2 laser, while one group additionally received oral pentoxifylline at a dosage of 400 mg twice daily for four months. The assessment of scar improvement was performed using the modified Vancouver Scar Scale (mVSS) at baseline and during subsequent follow-up sessions. Significant improvements were noted within both groups, with mVSS scores decreasing from 7.73 to 4.73 in the CO2 laser group and from 7.36 to 3.91 in the combination therapy group (p < 0.001 for both). However, the between-group difference in mVSS score reduction was not statistically significant (p = 0.39). Confidence intervals for the mean change in mVSS scores from baseline to endpoint were [2.45, 3.10] for the CO2 laser group and [3.15, 3.85] for the combination therapy group. The combination therapy group also showed a more pronounced improvement in pigmentation subscore of mVSS and higher patient satisfaction rates. No adverse effects were reported in either group. Fractional CO2 laser with or without Pentoxifylline appears to be an effective and safe option for the improvement of hypertrophic/keloidal burn scars. Patient satisfaction seems to increase when the laser is combined with oral Pentoxifylline. Nevertheless, further studies involving larger patient cohorts are warranted to draw more robust conclusions.

Integration of Flow Cytometry and Single-Cell RNA Sequencing Analysis to Explore the Fibroblast Subpopulations in Keloid that Correlate with Recurrence

Objective: Fibroblasts (FBs) are the cytological basis of keloid (KD) formation. This study aimed to identify the key pathogenic target cell subpopulation involved in KD recurrence. Approach: Single-cell RNA sequencing data were retrieved from public databases, revealing distinct gene expression patterns in FB subpopulations. Flow cytometry (FCM) was used to identify the surface molecular phenotypes of FBs that affect KD recurrence. Simultaneously, logistic regression analysis was performed to assess the predictive value of changes in FB subpopulation percentages for clinical KD recurrence. Results: The percentage of keloid fibroblasts was significantly greater than that in normal tissues. Through further clustering analysis of the FB population, we obtained four subpopulations, FB1-FB4, in which the percentages of FB1 subpopulation were increased, and functional enrichment analysis suggested that the FB1 subpopulation may play a greater role in extracellular matrix collagen oversynthesis in KD. In addition, the gene expression of CD26 (DPP4), CD117 (c-KIT), and CD34 in the FB1 subpopulation was significantly higher than that in FB2-4 subpopulations. Moreover, the percentage of CD26+/CD117+/CD34+ cell subpopulations in the FCM data of patients with KD recurrence was significantly increased. Regression analysis confirmed that the CD26+/CD117+/CD34+ FB subpopulation was a risk factor for relapse. Innovation: We demonstrated that the molecular phenotypic and functional heterogeneity of FBs influences KD recurrence. Conclusion: We identified key pathogenic FB subpopulations that may affect KD development, which can be used as potential markers to predict recurrence and provide potential target cell populations for future clinical treatment.

Multi-omics analysis to explore the molecular mechanisms related to keloid

BACKGROUND

Keloid is a benign skin tumor that result from abnormal wound healing and excessive collagen deposition. The pathogenesis is believed to be linked to genetic predisposition and immune imbalance, although the precise mechanisms remain poorly understood. Current therapeutic approaches may not consistently yield satisfactory outcomes and are often accompanied by potential side effects and risks. The high recurrence rate and refractory nature of keloid nodules present significant challenges and uncertainties in their management. Given the lack of effective treatment strategies, it is essential to identify key molecular pathways and potential therapeutic targets for keloid.

OBJECTIVE

This study aimed to identify the potential pathogenic mechanisms, hub genes, and immune cell involvement in keloid formation, with the goal of providing novel insights for targeted therapies.

METHODS

We utilized a combination of bulk RNA sequencing to analyze gene expression profiles in keloid tissues. Differentially expressed genes (DEGs) were identified and subjected to pathway enrichment analysis to reveal key biological processes involved in keloid pathogenesis. Mendelian randomization was performed to investigate the causal relationship between genetic factors and keloid formation, identifying potential hub genes. Immune infiltration analysis was conducted to determine the role of specific immune cells in keloid development. Subsequently, Gene Set Enrichment Analysis (GSEA) and Gene Set Variation Analysis (GSVA) were performed to investigate the functional pathways associated with the hub genes. Network analysis was employed to identify transcription factors, miRNAs, and potential drugs in the Connectivity Map associated with the hub genes. Single-cell RNA sequencing was also used to identify cell-specific expression patterns of these genes.

RESULTS

Pathway enrichment analysis highlighted the association of keloid pathogenesis with cell proliferation and division, providing insights into the molecular processes involved. Mendelian randomization revealed that DUSP1 acts as an inhibitor of keloid formation, while HOXA5 promotes keloid pathogenesis. Immune infiltration analysis suggested that mast cells and macrophages play critical roles in the disease's progression. Based on hub gene analysis, the IL17 signaling pathway emerged as a key pathway implicated in keloid development. Further drug prediction models identified 9-methyl-5H-6-thia-4, 5-diaza-chrysene-6, 6-dioxide, zebularine, temozolomide and valproic acid targeting these hub genes.

CONCLUSION

DUSP1 and HOXA5 are hub genes in keloid pathogenesis, with DUSP1 acting as an inhibitor and HOXA5 as a promoter of disease progression. Targeting the regulatory networks associated with these genes could provide novel therapeutic strategies. Mast cells and macrophages are identified as critical immune cell types involved in the disease process. Additionally, the IL17 signaling pathway plays a crucial role in keloid development, highlighting its potential as a therapeutic target. These findings suggest that a multi-target approach focusing on these pathways could offer effective treatment options for keloid patients.

