Single-cell transcriptomes of the human skin reveal age-related loss of fibroblast priming

Procyanidin C1 ameliorates aging-related skin fibrosis through targeting EGFR to inhibit TGFβ/SMAD pathway

BACKGROUND

Aging-related skin fibrosis (SF) is a complex condition with limited treatment options. Procyanidin C1 (PCC1), a natural polyphenolic compound with demonstrated senolytic activity, has emerged as a potential therapeutic agent for fibrotic disorders through its selective elimination of senescent cells. However, its therapeutic efficacy and mechanisms in aging-related SF remain unclear.

PURPOSE

This study aimed to investigate the mechanisms of PCC1 in aging-related SF.

RESULTS

In D-galactose-induced L929 cells, PCC1 treatment significantly attenuated the expression of both senescence-associated markers (IL-1β, P16, P21 and LMNB1) and fibrosis-related markers (α-SMA, LOXL2 and COL1). Network pharmacology and experimental validation (molecular docking, DARTS, CETSA, MST) identified EGFR as a primary target, with PCC1 directly binding to and inhibiting EGFR phosphorylation. Furthermore, PCC1 treatment effectively down-regulated TGFβ1 expression and suppressed SMAD2/3 phosphorylation in D-galactose-induced L929 cells. Notably, PCC1 blocked NSC228155-induced EGFR phosphorylation and inhibited ERK/MAPK, AKT/mTOR and TGFβ/SMAD pathway activation. In bleomycin-induced SF mice, PCC1 significantly attenuated epidermal hyperplasia, improved collagen structure, restored the collagen I/III ratio, and reduced EGFR phosphorylation along with TGFβ1 expression and SMAD2/3 phosphorylation.

CONCLUSION

This study elucidates that PCC1 exerts its anti-fibrotic effects through dual mechanisms: resistance to cellular senescence and modulation of fibroblast heterogeneity. By directly binding to EGFR and inhibiting its phosphorylation, PCC1 subsequently suppresses multiple downstream signaling cascades, ultimately ameliorating TGFβ/SMAD-mediated SF. These findings establish PCC1 as a promising therapeutic candidate for aging-related skin fibrosis, offering a novel approach through targeted EGFR inhibition and comprehensive pathway modulation.

Disturbed Spatial WNT Activation-A Potential Driver of the Reticularized Skin Phenotype in Systemic Sclerosis

OBJECTIVE

Little is known on the mechanisms necessary to maintain the physiologic adult human skin integrity. This study aims to quantitatively describe anatomic changes in systemic sclerosis (SSc)-skin compared with controls and investigate the underlying mechanisms.

METHODS

Skin morphology was histologically assessed in 23 patients with SSc, 18 controls, and 15 patients with hypertrophic scars. Spatial WNT/β-catenin-activation was analyzed by RNAscope and immunofluorescence staining. Enrichment of reticular marker genes in predefined fibroblast subpopulations was done using Gene Ontology (GO) enrichment and gene set enrichment analysis.

RESULTS

SSc skin showed a decrease in number (P < 0.0001/P = 0.0004), area (P < 0.0001), and height (P < 0.0001) of papillae compared with controls and hypertrophic scars, respectively. The expression of papillary/reticular marker genes shifted toward a reticular expression profile in SSc. On the level of previously defined fibroblast populations, the increase of reticular marker genes was particularly pronounced in the PI16+ and SFRP4+ populations (P < 0.0001, respectively). Mechanistically, the expression of the WNT/β-catenin target AXIN2 and the number of fibroblasts with nuclear β-catenin-staining-pattern increased in the papillary compared with the reticular dermis in healthy skin. This polarization was lost in SSc with a two-fold increase in β-catenin-positive fibroblasts and AXIN2-expressing fibroblasts throughout the dermis (P = 0.0095). Enrichment of genes related to WNT/β-catenin-regulation was found in the PI16+ population that also relocates from the reticular to the papillary dermis in SSc.

CONCLUSION

We demonstrate an association of the "reticularized" skin phenotype in SSc with a profound loss of physiologic spatial WNT/β-catenin-activation. Rescuing the spatial WNT/β-catenin-activation might help restore the physiologic skin organization in future therapeutic approaches of fibrosing disorders.

Imbalanced redox dynamics induce fibroblast senescence leading to impaired stem cell pools and skin aging

Skin function depends on a meticulously regulated dynamic interaction of distinct skin compartments such as the epidermis and dermis. Adaptive responses at the molecular and cellular level are essential for these interactions - and if dysregulated - drive skin aging and other pathologies. After defining the role of redox homeodynamics in physiology and aging pathology, we focus on the redox distress-dependent aging of dermal fibroblasts including their progenitors. We here discuss the prime role of senescent fibroblasts in the control of their own endogenous niche and stem cell niches for epidermal stem cells, hair follicle stem cells, adipocyte precursors and muscle stem cells. We here review that redox imbalance induced reduction in Insulin-like Growth Factor-1 drives skin aging by the depletion of stem cell pools. This IGF-1 reduction is mediated via the redox-sensitive transcription factor JunB and also by the redox-dependent changes in sphingolipid-metabolism, among others. In addition, we will discuss the changes in the extracellular matrix of the skin affecting cellular senescence and the skin integrity and function in aging. The aim is a deeper understanding of the two main redox-dependent hubs such as JunB-induced depletion of IGF-1, and the sphingolipid-mediated remodeling of the cell membrane with its impact on IGF-1, fibroblast heterogeneity, function, senescence and plasticity in skin aging.

The spatial and single-cell landscape of skin: Charting the multiscale regulation of skin immune function

Immune regulation is a key function of the skin, a barrier tissue that exhibits spatial compartmentalization of innate and adaptive immune cells. Recent advances in single-cell RNA sequencing (scRNA-seq) and spatial transcriptomics (ST) have facilitated systems-based investigations into the molecular and cellular features of skin immunity at single-cell resolution, identifying cell types that maintain homeostasis in a coordinated manner, and those that exhibit dysfunctional cell-cell interactions in disease. Here, we review how technological innovation is uncovering the multiple scales of heterogeneity in the immune landscape of the skin. The microanatomic scale encompasses the skin's diverse cellular components and multicellular spatial organization, which govern the functional cell interactions and behaviors necessary to protect the host. On the macroanatomic scale, understanding heterogeneity in cutaneous tissue architecture across anatomical sites promises to unearth additional functional immune variation and resulting disease consequences. We focus on how single-cell and spatial dissection of the immune system in experimental models and in humans has led to a deeper understanding of how each cell type in the skin contributes to overall immune function in a context-dependent manner. Finally, we highlight translational opportunities for adopting these technologies, and insights gleaned from them, into the clinic.

