Single-cell analysis uncovers fibroblast heterogeneity and criteria for fibroblast and mural cell identification and discrimination

Stiffness regulates extracellular matrix synthesis in fibroblasts by DDR1-TGF-β/STAT3 mechanotransduction axis

For a long time, research on atherosclerosis (AS) has mainly focused on endothelial cells (ECs) and smooth muscle cells (SMCs) in blood vessels. Fibroblasts, however, being the major component in adventitia, little is known about their role. Fibroblasts are highly plastic cells, capable of undergoing phenotypic changes in response to various extracellular signals. Once activated, fibroblasts can promote fibrosis by altering the secretion of extracellular matrix (ECM). In this study, the effect of ECM stiffness on fibroblasts was investigated. Polyacrylamide (PA) gels with varying elastic moduli (1 kPa, 20 kPa and 100 kPa) were used as models for matrix stiffness. Human fibroblasts were cultured on these substrates, and their phenotypic and functional changes were examined. The data revealed that a collagen-binding receptor, Discoidin Domain Receptor 1 (DDR1), plays a central role in sensing mechanical stimuli from ECM. Matrix stiffness-induced phosphorylation of DDR1 suppresses the synthesis of ECM proteins in fibroblasts. The expression of ECM proteins on the 1 kPa substrate was significantly higher than that on the 20 kPa and 100 kPa substrates, while the phosphorylation level of DDR1 was notably reduced. After knocking out DDR1, the difference in ECM proteins expression among the three substrates with different stiffness levels disappeared. The signal transduction from DDR1 to ECM synthesis is mediated by the TGF-β/STAT3 signaling axis. Our study reveals how matrix stiffness regulates the synthesis of ECM in fibroblasts and paves the way for understanding the regulation of fibrotic process in the pathogenesis of AS.

Auricular malformations are driven by copy number variations in a hierarchical enhancer cluster and a dominant enhancer recapitulates human pathogenesis

Enhancers, through the combinatorial action of transcription factors (TFs), dictate both the spatial specificity and the levels of gene expression, and their aberrations can result in diseases. While a HMX1 downstream enhancer is associated with ear malformations, the mechanisms underlying bilateral constricted ear (BCE) remain unclear. Here, we identify a copy number variation (CNV) containing three enhancers-collectively termed the positional identity hierarchical enhancer cluster (PI-HEC)-that drives BCE by coordinately regulating HMX1 expression. Each enhancer exhibits distinct activity-location-structure features, and the dominant enhancer with high mobility group (HMG)-box combined with Coordinator and homeodomain TF motifs modulating its activity and specificity, respectively. Mouse models demonstrate that neural crest-derived fibroblasts with aberrant Hmx1 expression in the basal pinna, along with ectopic distal pinna expression, disrupt outer ear development, affecting cartilage, muscle, and epidermis. Our findings elucidate mammalian ear morphogenesis and underscore the complexity of synergistic regulation among enhancers and between enhancers and transcription factors.

Single-Cell Transcriptomics and Lineage Tracing Unveil Parallels in Lymphatic Muscle and Venous Smooth Muscle Development, Identity, and Function

BACKGROUND

Lymphatic muscle cells (LMCs) are indispensable for lymphatic vessel contraction, and their aberrant recruitment or absence is associated with both primary and secondary lymphedema. Despite their critical role in lymphatic vessel function, the cellular and molecular bases that confer the unique contractile properties to LMCs are largely undefined, limiting the development of therapeutic interventions that precisely target LMCs.

METHODS

We used single-cell RNA sequencing, genetic lineage tracing, whole mount immunostaining, and intravital imaging to investigate the basis for the hybrid cardiomyocyte and blood vascular smooth muscle cell (SMC) characteristics that have been described for LMCs.