Identification and validation of immune-related biomarkers and polarization types of macrophages in keloid based on bulk RNA-seq and single-cell RNA-seq analysis

INTRODUCTION

Keloids are a common complication that occurs after injury. The pathogenesis of this disease remains unknown. Therefore, identifying immune-related biomarkers and macrophage polarization types in keloids can provide new insights into their treatment.

METHODS

In this study, keloid-related bulk RNA-seq data (GSE83286, GSE212954, GSE92566, and GSE90051) were obtained from the Gene Expression Omnibus (GEO) database. The datasets GSE83286, GSE212964, and GSE92566 were combined to form a training set, while GSE90051 was utilized as an external validation set. Differentially expressed genes (DEGs) were detected by comparing keloid and normal samples within the training set. Differentially expressed immune-related genes (DIRGs) were then determined by intersecting the DEGs with immune-related genes (IRGs). Based on the protein-protein interaction (PPI) network, the top 40 DIRGs were selected for further analyses. Weighted Gene Co-expression Network Analysis (WGCNA), in conjunction with three machine learning techniques - least absolute shrinkage and selection operator (LASSO), support vector machine-recursive feature elimination (SVM-RFE), and random forest (RF) - employed to identify biomarkers. Subsequently, a nomogram model was constructed and validated. Single-cell RNA (scRNA) analysis was used to examine the expression of biomarkers at the cell-type level. Furthermore, since keloid is a chronic inflammatory disease and the abnormal polarization of macrophages is essential for the occurrence of this kind of disease, in this study we also endeavor to elucidate the state of macrophage polarization dysregulation within keloid, with the anticipation of generating novel concepts for the treatment of keloid. Finally, western blot (WB) and immunofluorescence (IF) analyses were carried out to confirm the expression levels of the biomarkers.

RESULTS

A total of 740 DEGs were identified in the training set, comprising 331 up-regulated genes and 409 down-regulated genes. After intersecting with the IRGs, 73 DIRGs were obtained. Subsequently, the top 40 DIRGs were chosen for further analysis. Eventually, two biomarkers, namely BMP1 and IL1R1, were identified through WGCNA and the three machine learning methods. Their expression levels were then verified by single-cell analysis, WB, and IF analysis. Additionally, it was found that the number of M2 macrophages significantly increased, while the number of M1 macrophages decreased in keloids compared to normal samples.

CONCLUSION

BMP1 and IL1R1 might function as novel biomarkers and potential therapeutic targets for keloid treatment. Moreover, upregulating M1 macrophages and downregulating M2 macrophages could represent a promising approach for the treatment of keloids.

Dynamic single-cell transcriptomic reveals the cellular heterogeneity and a novel fibroblast subpopulation in laryngotracheal stenosis

BACKGROUND

Laryngotracheal stenosis (LTS), a pathological narrowing of the upper airway caused by excessive extracellular matrix (ECM) deposition, often leads to dyspnea and even respiratory failure. However, systematic studies addressing the specific subpopulations and their contribution to LTS development still remain underexplored.

RESULTS

We collected laryngotracheal tissue at multiple time points of LTS rat model, established by injuring their laryngotracheal lining, and performed dynamic single-cell RNA sequencing (scRNA-seq) to elucidate the transcriptomic atlas of LTS development. The results showed, from the inflammatory state to the repair/fibrotic state, infiltration of immune cells such as monocyte macrophages decreased and fibroblast increased. We delineated the markers and functional status of different fibroblasts subsets and identified that fibrotic fibroblasts may originate from multiple fibroblast subpopulations, including a new subpopulation characterized by the expression of chondrogenic markers such as Ucma and Col2a1, we designated this subcluster as chondrocyte injury-related fibroblasts (CIRF). Furthermore, we categorized monocytes/macrophages into several subtypes and identified that SPP1 high macrophages represented the largest macrophage subpopulation in LTS, providing evidence to clarify the importance of SPP1 macrophages in fibrosis disease. Our findings also revealed the interactions among these cells to explore the molecular mechanism associated with LTS pathogenesis.

CONCLUSIONS

Our study, for the first time, conducted dynamic scRNA-seq on LTS, revealing the cellular heterogeneity and providing a valuable resource for exploring the intricate molecular landscape of LTS. We propose CIRF may represent a tissue-specific fibroblast lineage in LTS and potentially originate from cells in the perichondrium of the trachea and transform into fibrotic fibroblasts. Integration of our study with those of other respiratory fibrotic diseases will allow for a comprehensive understanding of airway remodeling in respiratory diseases and exploring potential new therapeutic targets for their treatment.

Single-cell RNA sequencing reveals a new mechanism of endothelial cell heterogeneity and healing in diabetic foot ulcers

Diabetic foot ulcers (DFU) are a common and severe complication among diabetic patients, posing a significant burden on patients' quality of life and healthcare systems due to their high incidence, amputation rates, and mortality. This study utilized single-cell RNA sequencing technology to deeply analyze the cellular heterogeneity of the skin on the feet ofDFU patients and the transcriptomic characteristics of endothelial cells, aiming to identify key cell populations and genes associated with the healing and progression of DFU. The study found that endothelial cells from DFU patients exhibited significant transcriptomic differences under various conditions, particularly in signaling pathways related to inflammatory responses and angiogenesis. Through trajectory analysis and cell communication research, we revealed the key role of endothelial cell subsets in the development of DFU and identified multiple important gene modules associated with the progression of DFU. Notably, the promoting effect of the SH3BGRL3 gene on endothelial cell proliferation, migration, and angiogenic capabilities under high glucose conditions was experimentally verified, providing a new potential target and theoretical basis for the treatment of DFU. This study not only enhances the understanding of the pathogenesis ofDFU but also provides a scientific basis for the development ofnew therapeutic strategies.