The antioxidant stress effect of granulin precursor in vitiligo

The imbalance of the skin redox system is regarded as a crucial factor contributing to the loss of melanocytes in vitiligo. However, it remains unclear whether alterations in signal transmission between melanocytes and other cells impact the homeostasis of the skin microenvironment. Hence, leveraging single-cell sequencing and microarray data, we investigated the role of cell-cell and ligand receptor interactions in the pathogenesis of vitiligo. We discovered that the granulin-sortilin 1 ligand-receptor serves as an essential bridge for communication between melanocytes and other skin cells in normal skin, yet it is significantly downregulated in vitiligo lesions. Enrichment analysis indicates that the activation of granulin-sortilin 1 ligand-receptor is closely associated with the regulation of oxidative stress. In vitro experiments have verified that progranulin, the protein encoded by the granulin gene, enhances the ability of melanocytes to resist cell death induced by reactive oxygen species and markedly upregulates the expression of nuclear factor erythroid 2-related factor 2 and Heme Oxygenase-1. Notably, this process can be impeded by the interaction inhibitor. Moreover, the expression of nuclear factor erythroid 2-related factor 2 might be linked to the transcription of transcription factor EB activated by progranulin. In conclusion, the granulin-sortilin 1 ligand-receptor can activate the intracellular antioxidant system to counteract melanocyte death. The impairment of the granulin-sortilin 1 ligand-receptor may be implicated in melanocyte loss in vitiligo.

Angiopoietin-TIE2 feedforward circuit promotes PIK3CA-driven venous malformations

Venous malformations (VMs) are vascular anomalies lacking curative treatments, often caused by somatic PIK3CA mutations that hyperactivate the PI3Kα-AKT-mTOR signaling pathway. Here, we identify a venous-specific signaling circuit driving disease progression, where excessive PI3Kα activity amplifies upstream TIE2 receptor signaling through autocrine and paracrine mechanisms. In Pik3caH1047R-driven VM mouse models, single-cell transcriptomics and lineage tracking revealed clonal expansion of mutant endothelial cells with a post-capillary venous phenotype, characterized by suppression of the AKT-inhibited FOXO1 and its target genes, including the TIE2 antagonist ANGPT2. An imbalance in TIE2 ligands, likely exacerbated by aberrant recruitment of smooth muscle cells producing the agonist ANGPT1, increased TIE2 activity in both mouse and human VMs. While mTOR blockade had limited effects on advanced VMs in mice, inhibiting TIE2 or ANGPT effectively suppressed their growth. These findings uncover a PI3K-FOXO1-ANGPT-TIE2 circuit as a core driver of PIK3CA-related VMs and highlight TIE2 as a promising therapeutic target.

Gene set optimization for single cell transcriptomics

Although single cell RNA-sequencing (scRNA-seq) provides unprecedented insights into the biology of complex tissues, analyzing such data on a gene-by-gene basis is challenging due to the large number of tested hypotheses and consequent low statistical power and difficult interpretation. These issues are magnified by the increased noise, significant sparsity and multi-modal distributions characteristic of single cell data. One promising approach for addressing these challenges is gene set testing, or pathway analysis. Unfortunately, statistical and biological differences between single cell and bulk transcriptomic data make it challenging to use existing gene set collections, which were developed for bulk tissue analysis, on scRNA-seq data. In this paper, we describe a procedure for customizing gene set collections originally created for bulk tissue analysis to reflect the structure of gene activity within specific cell types. Our approach leverages information about mean gene expression in the 81 human cell types profiled via scRNA-seq by the Human Protein Atlas (HPA) Single Cell Type Atlas. This HPA information is used to compute cell type-specific gene and gene set weights that can be used to filter or weight gene set collections. As demonstrated through the analysis of immune cell scRNA-seq data using gene sets from the Molecular Signatures Database (MSigDB), accounting for cell type-specificity can significantly improve gene set testing power and interpretability.

Protocol for detecting 3D dermal fibroblast cellular dynamics in mice using an intravital imaging technique

Dermal fibroblasts play a central role in the production and remodeling of dermal extracellular matrix. Their spatially distinct subpopulations exhibit different functions during skin homeostasis, wound healing, and other diseases such as fibrosis and cancer. Here, we present a protocol for detecting 3D dermal fibroblast cellular dynamics in mice without fixing the tissue using an intravital imaging technique. We describe steps for preparing, labeling, and mounting mice. We then describe detailed procedures for intravital imaging, recovery, and quantification. For complete details on the use and execution of this protocol, please refer to Rognoni et al.1.

Deciphering the Dysregulating IGF-1-SP1-CD248 Pathway in Fibroblast Functionality during Diabetic Wound Healing

Reduced fibroblast activity is a critical factor in the progression of diabetic ulcers. CD248, a transmembrane glycoprotein prominently expressed in activated fibroblasts, plays a pivotal role in wound healing. However, the role of CD248 in diabetic wound healing and the CD248 regulatory pathway remains largely unexplored. Our study shows that CD248 expression is significantly reduced in skin wounds from both patients and mice with diabetes. Single-cell transcriptome data analyses reveal a marked reduction of CD248-enriched secretory-reticular fibroblasts in diabetic wounds. We identify IGF-1 as a key regulator of CD248 expression through the protein kinase B/mTOR signaling pathway and the SP1 transcription factor. Overexpression of CD248 enhances fibroblast motility, elucidating the under-representation of CD248-enriched fibroblasts in diabetic wounds. Immunohistochemical staining of diabetic wound samples further confirms low SP1 expression and fewer CD248-positive secretory-reticular fibroblasts. Further investigation reveals that elevated TNFα levels in diabetic environment promotes IGF-1 resistance, and inhibiting IGF-1 induced CD248 expression. In summary, our findings underscore the critical role of the IGF1-SP1-CD248 axis in activating reticular fibroblasts during wound-healing processes. Targeting this axis in fibroblasts could help develop a therapeutic regimen for diabetic ulcers.

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.

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.