RESULTS

Using single-cell RNA sequencing, the transcriptomes of LMCs and venous SMCs exhibited more similarities than differences, with both cell types exhibiting enrichment in overlapping molecular markers. Notably, LMCs and venous SMCs were both markedly distinct from that of arteriole SMCs. Functionally, both lymphatic vessels and blood vessels in the murine hind limb displayed pulsatile contractility, and their functions were regulated by gabapentin and nifedipine, which target the activity of voltage-gated calcium channels. Although LMCs express genes that overlap with the venous SMC transcriptome, lineage tracing demonstrates that LMCs do not originate from Myh11 (myosin heavy chain 11) lineage-derived SMCs, Nkx2.5 (NK2 homeobox 5) cardiomyocyte progenitors, or Wnt1 (Wnt family member 1) neural crest progenitors. Instead, most LMCs and SMCs in the hind limb and inguinal-axillary region originate from WT1+ (Wilms tumor gene 1) mesodermal progenitors from the lateral plate mesoderm. LMCs derived from WT1+ progenitors were critical for the maintenance of lymphatic vessel contractility.

CONCLUSIONS

Overall, our findings suggest that venous SMCs and LMCs derive from a related mesodermal progenitor and acquire a similar gene expression program that facilitates their contractile properties.

Fibroblasts in immune responses, inflammatory diseases and therapeutic implications

Once regarded as passive bystander cells of the tissue stroma, fibroblasts have emerged as active orchestrators of tissue homeostasis and disease. From regulating immunity and controlling tissue remodelling to governing cell growth and differentiation, fibroblasts assume myriad roles in guiding normal tissue development, maintenance and repair. By comparison, in chronic inflammatory diseases such as rheumatoid arthritis, fibroblasts recruit and sustain inflammatory leukocytes, become dominant producers of pro-inflammatory factors and catalyse tissue destruction. In other disease contexts, fibroblasts promote fibrosis and impair host control of cancer. Single-cell studies have uncovered striking transcriptional and functional heterogeneity exhibited by fibroblasts in both normal tissues and diseased tissues. In particular, advances in the understanding of fibroblast pathology in rheumatoid arthritis have shed light on pathogenic fibroblast states in other chronic diseases. The differentiation and activation of these fibroblast states is driven by diverse physical and chemical cues within the tissue microenvironment and by cell-intrinsic signalling and epigenetic mechanisms. These insights into fibroblast behaviour and regulation have illuminated therapeutic opportunities for the targeted deletion or modulation of pathogenic fibroblasts across many diseases.

Interleukin-11 expressed in the polyp-enriched fibroblast subset is a potential therapeutic target in Peutz-Jeghers syndrome

Peutz-Jeghers syndrome (PJS) is associated with early-onset gastrointestinal polyposis caused by hereditary inactivating pathogenic variants in the tumor suppressor gene STK11 (LKB1). Due to lack of prophylactic therapies, management of PJS polyps requires frequent surveillance. Interestingly, studies in mouse models have revealed that stromal cells drive the polyp formation, but detailed understanding of the cell types and interactions involved has been lacking. Using single-cell RNA sequencing of PJS mouse model polyps, we here identify a polyp-enriched crypt top fibroblast (pCTF) cluster characterized by a transcriptional signature also enriched in PJS patient polyps. The pCTF signature was also noted in primary fibroblasts in vitro following acute STK11 loss. Targeted deletion of Stk11 in crypt top fibroblasts using Foxl1-Cre led to upregulation of the pCTF signature genes and later to polyposis. pCTFs displayed similarity to inflammation-associated fibroblasts, and polyposis was exacerbated by inflammation. Cell-cell communication analysis identified interleukin 11 (IL-11) as a potential pCTF inducer, and consistent with this, IL-11 was required for fibroblast reprogramming toward pCTFs following STK11 loss. Importantly, a neutralizing IL-11 antibody efficiently reduced polyp formation in a PJS model indicating a key, targetable role for IL-11 in polyp development. Together the results characterize pCTFs as a PJS polyp-enriched fibroblast subset and identify IL-11 as a key mediator of fibroblast reprogramming and a potential therapeutic target in PJS. © 2025 The Pathological Society of Great Britain and Ireland.

Distinct Transcriptomic Profiles of Cultured Anterior and Posterior Populations of Human Infant Scleral Fibroblasts: Including Dopamine Receptors

Purpose

The transcriptomic profiling of scleral fibroblasts remains largely unexplored. To elucidate their heterogeneity, we performed single-cell RNA sequencing (scRNA-seq) on primary infant scleral fibroblasts.