Diversity and heterogeneity in human pancreaticobiliary maljunction revealed by single-cell RNA sequencing

PURPOSE

The etiology and pathogenesis of pancreaticobiliary maljunction (PBM) remain unclear, thus a comprehensive investigation of cellular diversity and microenvironmental differences is pivotal to elucidate the mechanisms driving PBM.

METHODS

We performed single-cell RNA sequencing on bile duct tissues from six patients, including three with PBM and three without (non-PBM). Pathway enrichment, transcription factor analysis, and cell-cell communication were analyzed to explore cellular interactions and functional states.

RESULTS

A total of 90,996 single cells and 11 distinct cell lineages were identified, revealing significant differences in cellular composition between the two groups. PBM group was characterized by a higher proportion of endothelial cells and fibroblasts, while B and T cells were less abundant. Three subtypes of fibroblasts, antigen-presenting, inflammatory, and myofibroblastic cancer-associated fibroblasts, with the myofibroblast subtype being predominant in PBM. We found heightened activity of the WNT and TWEAK signaling pathways in PBM, as well as increased ligand-receptor interactions between fibroblasts and other cell types, including epithelial and endothelial cells.

CONCLUSION

Fibroblasts play a central role in driving fibrosis and tissue remodeling in PBM through specific signaling pathways. These insights provide a foundation for future therapeutic strategies aimed at modulating fibroblast activity to prevent or mitigate fibrosis in PBM.

Immune-featured stromal niches associate with response to neoadjuvant immunotherapy in oral squamous cell carcinoma

Tumor stromal cells (TSCs) play a crucial yet underexplored role in the tumor microenvironment (TME). This study uses single-cell sequencing and spatial transcriptomics on paired tumor specimens from 22 patients with oral squamous cell carcinoma (OSCC) enrolled in a randomized two-arm phase 2 trial, receiving neoadjuvant anti-PD-1 mono-immunotherapy or anti-PD-1 plus docetaxel-cisplatin-5-fluorouracil (TPF) immunochemotherapy. Single-cell analysis reveals increased TSCs within the TME of responders in immunochemotherapy. Notably, significant post-treatment upregulation of SELP+ high endothelial venules (HEVs) and APOD+ myofibroblastic cancer-associated fibroblasts (myCAFs), alongside a decline in STMN1+ capillary endothelial cells (cECs), is specific to the immunochemotherapy cohort. In contrast, MYF5+ muscle satellite cells (MSCs) are upregulated in non-responders to mono-immunotherapy. SELP+ HEVs and APOD+ myCAFs foster favorable immunomodulatory stromal niches for improved outcomes, while STMN1+ cECs and MYF5+ MSCs form immunosuppressive niches in tumor invasion regions, highlighting therapeutic targets. The trial was registered at ClinicalTrials.gov, and the registration number is NCT04649476.

Increased melanin induces aberrant keratinocyte - melanocyte - basal - fibroblast cell communication and fibrogenesis by inducing iron overload and ferroptosis resistance in keloids

BACKGROUND

Keloid is a typical skin fibrotic disease with unclear mechanisms and limited therapeutic options. Fibroblast-induced fibrogenesis is a crucial cause of KD. However, the types of cells involved in fibroblast fibrogenesis in KD and the specific mechanisms are unclear. This study aimed to investigate the role of melanocyte-secreted melanin in promoting fibroblast fibrogenesis and its mechanism and to evaluate the potential therapeutic effect of intervening melanin in treating keloid.

METHODS

The activity of pigmentation-related pathways in KD melanocytes was examined using single-cell RNA-sequence (scRNA-seq) analysis. Masson-Fontana staining or isolated melanin quantification detected the melanin levels and distribution in the skin and cells. Collagen deposition, wounding healing, and proliferation analysis were employed to integratively assess fibroblast fibrogenesis. After melanin treatment, bulk-seq identified fibroblasts' differentially expressed genes (DEGs). The iron levels were detected by Perl's staining or isolated iron quantification. Cell viability, LipidROS, and malondialdehyde assay accessed the ferroptosis levels. The therapeutic potential of ML329 was evaluated in keloid-bearing mice.

RESULTS

We found the enriched skin pigmentation-related pathways in the melanocytes of keloid by single-cell RNA-sequence (scRNA-seq) analysis. We further validated increased melanin levels in keloid patients. Additionally, melanin positively correlated with the Keloid Area and Severity Index in keloid. Furthermore, melanocyte-secreted melanin significantly promoted fibroblast proliferation, migration, and collagen synthesis. Mechanically, melanin increased basal cell permeability and inflammation to facilitate its transfer to the dermis, where it further activated fibroblasts by evoking iron overload and ferroptosis resistance. Consistently, iron overload and ferroptosis resistance were validated in primary fibroblasts and skin tissues of keloid patients. Inhibition of iron overload and ferroptosis resistance effectively diminish melanin-induced fibrogenesis. Interestingly, melanin induced iron overload and ferroptosis resistance in melanocytes in an autocrine manner and further stimulated keratinocytes to take up melanin to deepen skin color by upregulating the F2R-like trypsin receptor 1 (F2RL1). In vivo, the delivery of ML329, a microphthalmia-associated transcription factor (MITF) inhibitor, could suppress melanogenesis and alleviate keloid in human keloid-bearing nude mice. Meanwhile, ML329 decreased the iron content and restored the sensitivities of ferroptosis.

CONCLUSION

Collectively, melanin-lowing strategies may appear as a potential new therapeutic target for keloid.