Heterogeneity of the tumor immune cell microenvironment revealed by single-cell sequencing in head and neck cancer

Head and neck cancer (HNC) is the sixth most common disease in the world. The recurrence rate of patients is relatively high, and the heterogeneity of tumor immune microenvironment (TIME) cells may be an important reason for this. Single-cell sequencing (SCS) is currently the most promising and mature application in cancer research. It can identify unique genes expressed in cells and study tumor heterogeneity. According to current research, the heterogeneity of immune cells has become an important factor affecting the occurrence and development of HNC. SCSs can provide effective therapeutic targets and prognostic factors for HNC patients through analyses of gene expression levels and cell heterogeneity. Therefore, this study analyzes the basic theory of HNC and the development of SCS technology, elaborating on the application of SCS technology in HNC and its potential value in identifying HNC therapeutic targets and biomarkers.

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.

Beyond circulating B cells: Characteristics and role of tissue-infiltrating B cells in systemic sclerosis

B cells play a key role in the pathophysiology of systemic sclerosis (SSc). While they are less characterized than their circulating counterparts, tissue-infiltrating B cells may have a more direct pathological role in tissues. In this review, we decipher the multiple evidence of B cells infiltration in the skin and lungs of SSc patients and animal models of SSc but also of other chronic fibrotic diseases with similar pathological mechanisms such as chronic graft versus host disease, idiopathic pulmonary fibrosis or morphea. We also recapitulate the current knowledge about mechanisms of B cells infiltration and their functions in tissues. Finally, we discuss B cell targeted therapies, and their specific impact on infiltrated B cells. Understanding the local consequences of infiltrating B cells is an important step for a better management of patients and the improvement of therapies in SSc.

Single-cell morphology encodes functional subtypes of senescence in aging human dermal fibroblasts

Cellular senescence, a hallmark of aging, reveals context-dependent phenotypes across multiple biological length scales. Despite its mechanistic importance, identifying and characterizing senescence across cell populations is challenging. Using primary dermal fibroblasts, we combined single-cell imaging, machine learning, several induced senescence conditions, and multiple protein biomarkers to define functional senescence subtypes. Single-cell morphology analysis revealed 11 distinct morphology clusters. Among these, we identified three as bona fide senescence subtypes (C7, C10, and C11), with C10 exhibiting the strongest age dependence within an aging cohort. In addition, we observed that a donor's senescence burden and subtype composition were indicative of susceptibility to doxorubicin-induced senescence. Functional analysis revealed subtype-dependent responses to senotherapies, with C7 being most responsive to the combination of dasatinib and quercetin. Our single-cell analysis framework, SenSCOUT, enables robust identification and classification of senescence subtypes, offering applications in next-generation senotherapy screens, with potential toward explaining heterogeneous senescence phenotypes based on the presence of senescence subtypes.

miRNA-29 regulates epidermal and mesenchymal functions in skin repair

MicroRNAs (miRNAs) control organogenesis in mammals by inhibiting translation of mRNA. Skin is an excellent model to study the role of miRNAs in epidermis and the mesenchyme. Previous research demonstrated miRNA-29 family functions in skin; however, the mRNA targets and the downstream mechanisms of miRNA-29-mediated regulation are missing. We used the miRNA crosslinking and immunoprecipitation method to find direct targets of miRNA-29 in keratinocytes and fibroblasts from human skin. miRNA-29 inhibition using modified antisense oligonucleotides in 2D and 3D cultures of keratinocytes and fibroblasts enhanced cell-to-matrix adhesion through autocrine and paracrine mechanisms of miRNA-29-dependent tissue growth. We reveal a full transcriptome of human keratinocytes with enhanced adhesion to the matrix, which supports regeneration of the epidermis and is regulated by miRNA-29. Impact statement The functions of small, therapeutically targetable microRNA molecules identified in our study can provide a new approach to improve wound healing by restoring and enhancing the inner molecular mechanisms of a cell and its surrounding matrix. We also provide a plethora of new mRNA targets for follow-up studies of cell adhesion and extracellular matrix formation in humans.

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.

Recent Developments in Single-Cell Metabolomics by Mass Spectrometry─A Perspective

Recent advancements in single-cell (sc) resolution analyses, particularly in sc transcriptomics and sc proteomics, have revolutionized our ability to probe and understand cellular heterogeneity. The study of metabolism through small molecules, metabolomics, provides an additional level of information otherwise unattainable by transcriptomics or proteomics by shedding light on the metabolic pathways that translate gene expression into functional outcomes. Metabolic heterogeneity, critical in health and disease, impacts developmental outcomes, disease progression, and treatment responses. However, dedicated approaches probing the sc metabolome have not reached the maturity of other sc omics technologies. Over the past decade, innovations in sc metabolomics have addressed some of the practical limitations, including cell isolation, signal sensitivity, and throughput. To fully exploit their potential in biological research, however, remaining challenges must be thoroughly addressed. Additionally, integrating sc metabolomics with orthogonal sc techniques will be required to validate relevant results and gain systems-level understanding. This perspective offers a broad-stroke overview of recent mass spectrometry (MS)-based sc metabolomics advancements, focusing on ongoing challenges from a biologist's viewpoint, aimed at addressing pertinent and innovative biological questions. Additionally, we emphasize the use of orthogonal approaches and showcase biological systems that these sophisticated methodologies are apt to explore.

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.

High resolution tissue and cell type identification via single cell transcriptomic profiling

Tissue identification can be instrumental in reconstructing a crime scene but remains a challenging task in forensic investigations. Conventionally, identifying the presence of certain tissue from tissue mixture by predefined cell type markers in bulk fashion is challenging due to limitations in sensitivity and accuracy. In contrast, single-cell RNA sequencing (scRNA-Seq) is a promising technology that has the potential to enhance or even revolutionize tissue and cell type identification. In this study, we developed a high sensitive general purpose single cell annotation pipeline, scTissueID, to accurately evaluate the single cell profile quality and precisely determine the cell and tissue types based on scRNA profiles. By incorporating a crucial and unique reference cell quality differentiation phase of targeting only high confident cells as reference, scTissueID achieved better and consistent performance in determining cell and tissue types compared to 8 state-of-art single cell annotation pipelines and 6 widely adopted machine learning algorithms, as demonstrated through a large-scale and comprehensive comparison study using both forensic-relevant and Human Cell Atlas (HCA) data. We highlighted the significance of cell quality differentiation, a previously undervalued factor. Thus, this study offers a tool capable of accurately and efficiently identifying cell and tissue types, with broad applicability to forensic investigations and other biomedical research endeavors.