Methods

Primary scleral fibroblasts, cultured at passage 2 from the anterior, equatorial, and posterior regions of infant sclera (3 months to 2 years of age) were subjected to scRNA-seq using the 10x Genomics platform. In-depth analysis revealed distinct transcriptomic profiles between anterior and posterior scleral fibroblasts, including differential expression of dopamine (DA) receptors, which was subsequently validated both in vitro and in situ. Furthermore, the regulatory role of DA in scleral remodeling was assessed using an in vitro collagen gel contraction assay, and the involvement of DA receptor activity and expression in this process was further explored through pharmacological manipulation and gene silencing approaches.

Results

Infant scleral fibroblasts have anterior and posterior subpopulations, each exhibiting distinct transcriptomic profiles. Anterior scleral fibroblasts show increased expression of D1-like receptors, but posterior scleral fibroblasts exhibit elevated expression of D2-like receptors. D1-like receptor activity enhances the inhibitory effect of DA on scleral remodeling in anterior sclera, whereas D2-like receptor activity, particularly that of DRD2 in the posterior sclera, counteracts this effect. Gene silencing of DRD4 significantly enhances DA-mediated inhibition of scleral remodeling in the posterior sclera.

Conclusions

To our knowledge, this study presents the first comprehensive transcriptomic profiling of infant scleral fibroblasts, revealing their heterogeneity. The investigation of the regulatory role of DA receptor activity and expression in DA-mediated inhibition of scleral fibroblast contraction provides new insights into how DA signaling modulates scleral remodeling.

Universal fibroblasts across tissues can differentiate into niche cells for hematopoietic stem cells

Hematopoietic stem cells (HSCs) generating all blood cells are maintained by their niche cells, termed CXCL12-abundant reticular (CAR) cells, which strongly overlap with leptin-receptor-expressing (LepR+) cells in the bone marrow. A meta-analysis of single-cell RNA sequencing datasets across tissues hypothesized that universal fibroblasts present in all organs give rise to distinct tissue-specific fibroblast subsets designated as specialized fibroblasts, including CAR/LepR+ cells. However, there is no direct evidence that universal fibroblasts can differentiate into specialized fibroblasts at a distant location. Here, we demonstrated that CD248+ universal fibroblasts from the lung and colon outside the skeletal system, as well as from muscle, generated CAR/LepR+ cells characterized by HSC niche functions and expression of cytokines and transcription factors essential for HSC maintenance during ectopic bone formation or after intra-bone marrow transplantation. These results demonstrate that universal fibroblasts with the potential to differentiate into bone marrow-specific HSC niche cells are scattered throughout the entire body.

Systematic evaluation of the isolated effect of tissue environment on the transcriptome using a single-cell RNA-seq atlas dataset

BACKGROUND

Understanding cellular diversity throughout the body is essential for elucidating the complex functions of biological systems. Recently, large-scale single-cell omics datasets, known as omics atlases, have become available. These atlases encompass data from diverse tissues and cell-types, providing insights into the landscape of cell-type-specific gene expression. However, the isolated effect of the tissue environment has not been thoroughly investigated. Evaluating this isolated effect is challenging due to statistical confounding with cell-type effects, which arises from the highly limited subset of tissue-cell-type combinations that are biologically realized compared to the vast number of theoretical possibilities.

RESULTS

This study introduces a novel data analysis framework, named the Combinatorial Sub-dataset Extraction for Confounding Reduction (COSER), which addresses statistical confounding by using graph theory to enumerate appropriate sub-datasets. COSER enables the assessment of isolated effects of discrete variables in single cells. Applying COSER to the Tabula Muris Senis single-cell transcriptome atlas, we characterized the isolated impact of tissue environments. Our findings demonstrate that some genes are markedly affected by the tissue environment, particularly in modulating intercellular diversity in immune responses and their age-related changes.

CONCLUSION

COSER provides a robust, general-purpose framework for evaluating the isolated effects of discrete variables from large-scale data mining. This approach reveals critical insights into the interplay between tissue environments and gene expression.

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.