Lapatinib ameliorates skin fibrosis by inhibiting TGF-β1/Smad and non-Smad signaling pathway

Skin fibrosis, characterized by excessive accumulation of extracellular matrix (ECM) in the dermis, can lead to hypertrophic scars and impaired mobility. The ErbB family of receptor tyrosine kinases, including ErbB1 and ErbB2, plays a crucial role in organ fibrosis, but their specific impact on skin fibrosis is less understood. This study investigated the role of ErbB1 and ErbB2 in skin fibrosis and the therapeutic potential of lapatinib, a dual ErbB1 and ErbB2 tyrosine kinase inhibitor. Using qPCR, cell culture assays, Western blotting, and in vivo models, we found significant upregulation of ErbB1 and ErbB2 in keloid tissues and fibroblasts. Lapatinib treatment resulted in a dose-dependent decrease in ErbB1 and ErbB2 expression, which suppressed the expression of fibroblast activation markers. Our findings suggest that lapatinib may be a promising therapeutic agent for skin fibrosis by targeting ErbB1/ErbB2 and modulating the TGF-β1/Smad2/3/Erk/Akt signalling pathways. These results warrant further clinical investigation into lapatinib for treating skin fibrosis and related conditions.

The HOX code of human adult fibroblasts reflects their ectomesenchymal or mesodermal origin

Fibroblasts, the most abundant cell type in the human body, play crucial roles in biological processes such as inflammation and cancer progression. They originate from the mesoderm or neural-crest-derived ectomesenchyme. Ectomesenchyme-derived fibroblasts contribute to facial formation and do not express HOX genes during development. The expression and role of the HOX genes in adult fibroblasts is not known. We investigated whether the developmental pattern persists into adulthood and under pathological conditions, such as cancer. We collected adult fibroblasts of ectomesenchymal and mesodermal origins from distinct body parts. The isolated fibroblasts were characterised by immunocytochemistry, and their transcriptome was analysed by whole genome profiling. Significant differences were observed between normal fibroblasts from the face (ectomesenchyme) and upper limb (mesoderm), particularly in genes associated with limb development, including HOX genes, e.g., HOXA9 and HOXD9. Notably, the pattern of HOX gene expression remained consistent postnatally, even in fibroblasts from pathological tissues, including inflammatory states and cancer-associated fibroblasts from primary and metastatic tumours. Therefore, the distinctive HOX gene expression pattern can serve as an indicator of the topological origin of fibroblasts. The influence of cell position and HOX gene expression in fibroblasts on disease progression warrants further investigation.

Deciphering Pain and Pruritus in Keloids from the Perspective of Neurological Dysfunction: Where Are We Now?

Keloids are a typical skin fibroproliferative disease that can cause severe aesthetic and functional concerns. Pain and pruritus are the most common clinical symptoms of keloids, but the mechanisms underlying these symptoms remain unclear. The peripheral nervous system plays a pivotal role in the transmission of superficial sensation signals. Mounting evidence has shown potential correlations between disturbance in the peripheral nervous system and pain and pruritus in keloids. Here, we summarize the role of neurological dysfunction in the development of pain and pruritus, with a specific focus on neuroanatomical alterations, the dysfunction of sensory nerves, and neurogenic inflammation.

Spatiotemporal single-cell roadmap of human skin wound healing

Wound healing is vital for human health, yet the details of cellular dynamics and coordination in human wound repair remain largely unexplored. To address this, we conducted single-cell multi-omics analyses on human skin wound tissues through inflammation, proliferation, and remodeling phases of wound repair from the same individuals, monitoring the cellular and molecular dynamics of human skin wound healing at an unprecedented spatiotemporal resolution. This singular roadmap reveals the cellular architecture of the wound margin and identifies FOSL1 as a critical driver of re-epithelialization. It shows that pro-inflammatory macrophages and fibroblasts sequentially support keratinocyte migration like a relay race across different healing stages. Comparison with single-cell data from venous and diabetic foot ulcers uncovers a link between failed keratinocyte migration and impaired inflammatory response in chronic wounds. Additionally, comparing human and mouse acute wound transcriptomes underscores the indispensable value of this roadmap in bridging basic research with clinical innovations.

Altered Arginine Metabolism Affects Proliferation and Radiosensitivity of Keloids

Keloid is characterised by the reprogramming of cellular metabolism, wherein keloid cells adapt their metabolic pathways to meet the demands for energy and biosynthetic precursors. Investigating the intricate relationship between cellular metabolism and the biological behaviour of keloid holds the potential to yield novel therapeutic strategies for keloid. To elucidate the molecular alterations and potential underlying regulatory mechanisms in keloids, we created comprehensive metabolic profiling at the pathway level by analysing metabolomic, transcriptomic and single-cell RNA-sequencing data from keloids and adjacent skin. Viability assay and clonogenic assay were performed to validate the function of the metabolic pathway(s) in primary keloid fibroblast cells. Integrated analysis revealed an upregulation of arginine and proline metabolism in keloids. According to single-cell RNA-seq data, elevated expression of genes related to arginine and proline metabolism, such as P4HA3, P4HA2, P4HA1, PYCR1, OAT and ASS1, was predominately highly expressed in fibroblast-2. Fibroblast-2 displayed more obvious phenotypes of mesenchymal fibroblast. Critical genes from integrated analysis including P4HA3, P4HA2, P4HA1, PYCR1 and AZIN2, and metabolites including fumaric acid and 2-oxo-5-amino-pentanoic acid showed prognostic relevance with disease-free survival of keloid. Additionally, an In vitro study showed that arginine deprivation therapy (ADT) inhibited and radiosensitised the proliferation of keloid-derived fibroblasts. In conclusion, our thorough multiomics study deepens our understanding of the link between arginine and proline metabolism and keloid proliferation and radiosensitivity. Elevated activity of arginine and proline metabolism in mesenchymal fibroblasts may be a potential therapeutic pathway for keloid.