The Skin-to-Mucosa Ratio Defines the Osteogenic Potential of Lip Fibroblasts

Fibroblasts isolated from discarded lip tissue obtained during cheiloplasty in patients with cleft lip/palate (CLP) show promising osteogenic potential and may be an appealing cell source for autologous bone regeneration. As the lip is a mucocutaneous junction, explant cultures from unseparated lip biopsies produce mesenchymal outgrowths composed of skin- and mucosa-derived fibroblasts. The proportions of the 2 fibroblast populations, however, differ among CLP patients and depend on the morphology of the excised sample, which is unique for each donor. Understanding the osteogenic activities of CLP fibroblast populations with varying skin-to-mucosa ratios is critical for their therapeutic application. We isolated CLP fibroblasts from 10 unseparated lip biopsies and comprehensively evaluated them for their bone differentiation capacities in vitro, demonstrating heterogeneous osteogenic potentials. Because there are no markers that can distinguish skin from mucosa fibroblasts, we used the respective and matching CLP keratinocytes to ascertain the skin-to-mucosa ratio of the 10 specimens. Thus, we found that CLP fibroblasts isolated from biopsies with high skin-to-mucosa ratios had a much higher osteogenic capacity than those derived from biopsies with low skin-to-mucosa ratios. To validate and solidify these findings, we carefully separated skin and mucosa tissues during corrective lip surgery to isolate pure skin and mucosa CLP lip fibroblasts. Indeed, skin had a higher osteogenic potential than their mucosal counterparts did. Furthermore, we discovered that the high osteogenic activity in skin was limited to specific subpopulations of yet unknown identities. Our findings indicate that skin fibroblasts perform better than their mucosal counterparts do, even though both types of fibroblasts can differentiate into bone-forming cells.

Inflammatory Transformation of Skin Basal Cells as a Key Driver of Cutaneous Aging

This study comprehensively investigated keratinocyte subpopulation heterogeneity and developmental trajectories during skin aging using single-cell sequencing, transcriptomics, and facial aging-related genome-wide association studies (GWAS) data. We identified three major subpopulations: basal cells (BCs), spinous cells (SCs), and IFI27+ keratinocytes. Single-cell pseudotime analysis revealed that basal cells can differentiate along two distinct paths: toward spinous differentiation or the inflammatory state. With aging, the proportion of IFI27+ cells significantly increased, displaying more active inflammatory and immunomodulatory signals. Through cell-cell communication analysis, we found that the signaling pathways, including NOTCH, PTPR, and PERIOSTIN, exhibited distinct characteristics along different branches. Integration of the GWAS data revealed significant loci on chromosomes 2, 3, 6, and 9 that were spatially correlated with key biological pathways (including antigen processing, oxidative stress, and apoptosis). These findings reveal the complex cellular and molecular mechanisms underlying skin aging, offering potential targets for novel diagnostic approaches and therapeutic interventions.

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.

Integrated Single-Cell Analysis Reveals Spatially and Temporally Dynamic Heterogeneity in Fibroblast States during Wound Healing

Wound healing is a dynamic process over temporal and spatial scales. Key to repair outcomes are fibroblasts; yet, how they modulate healing across time and in different wound regions remains incompletely understood. By integrating single-cell RNA-sequencing datasets of mouse skin and wounds, we infer that fibroblasts are the most transcriptionally dynamic skin-resident cells, evolving during postnatal skin maturation and rapidly after injury toward distinct late scar states. We show that transcriptional dynamics in fibroblasts are largely driven by genes encoding extracellular matrix and signaling factors. Lineage trajectory inference and spatial gene mapping reveal that Prg4-expressing fibroblasts transiently emerge along early wound edges. Within days, they become replaced by long-lasting and likely noninterconverting fibroblast populations, including Col25a1-expressing and Pamr1-expressing fibroblasts that occupy subepidermal and deep scar regions, respectively, where they engage in reciprocal signaling with immune cells. Signaling inference shows that fibroblast-immune crosstalk repeatedly uses some signaling pathways across wound healing time, whereas use of other signaling pathways is time and space limited. Collectively, we uncovered high transcriptional plasticity by wound fibroblasts, with early states transiently forming distinct microniches along wound edges and in the fascia, followed by stable states that stratify scar tissue into molecularly dissimilar upper and lower layers.

How Can Spatial Transcriptomic Profiling Advance Our Understanding of Skin Diseases?

Spatial transcriptomic (ST) profiling is the mapping of gene expression within cell populations with preservation of positional context and represents an exciting new approach to develop our understanding of local and regional influences upon skin biology in health and disease. With the ability to probe from a few hundred transcripts to the entire transcriptome, multiple ST approaches are now widely available. In this paper, we review the ST field and discuss its application to dermatology. Its potential to advance our understanding of skin biology in health and disease is highlighted through the illustrative examples of 3 research areas: cutaneous aging, tumorigenesis, and psoriasis.

Senescence as a molecular target in skin aging and disease

Skin aging represents a multifactorial process influenced by both intrinsic and extrinsic factors, collectively known as the skin exposome. Cellular senescence, characterized by stable cell cycle arrest and secretion of pro-inflammatory molecules, has been implicated as a key driver of physiological and pathological skin aging. Increasing evidence points towards the role of senescence in a variety of dermatological diseases, where the accumulation of senescent cells in the epidermis and dermis exacerbates disease progression. Emerging therapeutic strategies such as senolytics and senomorphics offer promising avenues to target senescent cells and mitigate their deleterious effects, providing potential treatments for both skin aging and senescence-associated skin diseases. This review explores the molecular mechanisms of cellular senescence and its role in promoting age-related skin changes and pathologies, while compiling the observed effects of senotherapeutics in the skin and discussing the translational relevance.

Unraveling aging from transcriptomics

Research into aging constitutes a pivotal endeavor aimed at elucidating the underlying biological mechanisms governing aging and age-associated diseases, as well as promoting healthy longevity. Recent advances in transcriptomic technologies, such as bulk RNA sequencing (RNA-seq), single-cell transcriptomics, and spatial transcriptomics, have revolutionized our ability to study aging at unprecedented resolution and scale. These technologies present novel opportunities for the discovery of biomarkers, elucidation of molecular pathways, and development of targeted therapeutic strategies for age-related disorders. This review surveys recent breakthroughs in different types of transcripts on aging, such as mRNA, long noncoding (lnc)RNA, tRNA, and miRNA, highlighting key findings and discussing their potential implications for future studies in this field.