Novel Directly Reprogrammed Smooth Muscle Cells Promote Vascular Regeneration as Microvascular Mural Cells

BACKGROUND

Although cell therapy has emerged as a promising approach to promote neovascularization, its effects are mostly limited to capillaries. To generate larger or more stable vessels, layering of mural cells such as smooth muscle cells (SMCs) or pericytes is required. Recently, direct reprogramming approaches have been developed for generating SMCs. However, such reprogrammed SMCs lack genuine features of contractile SMCs, a native SMC phenotype; thus, their therapeutic and vessel-forming potential in vivo was not explored. Therefore, we aimed to directly reprogram human dermal fibroblasts toward contractile SMCs (rSMCs) and investigated their role for generating vascular mural cells in vivo and their therapeutic effects on ischemic disease.

METHODS

We applied myocardin and all-trans retinoic acid with specific culture conditions to directly reprogram human dermal fibroblasts into rSMCs. We characterized their phenotype as contractile SMCs through quantitative reverse-transcriptase polymerase chain reaction, flow cytometry, and immunostaining. We then explored their contractility using a vasoconstrictor, carbachol, and through transmission electron microscope and bulk RNA sequencing. Next, we evaluated whether transplantation of rSMCs improves blood flow and induces vessel formation as mural cells in a mouse model of hindlimb ischemia with laser Doppler perfusion imaging and histological analysis. We also determined their paracrine effects.

RESULTS

Our novel culture conditions using myocardin and all-trans retinoic acid efficiently reprogrammed human dermal fibroblasts into SMCs. These rSMCs displayed characteristics of contractile SMCs at the mRNA, protein, and cellular levels. Transplantation of rSMCs into ischemic mouse hind limbs enhanced blood flow recovery and vascular repair and improved limb salvage. Histological examination showed that vascular density was increased and the engrafted rSMCs were incorporated into the vascular wall as pericytes and vascular SMCs, thereby contributing to formation of more stable and larger microvessels. Quantitative reverse-transcriptase polymerase chain reaction analysis revealed that these transplanted rSMCs exerted pleiotropic effects, including angiogenic, arteriogenic, vessel-stabilizing, and tissue regenerative effects, on ischemic limbs.

CONCLUSIONS

A combination of myocardin and all-trans retinoic acid in defined culture conditions efficiently reprogrammed human fibroblasts into contractile and functional SMCs. The rSMCs were shown to be effective for vascular repair and contributed to neovascularization through mural cells and various paracrine effects. These human rSMCs could represent a novel source for cell-based therapy and research.

Fibroblast hierarchy dynamics during mammary gland morphogenesis and tumorigenesis

Fibroblasts form a major component of the stroma in normal mammary tissue and breast tumors. Here, we have applied longitudinal single-cell transcriptome profiling of >45,000 fibroblasts in the mouse mammary gland across five different developmental stages and during oncogenesis. In the normal gland, diverse stromal populations were resolved, including lobular-like fibroblasts, committed preadipocytes and adipogenesis-regulatory, as well as cycling fibroblasts in puberty and pregnancy. These specialized cell types appear to emerge from CD34high mesenchymal progenitor cells, accompanied by elevated Hedgehog signaling. During late tumorigenesis, heterogeneous cancer-associated fibroblasts (CAFs) were identified in mouse models of breast cancer, including a population of CD34- myofibroblastic CAFs (myCAFs) that were transcriptionally and phenotypically similar to senescent CAFs. Moreover, Wnt9a was demonstrated to be a regulator of senescence in CD34- myCAFs. These findings reflect a diverse and hierarchically organized stromal compartment in the normal mammary gland that provides a framework to better understand fibroblasts in normal and cancerous states.

Adventitial fibroblasts direct smooth muscle cell-state transition in pulmonary vascular disease

Background

Pulmonary vascular remodeling is a progressive pathological process characterized by functional alterations within pulmonary artery smooth muscle cells (PASMCs) and adventitial fibroblasts (PAAFs). Mechanisms driving the transition to a diseased phenotype remain elusive.

Methods

We combined transcriptomic and proteomic profiling with phenotypic characterization of source-matched cells from healthy controls and individuals with idiopathic pulmonary arterial hypertension (IPAH). Bidirectional cellular crosstalk was examined using direct and indirect co-culture models, and phenotypic responses were assessed via transcriptome analysis.