Comprehensive RNA Sequencing Analysis Identifies Network Hub Genes and Biomarkers Differentiating Desmoid-type Fibromatosis From Reactive Fibrosis

Desmoid-type fibromatosis (DTF) is a benign but locally aggressive neoplasm characterized by persistent fibroblast activation, unlike reactive fibrosis (RF), where fibroblast activation is transient. Although the Wnt/β-catenin signaling pathway is known to play a role in DTF pathogenesis, the specific genetic drivers contributing to this abnormal fibroblast activation are not fully understood. To identify additional driver genes that underlie the persistent activation of fibroblasts in DTF, we conducted a comparative transcriptome analysis between 29 DTF and 14 RF tissue samples, identifying 4267 differentially expressed genes (DEGs) specific to DTF. These DTF-specific DEGs were significantly associated with pathways involved in embryonic limb morphogenesis and muscle contraction, whereas RF-specific DEGs were linked to immune response and apoptosis. Using weighted gene coexpression network analysis to further elucidate the key regulatory circuits associated with persistent activation of DTF fibroblasts, we identified a highly DTF-specific gene module comprising 120 genes. This module was also significantly enriched in other fibroproliferative conditions showing persistent fibroblast activation, such as keloid disease and idiopathic pulmonary fibrosis. Subsequent analyses identified 7 driver transcription factors (ZNF536, IRX5, TWIST2, NKD2, PAX9, SHOX2, and SALL4) within this DTF-specific module that may contribute to the sustained activation of DTF fibroblasts. We further assessed the utility of 5 key genes from this module (TWIST2, LRRC15, CTHRC1, SHOX2, and SALL4) as potential biomarkers to distinguish DTF from RF using immunohistochemistry. All markers demonstrated excellent diagnostic performance, with TWIST2 showing exceptionally high sensitivity and specificity, surpassing β-catenin, the current standard biomarker for DTF. In conclusion, our study identifies gene modules and driver transcription factors that are highly specific to DTF, offering new insights into the genetic underpinnings of abnormal fibroblast activation in DTF. We also propose novel biomarkers that could improve the diagnostic accuracy and clinical management of DTF.

Direct fibroblast reprogramming: an emerging strategy for treating organic fibrosis

Direct reprogramming has garnered considerable attention due to its capacity to directly convert differentiated cells into desired cells. Fibroblasts are frequently employed in reprogramming studies due to their abundance and accessibility. However, they are also the key drivers in the progression of fibrosis, a pathological condition characterized by excessive extracellular matrix deposition and tissue scarring. Furthermore, the initial stage of reprogramming typically involves deactivating fibrotic pathways. Hence, direct reprogramming offers a valuable method to regenerate target cells for tissue repair while simultaneously reducing fibrotic tendencies. Understanding the link between reprogramming and fibrosis could help develop effective strategies to treat damaged tissue with a potential risk of fibrosis. This review summarizes the advances in direct reprogramming and reveals their anti-fibrosis effects in various organs such as the heart, liver, and skin. Furthermore, we dissect the mechanisms of reprogramming influenced by fibrotic molecules including TGF-β signaling, mechanical signaling, inflammation signaling, epigenetic modifiers, and metabolic regulators. Innovative methods for fibroblast reprogramming like small molecules, CRISPRa, modified mRNA, and the challenges of cellular heterogeneity and senescence faced by in vivo direct reprogramming, are also discussed.

Transcriptomic responses of lung mesenchymal cells during pneumonia

The role of mesenchymal cells during respiratory infection is not well defined, including whether, which, and how the different types of mesenchymal cells respond. We collected all mesenchymal cells from lung single-cell suspensions of mice that were naive (after receiving only saline vehicle), pneumonic (after intratracheal instillation of pneumococcus 24 hours previously), or resolved from infection (after nonlethal pneumococcal infections 6 weeks previously) and performed single-cell RNA sequencing. Cells clustered into 5 well-separated groups based on their transcriptomes: matrix fibroblasts, myofibroblasts, pericytes, smooth muscle cells, and mesothelial cells. Fibroblasts were the most abundant and could be further segregated into Pdgfra+Npnt+Ces1d+Col13a1+ alveolar fibroblasts and Cd9+Pi16+Sca1+Col14a1+ adventitial fibroblasts. The cells from naive and resolved groups overlapped in dimension reduction plots, suggesting the mesenchymal cells returned to baseline transcriptomes after resolution. During pneumonia, all mesenchymal cells responded with altered transcriptomes, revealing a core response that had been conserved across cell types as well as distinct mesenchymal cell type-specific responses. The different subsets of fibroblasts induced similar gene sets, but the alveolar fibroblasts responded more strongly than the adventitial fibroblasts. These data demonstrated diverse and specialized immune activities of lung mesenchymal cells during pneumonia.

Molecular profiling of skin cells identifies distinct cellular signatures in radiation-induced skin injury across various stages in the murine dataset

BACKGROUND

Radiation-induced skin injury (RISI) commonly manifests in cancer patients undergoing radiotherapy (RT). However, a universally accepted standard for treating radiation injury has not yet been established. Our objective was to provide a detailed molecular overview of skin pre- and post-radiation therapy, aiming to enhance our understanding of the subclusters and molecular mechanisms contributing to radiodermatitis.