Regulation of pathologic fibroblast functions in digestive diseases: a role for hypoxia?

The recent uncovering of fibroblast heterogeneity has given great insight into the versatility of the stroma. Among other cellular processes, fibroblasts are now thought to contribute to the coordination of immune responses in a range of chronic inflammatory diseases and cancer. Although the pathologic roles of myofibroblasts, inflammatory fibroblasts, and cancer-associated fibroblasts in disease are reasonably well understood, the mechanisms behind their activation remain to be uncovered. In the gastrointestinal (GI) tract, several interleukins and tumor necrosis factor superfamily members have been identified as possible mediators driving the acquisition of inflammatory and fibrotic properties in fibroblasts. In addition to cytokines, other microenvironmental factors such as nutrient and oxygen availability are likely contributors to this process. In this respect, the phenomenon of low cellular oxygen levels known as hypoxia is common in a plethora of GI diseases. Indeed, the cross talk between hypoxia and inflammation is well-documented, with an abundance of studies suggesting that oxygen-sensing enzymes may have regulatory effects on inflammatory signaling pathways such as NF-κB. However, the impact that this has in GI fibroblasts in the context of chronic diseases has not been fully uncovered. Here we discuss the role of fibroblasts in GI diseases, the mediators that have emerged as regulators of their functions and the potential impact of hypoxia in this process, highlighting areas that require further investigation.

SenSkin™: a human skin-specific cellular senescence gene set

Cellular senescence gene sets have been leveraged to overcome the inadequate sensitivity or specificity of single markers. However, growing evidence of heterogeneity among tissues in senescent cell phenotypes and gene expression profiles has highlighted the need for tissue-specific gene sets. SenSkin™ was curated by an expert review of literature on cellular senescence in the skin and characterized with pathway analysis. To validate SenSkin™, it was evaluated for enrichment with chronological aging in a bulk RNA-sequencing (RNA-seq) dataset and a pseudobulk RNA-seq dataset. Further, changes to SenSkin™ in different skin cell types with photoaging were evaluated in two single-cell RNA-seq datasets. SenSkin™ predominantly included genes related to the senescence-associated secretory phenotype (SASP), which were associated with metabolism and multiple aspects of immune responses. SenSkin™ was more enriched in chronologically aged skin than other commonly used cellular senescence and aging gene sets. In scRNA-seq, SenSkin™ displayed significant upregulation due to photoaging in ten skin cell types. In conclusion, SenSkin™ is a human skin-specific senescence gene set validated in chronological aging and photoaging, which may be more effective at detecting senescent cells in the skin than non-tissue-specific gene sets.

THSD4 promotes hair growth by facilitating dermal papilla and hair matrix interactions

Introduction: Aging causes striking changes in the extracellular matrix (ECM) in hair follicles, which has a profound influence on hair growth. How the ECM of dermal papilla (DP), the master regulator of hair growth, changes during aging remains largely unknown. Methods: Herovici staining, Western Blotting and immunofluorescence were used to assess DP ECM and protein expression in hair follicles. Bulk and single cell RNA-sequencing were used to analyze gene expression and predict upstream and downstream regulators of target genes. Skin organoid and mouse models were used for functional validation of molecular mechanisms. Results: Aged follicle DP shows drastic depletion of ECM in which Thrombospondin Type 1 Domain Containing 4 (Thsd4) is highly downregulated. THSD4 is specifically expressed in the interface between DP and hair matrix (HM). It promotes hair growth by enhancing the interaction between dermal (DP) and epithelial cells (HM) through the SDC4-THSD4-CXCL1 signaling axis in both skin organoids and mouse models. Murine dorsal hair follicles show upregulated THSD4, enhanced DP-HM interaction, and hair growth following exposure to low temperature. Conclusions: THSD4 is a key micro- and macro-environmental mediator to promote hair growth by facilitating epidermal-mesenchymal interactions during aging. These findings demonstrate the therapeutic potential of low-temperature treatment for treating unwanted hair loss.

Identifying differentiation markers between dermal fibroblasts and adipose-derived mesenchymal stromal cells (AD-MSCs) in human visceral and subcutaneous tissues using single-cell transcriptomics

BACKGROUND

Adipose-derived mesenchymal stromal cells (AD-MSCs) and fibroblasts are both widely used in regenerative medicine, demonstrating significant potential for personalized cell therapy. A major challenge in their use lies in their high biological similarity, encompassing morphology, differentiation capabilities, and flow cytometric markers, making their distinction difficult.

METHODS

In our study, we aimed to compare AD-MSCs obtained from two types of adipose tissue, subcutaneous and visceral, alongside skin fibroblasts. Notably, all tissue samples were sourced from the same donors. We analyzed the cells for surface antigens via flow cytometry and conducted single-cell RNA sequencing, followed by verification with quantitative PCR (qPCR).

RESULTS

Our results revealed phenotypic similarities between the isolated AD-MSCs and dermal fibroblasts, particularly in the expression of markers characteristic of AD-MSCs. However, through in-depth analyses, we identified distinct differences between these cell types. Specifically, we pinpointed 30 genes exhibiting the most significant variations in expression between AD-MSCs and fibroblasts. These genes are associated with biological processes such as tissue remodeling, cell movement, and activation in response to external stimuli. Among them, MMP1, MMP3, S100A4, CXCL1, PI16, IGFBP5, COMP were further validated using qPCR, clearly demonstrating their potential to differentiate between AD-MSCs and fibroblasts.

CONCLUSIONS

Our scRNA-seq analysis elucidates the transcriptional landscape of AD-MSCs and fibroblasts with unprecedented resolution, highlighting both the population-specific markers and the intrapopulation heterogeneity. Our findings underscore the importance of employing high-resolution techniques for cell identification.

Carboxylesterase 1-mediated endocannabinoid metabolism in skin: role in melanoma progression in BRafV600E/Pten-/- mice

BACKGROUND

Melanoma is a highly aggressive skin cancer with a poor prognosis. The endocannabinoids 2-arachidonoylgylcerol (2-AG) and anandamide have been linked to melanoma progression, though their roles remain unclear. We hypothesized that the 2-AG-arachidonate-prostaglandin axis could drive aggressive melanoma progression.