Results

PASMC and PAAF undergo distinct phenotypic shifts during pulmonary vascular remodeling, with limited shared features, such as reduced mitochondrial content and hyperpolarization. IPAH-PASMC exhibit increased glycosaminoglycan production and downregulation of contractile machinery, while IPAH-PAAF display a hyperproliferative phenotype. We identified alterations in extracellular matrix components, including laminin and collagen, alongside pentraxin-3 and hepatocyte growth factor, as potential regulators of PASMC phenotypic transitions mediated by PAAF.

Conclusions

While PASMCs and PAAFs retain their core cellular identities, they acquire distinct disease-associated states. These findings provide new insights into the dynamic interplay of pulmonary vascular mesenchymal cells in disease pathogenesis.

Funding

This work was supported by Cardio-Pulmonary Institute EXC 2026 390649896 (GK) and Austrian Science Fund (FWF) grant I 4651-B (SC).

Fibroblast heterogeneity and its role in generating protective immunity in the secondary lymphoid organs

Fibroblasts are cells of mesenchymal origin with a range of phenotypic diversity and heterogeneity. One of the major functions of fibroblasts is the formation and turnover of the extracellular matrix and establishing a tissue structure by forming a matrisome from embryonic development to the adult stage. It plays an indispensable role in extracellular matrix remodeling during injury, repair, and infection, providing a scaffold for cell-to-cell interaction. Despite their important pathophysiological roles, molecular markers for tissue-resident fibroblasts are only now being identified. Fibroblasts acquire molecular signatures based on anatomical locations, thus impacting their phenotypic heterogeneity despite their overlapping morphology. Fibroblasts are now recognized as key immune sentinel cells, capable of regulating the inflammatory milieu through their distinct functional subsets that are designed to respond differently with unique immune signatures. Fibroblasts can detect pathogenic and danger signals through their diverse pattern recognition receptors (PRRs) and release soluble mediators that can modulate the immune infiltrates at the site of tissue injury and repair. This review discusses the diversity and heterogeneity of fibroblasts in secondary lymphoid organs such as lymph nodes, spleen, and Peyer's patches, and their contributions to a range of pathological and physiological processes. The role of trans-differentiated effector fibroblast phenotypes that modulate the expression and function of various innate immune components (PRRs, cytokines, chemokines, and complement) in maintaining homeostasis has also been discussed.

Establishment and characterization of a novel immortalized human aortic valve interstitial cell line

Primary human aortic valvular interstitial cells (pHAVICs) play crucial roles in maintaining the mechanical structure and microenvironmental homeostasis of aortic valves. Pathologic processes such as inflammation, senescence, apoptosis, and metabolic disorders of valvular interstitial cells often lead to calcified aortic valve disease (CAVD). However, the lack of clinically relevant cellular models has impeded our understanding of CAVD. Here, we immortalized primary HAVICs with SV40 LTA. The iHAVICs (immortalized human aortic valvular interstitial cells) were maintained in a nonsenescent state and still had the potential to be induced into a senescent phenotype. In calcification induction experiments, iHAVICs can be induced to transform into osteogenic phenotypes via different stimuli via different pathways, accompanied by variations in different markers. In conclusion, we established and characterized a novel human immortalized aortic valve interstitial cell line as a practical in vitro experimental tool for the study of aortic valve calcification disease.

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.

Fibrosis: cross-organ biology and pathways to development of innovative drugs

Fibrosis is a pathophysiological mechanism involved in chronic and progressive diseases that results in excessive tissue scarring. Diseases associated with fibrosis include metabolic dysfunction-associated steatohepatitis (MASH), inflammatory bowel diseases (IBDs), chronic kidney disease (CKD), idiopathic pulmonary fibrosis (IPF) and systemic sclerosis (SSc), which are collectively responsible for substantial morbidity and mortality. Although a few drugs with direct antifibrotic activity are approved for pulmonary fibrosis and considerable progress has been made in the understanding of mechanisms of fibrosis, translation of this knowledge into effective therapies continues to be limited and challenging. With the aim of assisting developers of novel antifibrotic drugs, this Review integrates viewpoints of biologists and physician-scientists on core pathways involved in fibrosis across organs, as well as on specific characteristics and approaches to assess therapeutic interventions for fibrotic diseases of the lung, gut, kidney, skin and liver. This discussion is used as a basis to propose strategies to improve the translation of potential antifibrotic therapies.