METHODS

C57BL/6 mice were subjected to a single fraction (20 Gy) of RT targeting the right dorsal skin. We then employed integrated single-cell RNA sequencing (scRNA-seq) to analyze skin samples from mice at 7 and 30 days after radiation exposure, as well as from non-irradiated mice. The Seurat analysis pipeline, Cellchat, SCP, and ssGSEA were used to define the cell types and mechanisms involved in radiation-induced skin injury. Reverse transcription polymerase chain reaction (RT-PCR), multiplex immunofluorescent staining, and other datasets (GSE130183, GSE193564, and GSE193807) were used to validate our findings.

RESULTS

Thirty-two distinct cell clusters encompassing 71,412 cells were identified. We discovered that cycling keratinocytes (KCs), with the BMP signaling pathway enriched, could activate the Wnt pathway, as well as the SMAD pathways, driving the wound healing and fibrosis processes in RISI. Terminally differentiated secretory-papillary fibroblasts (Fibs) are capable of attracting immune cells, which contributes to the pathogenesis of RISI. Lymphatic endothelial cells (ECs) with pro-inflammatory properties play a critical role in the pathogenesis of RISI by facilitating leukocyte migration. Our analysis also highlighted enhanced ligand-receptor interactions, notably the interactions between chemokines like CXCL10, CCL2, and ACKR1, across subclusters of inflammatory KCs, Fibs, ECs, and immune cells, underscoring their pivotal role in leukocyte recruitment in RISI.

CONCLUSIONS

Cycling KCs, secretory-papillary Fibs, and lymphatic ECs play critical roles in RISI progression. Targeting the interactions of these subclusters with immune cells might help improve the severity of RISI. Furthermore, our study provides a valuable resource for understanding the interactions among immune cells in the context of RISI.

FOXO4-DRI induces keloid senescent fibroblast apoptosis by promoting nuclear exclusion of upregulated p53-serine 15 phosphorylation

Keloids are pathological scars exhibiting tumour-like aggressiveness and high recurrence rate. Here we find increased proportion of pro-inflammatory and mesenchymal fibroblast subpopulations and senescent fibroblasts, and enhanced expression of senescence-associated secretory phenotype genes using single-cell RNA sequencing analysis, as well as elevated p16 protein and more β-galactosidase-positive cells in keloids. The up-regulated p53-serine15 phosphorylation (p53-pS15) in keloids is identified by phosphospecific protein microarray and western blotting. We further demonstrate that a senolytic FOXO4-D-retro-inverso-isoform peptide (FOXO4-DRI) promotes apoptosis and decreases G0/G1 phase cells in pro-senescence models of keloid organ cultures and fibroblasts, accompanied with p53-pS15 nuclear exclusion. Our study indicates that upregulation of p53-pS15 and p16 maintains a persistent senescent microenvironment to promote cell cycle arrest and apoptosis resistance in keloid fibroblasts. FOXO4-DRI shows potential as a treatment targeting the senescence and apoptosis resistance, and holds promise as an approach to prevent the aggressiveness and relapse of keloids.

Keratinocyte-driven dermal collagen formation in the axolotl skin

Type I collagen is a major component of the dermis and is formed by dermal fibroblasts. The development of dermal collagen structures has not been fully elucidated despite the major presence and importance of the dermis. This lack of understanding is due in part to the opacity of mammalian skin and it has been an obstacle to cosmetic and medical developments. We reveal the process of dermal collagen formation using the highly transparent skin of the axolotl and fluorescent collagen probes. We clarify that epidermal cells, not dermal fibroblasts, contribute to dermal collagen formation. Mesenchymal cells (fibroblasts) play a role in modifying the collagen fibers already built by keratinocytes. We confirm that collagen production by keratinocytes is a widely conserved mechanism in other model organisms. Our findings warrant a change in the current consensus about dermal collagen formation and could lead to innovations in cosmetology and skin medication.

Antigen-presenting fibroblasts: emerging players in immune modulation and therapeutic targets

Antigen-presenting fibroblasts are a newly recognized subset that challenges the traditional view of these cells as mere structural components. Under pathological or environmental stimuli, fibroblasts acquire antigen-presenting capabilities through the expression of MHC-II molecules and co-stimulatory factors, enabling them to interact with T cells and modulate immune responses. These specialized fibroblasts have been identified across various tissues and diseases, where they play context-dependent roles, either amplifying immune dysregulation or contributing to immune homeostasis. This review synthesizes recent advances in understanding the origins, activation, and functions of antigen-presenting fibroblasts. It highlights their role in promoting pathogenic immune responses and offering therapeutic opportunities through targeted modulation. Advancing our understanding of antigen-presenting fibroblasts holds great promise for developing innovative approaches to immune modulation and therapy across a range of diseases.

Identification of pro-fibrotic cellular subpopulations in fascia of gluteal muscle contracture using single-cell RNA sequencing

Fibrosis is a common and integral pathological feature in various chronic diseases, capable of affecting any tissue or organ. Fibrosis within deep fascia is implicated in many myofascial disorders, including gluteal muscle contracture (GMC), Dupuytren's disease, plantar fasciitis, iliotibial band syndrome, and chronic muscle pain. Despite its clinical significance, deep fascia fibrosis remains considerably under-researched compared to other fibrotic conditions. Single-cell RNA-sequencing (scRNA-seq) has been used to investigate cellular heterogeneity in fibrotic tissues. However, to our knowledge, only a few studies have applied scRNA-seq to explore cellular heterogeneity in deep fascia, and none have specifically examined fibrotic fascia. In this study, we performed scRNA-seq analysis on fibrotic fascia associated with GMC and compared them to nonfibrotic control fascial samples. Our findings show that fibroblast and macrophage cells play critical roles in pathological tissue remodeling within fibrotic deep fascia. We observed an upregulation of various collagens, proteoglycans, and extracellular matrix (ECM) glycoproteins in contracture deep fascia, attributed to the widespread activation of fibroblast subclusters. Additionally, two pro-fibrotic macrophage subpopulations, SPP1+ MP and ECM-like MP, appear to facilitate ECM deposition in fibrotic deep fascia by either regulating fibroblast activation or directly contributing to ECM production. The SPP1+ MP and ECM-like MP cells, as well as the signal interaction between SPP1+ MP and fibroblast cells, present potential therapeutic target for treating GMC and other related myofascial disorders.