METHODS

The genetically engineered melanoma mouse model B6-Tyr::CreERT2; BRafCA; PtenloxP was characterized by targeted metabolomics. Functionally expressed serine hydrolases in the tumor tissue were identified by chemoproteomics. Pharmacological inhibition of carboxylesterase 1 (CES1) was achieved through chronic in vivo i.p. treatment with JZL184 (10 mg/kg daily), confirmed by activity-based protein profiling (ABPP) and targeted lipidomics. CES1-mediated 2-AG hydrolysis was further confirmed in radiotracer-based assays using CES1-transfected cell lines.

RESULTS

The diacylglycerol and protein kinase C activator 1-stearoyl-2-arachidonoyl-sn-glycerol (SAG) was significantly elevated in the nodular-like melanoma tissues, along with 2-AG and arachidonic acid (ARA), compared to normal skin. AEA and other N-acylethanolamines were decreased, while, notably, prostaglandin levels remained unchanged. Significant changes in the levels of neuromodulators and neurotransmitters, including serotonin and adenosine, were observed. Pronounced differences between serine hydrolase activity in normal skin and melanoma tissue were identified by ABPP. Intriguingly, CES1 was identified as the only 2-AG-hydrolyzing enzyme in this melanoma tissue, as MAGL and ABHD6/12 were not expressed. The MAGL inhibitor JZL184 also efficiently inhibited CES1 in vitro and in vivo, increasing glycerol esters and reducing tumor progression. Additionally, scRNA-seq data from previous studies revealed divergent MAGL/CES1 expression patterns across different human melanoma subtypes.

CONCLUSIONS

A role of CES1 expression in skin is demonstrated for the first time. Our study suggests that 2-AG degradation to arachidonate favors melanoma progression, either reflecting the carcinogenic role of ARA or that monoacylglycerols like 2-AG and/or other CES1 substrates may exert antitumor effects, indicating that CES1 could be a potential therapeutic target. CES1 expression and high SAG, 2-AG, and ARA levels may be a signature of specific BRAF-driven malignant melanoma subtypes which are associated with discrete metabolic adaptations.

Exploring the heterogeneous targets of metabolic aging at single-cell resolution

Our limited understanding of metabolic aging poses major challenges to comprehending the diverse cellular alterations that contribute to age-related decline, and to devising targeted interventions. This review provides insights into the heterogeneous nature of cellular metabolism during aging and its response to interventions, with a specific focus on cellular heterogeneity and its implications. By synthesizing recent findings using single-cell approaches, we explored the vulnerabilities of distinct cell types and key metabolic pathways. Delving into the cell type-specific alterations underlying the efficacy of systemic interventions, we also discuss the complexity of integrating single-cell data and advocate for leveraging computational tools and artificial intelligence to harness the full potential of these data, develop effective strategies against metabolic aging, and promote healthy aging.

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.

Single-cell sequencing delineates T-cell clonality and pathogenesis of the parapsoriasis disease group

BACKGROUND

Mycosis fungoides (MF), the most common cutaneous T-cell lymphoma, is often underdiagnosed in early stages because of similarities with benign dermatoses such as atopic dermatitis (AD). Furthermore, the delineation from what is called "parapsoriasis en plaque", a disease that can appear either in a small- or large-plaque form, is still controversial.

OBJECTIVE

We sought to characterize the parapsoriasis disease spectrum.

METHODS

We performed single-cell RNA sequencing of skin biopsies from patients within the parapsoriasis-to-early-stage MF spectrum, stratified for small and large plaques, and compared them to AD, psoriasis, and healthy control skin.

RESULTS

Six of 8 large-plaque lesions harbored either an expanded alpha/beta or gamma/delta T-cell clone with downregulation of CD7 expression, consistent with a diagnosis of early-stage MF. In contrast, 6 of 7 small-plaque lesions were polyclonal in nature, thereby lacking a lymphomatous phenotype, and also revealed a less inflammatory microenvironment than early-stage MF or AD. Of note, polyclonal small- and large-plaque lesions characteristically harbored a population of NPY+ innate lymphoid cells and displayed a stromal signature of complement upregulation and antimicrobial hyperresponsiveness in fibroblasts and sweat gland cells, respectively. These conditions were clearly distinct from AD or psoriasis, which uniquely harbored CD3+CRTH2+ IL-13 expressing "TH2A" cells, or strong type 17 inflammation, respectively.

CONCLUSION

These data position polyclonal small- and large-plaque parapsoriasis lesions as a separate disease entity that characteristically harbors a so far undescribed innate lymphoid cell population. We thus propose a new term, "polyclonal parapsoriasis en plaque", for this kind of lesion because they can be clearly differentiated from early- and advanced-stage MF, psoriasis, and AD on several cellular and molecular levels.

SenPred: a single-cell RNA sequencing-based machine learning pipeline to classify deeply senescent dermal fibroblast cells for the detection of an in vivo senescent cell burden

BACKGROUND

Senescence classification is an acknowledged challenge within the field, as markers are cell-type and context dependent. Currently, multiple morphological and immunofluorescence markers are required. However, emerging scRNA-seq datasets have enabled an increased understanding of senescent cell heterogeneity.

METHODS

Here we present SenPred, a machine-learning pipeline which identifies fibroblast senescence based on single-cell transcriptomics from fibroblasts grown in 2D and 3D.

RESULTS

Using scRNA-seq of both 2D and 3D deeply senescent fibroblasts, the model predicts intra-experimental fibroblast senescence to a high degree of accuracy (> 99% true positives). Applying SenPred to in vivo whole skin scRNA-seq datasets reveals that cells grown in 2D cannot accurately detect fibroblast senescence in vivo. Importantly, utilising scRNA-seq from 3D deeply senescent fibroblasts refines our ML model leading to improved detection of senescent cells in vivo. This is context specific, with the SenPred pipeline proving effective when detecting senescent human dermal fibroblasts in vivo, but not the senescence of lung fibroblasts or whole skin.

CONCLUSIONS

We position this as a proof-of-concept study based on currently available scRNA-seq datasets, with the intention to build a holistic model to detect multiple senescent triggers using future emerging datasets. The development of SenPred has allowed for the detection of an in vivo senescent fibroblast burden in human skin, which could have broader implications for the treatment of age-related morbidities. All code for the SenPred pipeline is available at the following URL: https://github.com/bethk-h/SenPred_HDF .

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.

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.