Nrf2 phosphorylation contributes to acquisition of pericyte reprogramming via the PKCδ pathway

Pericytes (PCs) are vascular mural cells embedded in the basement membrane of micro blood vessels. It has been proposed using a C.B-17 mouse model of stroke that normal brain PCs are converted to ischemic PCs (iPCs), some of which express various stem cell markers. We previously reported that nuclear factor erythroid-2-related factor 2 (Nrf2) protected against oxidative stress following ischemia and promoted the PC reprogramming process. The present study examined the molecular mechanisms underlying the induction of Nrf2. We revealed that oxidative stress and pNrf2 induced by stroke proceeded the expression of nestin in meningeal cells and reactive PCs within the post-stroke area. PKCδ inhibitor treatment suppressed pNrf2 activation and restored the down-regulated expression of stem cell markers in iPCs in vitro. The PKCδ inhibitor treatment also suppressed the production of iPCs. These results suggest the potential of Nrf2 phosphorylation via PKCδ as a novel strategy for the treatment of ischemic injury.

Multi-modal refinement of the human heart atlas during the first gestational trimester

Forty first-trimester human hearts were studied to lay groundwork for further studies of the mechanisms underlying congenital heart defects. We first sampled 49,227 cardiac nuclei from three fetuses at 8.6, 9.0, and 10.7 post-conceptional weeks (pcw) for single-nucleus RNA sequencing, enabling the distinction of six classes comprising 21 cell types. Improved resolution led to the identification of previously unappreciated cardiomyocyte populations and minority autonomic and lymphatic endothelial transcriptomes, among others. After integration with 5-7 pcw heart single-cell RNA-sequencing data, we identified a human cardiomyofibroblast progenitor preceding the diversification of cardiomyocyte and stromal lineages. Spatial transcriptomic analysis (six Visium sections from two additional hearts) was aided by deconvolution, and key spatial markers validated on sectioned and whole hearts in two- and three-dimensional space and over time. Altogether, anatomical-positional features, including innervation, conduction and subdomains of the atrioventricular septum, translate latent molecular identity into specialized cardiac functions. This atlas adds unprecedented spatial and temporal resolution to the characterization of human-specific aspects of early heart formation.

Electrospinning strategies targeting fibroblast for wound healing of diabetic foot ulcers

The high incidence and prevalence of diabetic foot ulcers (DFUs) present a substantial clinical and economic burden, necessitating innovative therapeutic approaches. Fibroblasts, characterized by their intrinsic cellular plasticity and multifunctional capabilities, play key roles in the pathophysiological processes underlying DFUs. Hyperglycemic conditions lead to a cascade of biochemical alterations that culminate in the dysregulation of fibroblast phenotype and function, which is the primary cause of impaired wound healing in DFUs. Biomaterials, particularly those engineered at the nanoscale, hold significant promise for enhancing DFU treatment outcomes. Electrospun nanofiber scaffolds, with their structural and compositional similarities to the natural extracellular matrix, serve as an effective substrate for fibroblast adhesion, proliferation, and migration. This review comprehensively summarizes the biological behavior of fibroblasts in DFUs and the mechanism mediating wound healing. At the same time, the mechanism of biological materials, especially electrospun nanofiber scaffolds, to improve the therapeutic effect by regulating the activity of fibroblasts was also discussed. By highlighting the latest advancements and clinical applications, we aim to provide a clear perspective on the future direction of DFU treatment strategies centered on fibroblast-targeted therapies.

Protective role of the longevity-associated BPIFB4 gene on cardiac microvascular cells and cardiac aging

In recent years, the role of the cardiac microvasculature in modulating the symptoms and disease progression of patients affected by cardiac pathology has been reconsidered. The term cardiac microvascular disease (CMD) describes the set of functional and/or structural alterations of the cardiac microvasculature that reduce the ability of the heart to adequately increase its coronary blood flow to keep up with increased metabolic demand. CMD is involved in the evolution of heart disease of both ischemic and non-ischemic origin as well as in cardiac aging. The primary actors involved in this process are the cells of the stromal compartment, whose nature and biology are now investigated to a new level of detail thanks to single-cell omics studies. Recent studies on the genetics of extreme longevity have identified a polymorphic haplotype variant of the BPIFB4 gene that confers prolonged life span and health span, atheroprotective advantages, and an improved immune response. The aim of this review was to focus on the beneficial effects of the longevity-associated variant (LAV) of BPIFB4 on cardiac microvascular cell biology, providing novel and exciting mechanisms of its action directed against the development or progression of many age-related cardiovascular diseases, thus emphasizing its translational therapeutic potential.