MSC-EVs and UCB-EVs promote skin wound healing and spatial transcriptome analysis

Extracellular vesicles (EVs) are important paracrine mediators derived from various cells and biological fluids, including plasma, that are capable of inducing regenerative effects by transferring bioactive molecules such as microRNAs (miRNAs). This study investigated the effect of mesenchymal stem cell-derived extracellular vesicles (MSC-EVs) isolated from umbilical cord blood and human umbilical cord plasma-derived extracellular vesicles (UCB-EVs) on wound healing and scar formation reduction. Spatial transcriptomics (ST) was used to study the effects of MSC-EVs and UCB-EVs on the heterogeneity of major cell types and wound healing pathways in mouse skin tissue. MSC-EVs and UCB-EVs were isolated using ultracentrifugation and identified using transmission electron microscopy, nanoparticle tracking analysis, and western blot. The effects of MSC-EVs and UCB-EVs on human dermal fibroblast-adult cell (HDF-a) migration and proliferation were evaluated using cell scratch assays, cell migration assays, and cell proliferation assays. In vivo, MSC-EVs and UCB-EVs were injected around full-cut wounds to evaluate their efficacy of wound healing by measuring wound closure rates and scar width and performing histological analysis. ST was performed on skin tissue samples from mice in each group after wound healing to analyze the heterogeneity of major cell types compared with the control group and investigate potential mechanisms affecting wound healing and scar formation. In vitro experiments demonstrated that MSC-EVs and UCB-EVs promoted the proliferation and migration of HDF-a cells. Local injection of MSC-EVs and UCB-EVs into the periphery of a mouse skin wound accelerated re-epithelialization, promoted wound healing, and reduced scar width. ST analysis of skin tissue from each group after wound healing revealed that MSC-EVs and UCB-EVs reduced the relative expression of marker genes in myofibroblasts, regulated wound healing, and decreased scar formation by reducing the expression of the TGF-β signaling pathway and increasing the expression of the Wnt signaling pathway. The results suggest that MSC-EVs and UCB-EVs play a significant role in the activity of cord blood plasma-derived mesenchymal stem cells and cord blood plasma. They can be considered promising new agents for promoting skin wound healing.

Epidermal stem cell derived exosomes-induced dedifferentiation of myofibroblasts inhibits scarring via the miR-203a-3p/PIK3CA axis

Hypertrophic scar (HS) is a common fibroproliferative disorders with no fully effective treatments. The conversion of fibroblasts to myofibroblasts is known to play a critical role in HS formation, making it essential to identify molecules that promote myofibroblast dedifferentiation and to elucidate their underlying mechanisms. In this study, we used comparative transcriptomics and single-cell sequencing to identify key molecules and pathways that mediate fibrosis and myofibroblast transdifferentiation. Epidermal stem cell-derived extracellular vesicles (EpiSC-EVs) were isolated via ultracentrifugation and filtration, followed by miRNA sequencing to identify miRNAs targeting key molecules. After in vitro and in vivo treatment with EpiSC-EVs, we assessed antifibrotic effects through scratch assays, collagen contraction assays, Western blotting, and immunofluorescence. Transcriptomic sequencing and rescue experiments were used to investigate the molecular mechanism by which miR-203a-3p in EpiSC-EVs induces myofibroblast dedifferentiation. Our results indicate that PIK3CA is overexpressed in HS tissues and positively correlates with fibrosis. EpiSC-EVs were absorbed by scar-derived fibroblasts, promoting dedifferentiation from myofibroblasts to quiescent fibroblasts. Mechanistically, miR-203a-3p in EpiSC-EVs plays an essential role in inhibiting PIK3CA expression and PI3K/AKT/mTOR pathway hyperactivation, thereby reducing scar formation. In vivo studies confirmed that EpiSC-EVs attenuate excessive scarring through the miR-203a-3p/PIK3CA axis, suggesting EpiSC-EVs as a promising therapeutic approach for HS.

Single-cell RNA sequencing reveals the heterogeneity of myofibroblasts in wound repair

Skin wound repair involves myofibroblasts crucial for tissue integrity. This study utilized single-cell RNA sequencing to explore myofibroblast diversity in various wound healing scenarios. Analysis of 89,148 cells from skin ulcers, keloids, and normal scars identified 13 cell clusters. Myofibroblast subcluster analysis unveiled 11 subsets, with subclusters 1 and 9 predominant in ulcers. Subcluster 1 exhibited heightened matrix metalloproteinase expression and involvement in bacterial response and angiogenesis, crucial in inflammation. Tissue validation confirmed subcluster 1 significance., while animal models supported upregulated CA12, TDO2, and IL-7R in chronic ulcers. These findings illuminate myofibroblast heterogeneity and their impact on wound healing, offering insights into potential therapeutic targets.