Differentiation signals induce APOBEC3A expression via GRHL3 in squamous epithelia and squamous cell carcinoma

Two APOBEC DNA cytosine deaminase enzymes, APOBEC3A and APOBEC3B, generate somatic mutations in cancer, thereby driving tumour development and drug resistance. Here, we used single-cell RNA sequencing to study APOBEC3A and APOBEC3B expression in healthy and malignant mucosal epithelia, validating key observations with immunohistochemistry, spatial transcriptomics and functional experiments. Whereas APOBEC3B is expressed in keratinocytes entering mitosis, we show that APOBEC3A expression is confined largely to terminally differentiating cells and requires grainyhead-like transcription factor 3 (GRHL3). Thus, in normal tissue, neither deaminase appears to be expressed at high levels during DNA replication, the cell-cycle stage associated with APOBEC-mediated mutagenesis. In contrast, in squamous cell carcinoma we find that, there is expansion of GRHL3expression and activity to a subset of cells undergoing DNA replication and concomitant extension of APOBEC3A expression to proliferating cells. These findings suggest that APOBEC3A may play a functional role during keratinocyte differentiation, and offer a mechanism for acquisition of APOBEC3A mutagenic activity in tumours.

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.

Immune aging and infectious diseases

ABSTRACT

The rise in global life expectancy has led to an increase in the older population, presenting significant challenges in managing infectious diseases. Aging affects the innate and adaptive immune systems, resulting in chronic low-grade inflammation (inflammaging) and immune function decline (immunosenescence). These changes would impair defense mechanisms, increase susceptibility to infections and reduce vaccine efficacy in older adults. Cellular senescence exacerbates these issues by releasing pro-inflammatory factors, further perpetuating chronic inflammation. Moreover, comorbidities, such as cardiovascular disease and diabetes, which are common in older adults, amplify immune dysfunction, while immunosuppressive medications further complicate responses to infections. This review explores the molecular and cellular mechanisms driving inflammaging and immunosenescence, focusing on genomic instability, telomere attrition, and mitochondrial dysfunction. Additionally, we discussed how aging-associated immune alterations influence responses to bacterial, viral, and parasitic infections and evaluated emerging antiaging strategies, aimed at mitigating these effects to improve health outcomes in the aging population.

Unveiling Novel Protein Biomarkers for Psoriasis Through Integrated Analysis of Human Plasma Proteomics and Mendelian Randomization

Background

Current pharmacological treatments for psoriasis are generally non-specific and have significant limitations, particularly in the realm of targeted biologic therapies. There is an urgent need to identify and develop new therapeutic targets to improve treatment options.

Objective

The aim of this study was to explore the proteome associated with psoriasis in large population cohorts to discover novel biomarkers that could guide therapy.

Methods

We analyzed data from 54,306 participants enrolled in the UK Biobank Pharmacological Proteomics Project (UKB-PPP). We investigated the relationship between 2923 serum proteins and the risk of psoriasis using multivariate Cox regression models initially. This was complemented by two-sample Mendelian randomization (TSMR), Summary-data-based Mendelian Randomization (SMR), and coloc colocalization studies to identify genetic correlations with protein targets linked to psoriasis. A protein scoring system was created using the Cox proportional hazards model, and cumulative risk curves were generated to analyze psoriasis incidence variations.

Results

Our study pinpointed 62 proteins significantly linked to the risk of developing psoriasis. Further analysis through TSMR narrowed these down to ten proteins with strong causal relationships to the disease. Additional deep-dive analyses such as SMR, colocalization, and differential expression studies highlighted four critical proteins (MMP12, PCSK9, PRSS8, and SCLY). We calculated a protein score based on the levels of these proteins, with higher scores correlating with increased risk of psoriasis.

Conclusion

This study's integration of proteomic and genetic data from a European adult cohort provides compelling evidence of several proteins as viable predictive biomarkers and potential therapeutic targets for psoriasis, facilitating the advancement of targeted treatment strategies.

New insights into the structural role of EMILINs within the human skin microenvironment

Supramolecular extracellular matrix (ECM) networks play an essential role in skin architecture and function. Elastin microfibril interface-located proteins (EMILINs) comprise a family of three extracellular glycoproteins that serve as essential structural components of the elastin/fibrillin microfibril network, and exert crucial functions in cellular signaling. Little is known about the structural nature of EMILIN networks in skin. We therefore investigated the spatiotemporal localization of EMILIN-1, -2, -3 in human skin induced by aging, UV-exposure, fibrosis, and connective tissue disorder. Confocal immunofluorescence and immunogold electron microscopy analysis identified all EMILINs as components of elastic fibers and elastin-free oxytalan fibers inserted into the basement membrane (BM). Further, our ultrastructural analysis demonstrates cellular contacts of dermally localized EMILIN-1 positive fibers across the BM with the surface of basal keratinocytes. Analysis of skin biopsies and fibroblast cultures from fibrillin-1 deficient Marfan patients revealed that EMILINs require intact fibrillin-1 as deposition scaffold. In patients with scleroderma and the bleomycin-induced murine fibrosis model EMILIN-2 was upregulated. EMILIN-3 localizes to the tips of candelabra-like oxytalan fibers, and to specialized BMs engulfing hair follicles and sebaceous glands. Our data identify EMILINs as important markers to monitor rearrangements of the dermal ECM architecture induced by aging and pathological conditions.

Methylglyoxal impairs human dermal fibroblast survival and migration by altering RAGE-hTERT mRNA expression in vitro

Fibroblasts are native residents in dermal layer of human skin which are important for dermal regeneration and essential during cutaneous wound healing by releasing inflammatory markers and actively migrate to close an open wound. Premature skin ageing due to methylglyoxal (MGO) has recently caught the attention considering its potential to accelerate the emergence of skin ageing signs, however previous studies were only focused in primary neonatal dermal fibroblast and NIH3t3 fibroblast cell line. Therefore, thorough investigation is required to study the impact of MGO on primary human dermal fibroblast isolated from adult subject (HDFa). In our experiments, short exposure of MGO was observed to induced significant reductions in cell viability at concentrations of 7.5, 10, 12.5, 15, and 17.5 mM (p < 0.005) after 3 hours of treatment. The cellular death of HDFa at 10, 12.5 and 15 mM of MGO were also marked by increased in intracellular ROS level, indicating the involvement of oxidative stress-induced death in these cells. We also observed enlarge scratch areas of cells exposed with 7.5 and 10 mM MGO compared to control after 26 hours, thereby suggesting a decline in cell migration and viability in this group. We propose the increased ROS as the consequence of AGE-RAGE activation which was marked by significant elevation of RAGE mRNA on cells exposed to 10 mM MGO. Our data also suggest the occurrence of DNA damage events via ROS-induced oxidation or mediated by decline in hTERT mRNA expression.