CCN2 mediates fibroblast-macrophage interaction in knee arthrofibrosis based on single-cell RNA-seq analysis

Knee arthrofibrosis, characterized by excessive matrix protein production and deposition, substantially impairs basic daily functions, causing considerable distress and financial burden. However, the underlying pathomechanisms remain unclear. Here, we characterized the heterogeneous cell populations and cellular pathways by combination of flow cytometry and single-cell RNA-seq analysis of synovial tissues from six patients with or without knee arthrofibrosis. Increased macrophages and fibroblasts were observed with decreased numbers of fibroblast-like synoviocytes, endothelial cells, vascular smooth muscle cells, and T cells in the arthrofibrosis group compared with negative controls. Notably, fibroblasts were discovered to interact with macrophages, and lead to fibrosis through TGF-β pathway induced CCN2 expression in fibroblasts. CCN2 was demonstrated to be required for fibroblast pro-fibrotic functions (activation, proliferation, and migration) through TGFBR/SMAD pathway. The expression of CCN2 was positively correlated with the collagen volume and TGF-β expression and negatively associated with patient-reported outcome measures in another cohort of patients with knee arthrofibrosis. Our study reveals the role of CCN2 in the fibroblast-macrophage interaction through TGF-β pathway which might help to shed light on CCN2 as a potential biomarker.

Chronic Wound Initiation: Single-Cell RNAseq of Cutaneous Wound Tissue and Contributions of Oxidative Stress to Initiation of Chronicity

Chronic wounds (CWs) in humans affect millions of people in the US alone, cost billions of dollars, cause much suffering, and still there are no effective treatments. Patients seek medical care when wound chronicity is already established, making it impossible to investigate factors that initiate chronicity. In this study, we used a diabetic mouse model of CWs that mimics many aspects of chronicity in humans. We performed scRNAseq to compare the cell composition and function during the first 72 h post-injury and profiled 102,737 cells into clusters of all major cell types involved in healing. We found two types of fibroblasts. Fib 1 (pro-healing) was enriched in non-CWs (NCWs) whereas Fib 2 (non-healing) was in CWs. Both showed disrupted proliferation and migration, and extracellular matrix (ECM) deposition in CWs. We identified several subtypes of keratinocytes, all of which were more abundant in NCWs, except for Channel-related keratinocytes, and showed altered migration, apoptosis, and response to oxidative stress (OS) in CWs. Vascular and lymphatic endothelial cells were both less abundant in CWs and both had impaired migration affecting the development of endothelial and lymphatic microvessels. Study of immune cells showed that neutrophils and mast cells are less abundant in CWs and that NCWs contained more proinflammatory macrophages (M1) whereas CWs were enriched in anti-inflammatory macrophages (M2). Also, several genes involved in mitochondrial function were abnormally expressed in CWs, suggesting impaired mitochondrial function and/or higher OS. Heat shock proteins needed for response to OS were downregulated in CWs, potentially leading to higher cellular damage. In conclusion, the initiation of chronicity is multifactorial and involves various cell types and cellular functions, indicating that one type of treatment will not fix all problems, unless the root cause is fundamental to the cell and molecular mechanisms of healing. We propose that such a fundamental process is high OS and its association with wound infection/biofilm.

Cardiac Reprogramming and Gata4 Overexpression Reduce Fibrosis and Improve Diastolic Dysfunction in Heart Failure With Preserved Ejection Fraction

BACKGROUND

Heart failure with preserved ejection fraction (HFpEF) is a major health concern. Pathological stimuli and interactions between cardiac fibroblasts (CFs) and other cell types may lead to cardiac fibrosis and diastolic dysfunction, which are hallmarks of HFpEF. Interstitial and perivascular cardiac fibrosis correlates with poor prognosis in HFpEF; however, mechanisms of fibrosis remain poorly elucidated, and targeted therapies are lacking. Cardiac reprogramming is a promising therapeutic approach for myocardial infarction that facilitates cardiac regeneration and antifibrosis action through Mef2c/Gata4/Tbx5/Hand2 (MGTH) overexpression in resident CFs. However, the efficacy of this approach on HFpEF is yet to be established.