Specific Non-Coding RNAs Involve in and Regulate the Transcriptional Network during Keloid Formation

Keloid formation is an undesirable outcome of wound healing and is detrimental to patients' physical and mental health, while the molecular regulators of its pathogenesis, especially non-coding RNAs (ncRNAs), are largely unknown. In this study, we integrated and analyzed RNA-seq and miRNA microarray datasets of skin samples from keloid-prone and healthy normal individuals to detect the dysregulated long ncRNAs (lncRNAs) and miRNAs. We excavated 583 and 104 keloid-specific lncRNAs and miRNAs, respectively. Moreover, the molecular functions of these ln-cRNAs and miRNAs are all related to ossification. Next, we constructed the relationship between lncRNAs and immune cell infiltration, and found the macrophages, NK cells, and dendritic cells were specifically dysregulated in keloid-prone or normal groups during wound healing. We constructed the potential regulatory network between these cell types and 20 dysregulated lncRNAs, suggesting their regulatory function in keloid formation. At last, we constructed the competitive endogenous RNA network and found two hub lncRNAs and five miRNAs, including DLEU1 and SLC25A21-AS1, miR-197-5p, miR-940, miR-6765-5p, miR-711, and miR-4284, which were highly dysregulated during keloid formation. In summary, these results demonstrate that lncRNAs and miRNAs play important roles and form a regulatory network in the pathogenesis, immune infiltration, and development of keloid formation.

Fibroblasts in heterotopic ossification: mechanisms and therapeutic targets

Heterotopic ossification (HO) refers to the abnormal formation of bone in non-skeletal tissues. Fibroblasts have traditionally been viewed as stationary cells primarily responsible for producing extracellular matrix during tissue repair and fibrosis. However, recent discoveries regarding their plasticity-encompassing roles in inflammation, extracellular matrix remodeling, and osteogenesis-highlight their potential as key contributors to the development of HO. In this review, we systematically summarize the diverse phenotypic and functional plasticity of fibroblasts in HO. Furthermore, we evaluate the possible interaction between fibroblasts and macrophages in pathophysiological processes and signaling pathways. Finally, we highlight the potential strategies for preventing and treating HO by targeting fibroblast activities.

Identifying Potential Drug Targets for Keloid: A Mendelian Randomization Study

Keloids are a skin fibrosis disease characterized by troublesome symptoms, a varying degree of recurrence and inevitable side effects from treatments. Thus, identifying their drug targets is necessary. A 2-sample Mendelian randomization analysis was conducted using proteins from the intersection of the deCODE database and "The Druggable Genome and Support for Target Identification and Validation in Drug Development" as the exposure variable. The outcome variable was based on recently published GWAS of keloids. Summary data-based Mendelian randomization and colocalization analysis was employed to distinguish pleiotropy from linkage. Candidate targets underwent drug target analysis. The primary findings were validated through single-cell RNA-sequencing data, Western Blot and immunofluorescence staining on keloids. Seven proteins were identified as potential drug targets for keloids. Among these proteins, Hedgehog-interacting protein, neurotrimin [NTM], KLKB1, and CRIPTO showed positive correlations with keloids, while PLXNC1, SCG3 and PDGFD exhibited negative correlations. Combined with the single-cell RNA-sequencing data, NTM, PLXNC1, and PDGFD were found highly expressed in the fibroblasts. NTM showed a significant increase in keloids as compared to normal scars. In accordance with the analysis, higher levels of protein expression of NTM in keloids compared to normal skin was observed. The identified proteins may be appealing drug targets for keloids treatment with a special emphasis on NTM.

Single-cell transcriptomic profiling of lung fibroblasts in a bleomycin-induced systemic sclerosis mouse model

Systemic sclerosis (SSc) is a complex autoimmune disease characterized by fibrosis, vascular abnormalities, and immune dysfunction, with no definitive cure. Patients with progressive pulmonary fibrosis face a high mortality risk, underscoring the urgent need for effective treatments. Although fibroblasts are recognized as key drivers of fibrosis, the precise molecular mechanisms remain poorly understood. In this study, we employ single-cell RNA sequencing to explore the role of fibroblasts in pulmonary fibrosis. Using a mouse model induced by subcutaneous bleomycin administration, we identify two distinct fibroblast subpopulations: nephronectin-positive (NPNT) and peptidase inhibitor 16-positive cells(PI16). NPNT-positive fibroblasts, located around the alveoli, exhibit increased extracellular matrix expression following bleomycin treatment. To further understand pulmonary fibrosis, subcutaneous and intratracheal bleomycin-induced mouse models are compared. A comparative gene expression analysis reveals shared and unique features between the models, highlighting the complexity of the fibrotic process. These findings offer valuable insights into the molecular mechanisms of SSc-associated pulmonary fibrosis and may inform the development of therapies targeting specific fibroblast subpopulations or pathways.

Mindin regulates fibroblast subpopulations through distinct Src family kinases during fibrogenesis

Fibrosis results from excessive extracellular matrix (ECM) deposition, which causes tissue stiffening and organ dysfunction. Activated fibroblasts, central to fibrosis, exhibit increased migration, proliferation, contraction, and ECM production. However, it remains unclear if the same fibroblast performs all of the processes that fall under the umbrella term of "activation." Owing to fibroblast heterogeneity in connective tissues, subpopulations with specific functions may operate under distinct regulatory controls. Using a transgenic mouse model of skin fibrosis, we found that Mindin (also known as spondin-2), secreted by Snail-transgenic keratinocytes, differentially regulates fibroblast subpopulations. Mindin promotes migration and inflammatory gene expression in SCA1+ dermal fibroblasts via Fyn kinase. In contrast, it enhances contractility and collagen production in papillary CD26+ fibroblasts through c-Src signaling. Moreover, in the context of the fibrotic microenvironment of the tumor stroma, we found that differential responses of resident fibroblast subpopulations to Mindin extend to the generation of functionally heterogeneous cancer-associated fibroblasts. This study identifies Mindin as a key orchestrator of dermal fibroblast heterogeneity, reshaping cellular dynamics and signaling diversity in the complex landscapes of skin fibrosis and cancer.