Distribution and impact of p16INK4A+ senescent cells in elderly tissues: a focus on senescent immune cell and epithelial dysfunction

Cellular senescence, recognized as a key hallmark of aging, leads to the accumulation of senescent cells in various tissues over time. While the detrimental effects of these cells on age-related pathological conditions are well-documented, there is still limited information about how senescent cells are distributed in normal tissues of both young and aged organs. Our research indicates that fully senescent p16INK4A+ cells are rarely identified in the parenchyma of organic tissues and in the stromal cells crucial for structural maintenance, such as fibroblasts and smooth muscle cells. Instead, p16INK4A+ cells are more commonly found in immune cells, whether they reside in the organ or are infiltrating. Notably, p16INK4A+ senescent T cells have been observed to induce apoptosis and inflammation in colonic epithelial cells through Granzyme A-PARs signaling, compromising the integrity of the epithelial lining. This study showed that the senescence of immune cells could affect the phenotypical change of the parenchymal cells in the elderly and suggests that targeting immunosenescence might be a strategy to control functional decline in this population.

Integrative multiomics analysis reveals association of gut microbiota and its metabolites with susceptibility to keloids

Keloid scarring is a fibroproliferative disease of the skin, which can significantly impact one's quality of life through cosmetic concerns, physical discomfort (itchy; painful), restricted movement, and psychological distress. Owing to the poorly understood pathogenesis of keloids and their high recurrence rate, the efficacy of keloid treatment remains unsatisfactory, particularly in patients susceptible to multiple keloids. We conducted fecal metagenomic analyzes and both untargeted and targeted plasma metabolomics in patients with multiple keloids (MK, n = 56) and controls with normal scars (NS, n = 60); tissue-untargeted metabolomics (MK, n = 35; NS, n = 32), tissue-targeted metabolomics (MK, n = 41; NS, n = 36), and single-cell sequencing analyzes (GSE163973). Differences in the gut microbiota composition, plasma metabolites, and tissue metabolites were observed between the MK and NS groups; the core gut microbiota, Oxalobacter formigenes, Bacteroides plebeius, and Parabacteroides distasonis, were identified via the gut microbiome co-occurrence network. Single-cell data helped clarify the specific cells affected by plasma metabolites. An area under the curve analysis using a random forest model based on fecal metagenomics, plasma metabolomics, and tissue metabolomics revealed that gut bacteria, plasma, and tissue metabolites were effective in distinguishing between MK and NS groups. Decreased Bacteroides plebeius could lower uracil levels, altering systemic lipid metabolism, which may change the metabolic phenotype of secretory reticular fibroblasts in wounds, potentially leading to MK. These findings may open new avenues for understanding the multifactorial nature of keloid formation from the gut-skin axis and highlight the potential for novel therapeutic strategies targeting keloid lesions and the underlying systemic imbalances affected by the gut microbiome.

Flow Cytometry Analyses of Meningioma Immune Cell Composition Using a Short, Optimized Digestion Protocol

BACKGROUND

Current challenges in meningioma treatment, including post-surgical complications and cognitive impairments, highlight the need for new treatment alternatives. Immunological interventions have shown promise. However, there is a knowledge gap in characterizing infiltrating immune cells in meningioma and their interplay. Further studies on immune cells in single-cell suspensions from digested meningioma tissues could identify targetable mechanisms for non-surgical treatment options with fewer side effects. This study aimed to optimize a protocol for faster digestion of meningioma tissues into viable single-cell suspensions and to identify infiltrating immune cell populations.

METHODS

We modified a commercial kit intended for whole skin dissociation to digest resected meningioma tissues into viable single-cell suspensions. Tumor-infiltrating immune cell populations were characterized using flow cytometry.

RESULTS

Flow cytometry analyses revealed that the digested tissue was composed of viable immune cells, including predominantly CD14+ macrophages and CD3+ T cells, with minor populations of CD56+ NK cells and CD19+ B cells. In both of the two patient samples tested, half of the tumor-associated macrophages were TIM-3+, with a small proportion co-expressing CD83. Women were more likely to have a lower proportion of immune cells, B cells, and NK cells. Female patients with a high proportion of immune cells had a higher proportion of macrophages.

CONCLUSION

We successfully optimized a protocol for generating single-cell suspensions with viable immune cells from meningioma tissues, revealing infiltrating antigen-presenting cells with an immunosuppressive phenotype, and lymphocytes. This short protocol allows advanced analyses of tumor-infiltrating cells using techniques such as single-cell RNA sequencing and flow cytometry, which require live, dissociated cells.

ICAM1+ gingival fibroblasts modulate periodontal inflammation to mitigate bone loss

Tissue-resident fibroblasts are heterogeneous and provide an endogenous source of cytokines that regulate immunologic events in many osteolytic diseases. Identifying distinct inflammatory fibroblast subsets and conducting mechanistic in vivo studies are critical for understanding disease pathogenesis and precision therapeutics, which is poorly explored in periodontitis. Here, we surveyed published single-cell datasets for fibroblast-specific analysis and show that Intercellular Adhesion Molecule-1 (ICAM1) expression selectively defines a fibroblast subset that exhibits an inflammatory transcriptional profile associated with nuclear factor-κB (NF-κB) pathway. ICAM1+ fibroblasts expand in both human periodontitis and murine ligature-induced periodontitis model, which have upregulated expression of CCL2 and CXCL1 compared to other fibroblast populations. Using a mouse model to selectively target gingival stromal cells, we further show that disruption of an inflammatory pathway by inhibiting transcriptional activity of NF-κB in these cells accelerated periodontal bone loss. Mechanistically, this was linked to a reduction of CCL2 expression by the ICAM1+ fibroblasts, leading to impaired macrophage recruitment and efferocytosis that was associated with persistent neutrophilic inflammation. These results may have a significant therapeutic implication as ICAM1+ gingival fibroblasts exert a protective response by regulating innate immune responses that are needed for the controlled inflammatory events in early stages of periodontitis.