METHODS

Herein, we examined the effects of cardiac reprogramming in HFpEF using Tcf21iCre/Tomato/MGTH2A transgenic mice, which expressed both MGTH and reporter expression in CFs for cardiac reprogramming and lineage tracing upon tamoxifen administration. To establish HFpEF model mice, we used a combination of a high-fat diet and nitric oxide synthase inhibition. Bulk RNA-sequencing, single-cell RNA-sequencing, and spatial transcriptomics were conducted to determine fibrotic mechanisms and the efficacy of cardiac reprogramming in HFpEF. We generated new tamoxifen-inducible transgenic mice overexpressing each reprogramming factor in CFs to investigate the effect of single factors. Last, we analyzed the effect of reprogramming factors in human CFs.

RESULTS

Cardiac reprogramming with MGTH overexpression improved diastolic dysfunction, cardiac hypertrophy, fibrosis, inflammation, and capillary loss in HFpEF. Cardiac reprogramming converted approximately 1% of resident CFs into induced cardiomyocytes. Bulk RNA-seq indicated that MGTH overexpression upregulated genes related to heart contraction and suppressed the fetal gene program (Nppa and Nppb) and proinflammatory and fibrotic signatures. Single-cell RNA-sequencing and spatial transcriptomics revealed that multiple CF clusters upregulated fibrotic genes to induce diffuse interstitial fibrosis, whereas distinct CF clusters generated focal perivascular fibrosis in HFpEF. MGTH overexpression reversed these profibrotic changes. Among 4 reprogramming factors, only Gata4 overexpression in CFs reduced fibrosis and improved diastolic dysfunction in HFpEF by suppressing CF activation without generating new induced cardiomyocytes. Gata4 overexpression also suppressed profibrotic signatures in human CFs.

CONCLUSIONS

Overexpressing Gata4 in CFs may be a promising therapeutic approach for HFpEF by suppressing fibrosis and improving diastolic dysfunction.

Generation of iPSC-derived human venous endothelial cells for the modeling of vascular malformations and drug discovery

Venous malformations (VMs) represent prevalent vascular anomalies typically attributed to non-inherited somatic mutations within venous endothelial cells (VECs). The lack of robust disease models for VMs impedes drug discovery. Here, we devise a robust protocol for the generation of human induced VECs (iVECs) through manipulation of cell-cycle dynamics via the retinoic signaling pathway. We introduce an L914F mutation into the TIE2 gene locus of induced pluripotent stem cells (iPSCs) and show that the mutated iVECs form dilated blood vessels after transplantation into mice, thereby recapitulating the phenotypic characteristics observed in VMs. Moreover, utilizing a deep neural network and a high-throughput digital RNA with perturbation of genes sequencing (DRUG-seq) approach, we perform drug screening and demonstrate that bosutinib effectively rescues the disease phenotype in vitro and in vivo. In summary, by leveraging genome editing and stem cell technology, we generate VM models that enable the development of additional therapeutics.

Development of a 3D in vitro model to study corpus luteum of felids based on luteinized cells from antral follicles

The study aimed to establish a long-term 3D cell culture model using luteinized follicular cells to investigate the functionality and life cycle of the CL in felids. A mixture of cell types from antral follicles was luteinized in vitro and cultured for up to 23 days. The method, initially applied to the domestic cat, was later extended to Persian and Clouded leopards. Antral follicles were isolated and digested with enzymes; then, the cells were subjected to culture. Experimental subsets were treated with/without 1 µg/mL cloprostenol to validate the cell culture model's suitability for functional studies. In domestic cat samples, microscopic evaluation indicated luteinization, which was confirmed by increased progestagen concentrations and IHC staining for HSD3B and CYP11A1. The gene expression of selected steroidogenic factors (HSD3B1, STAR, CYP11A1) and hormone receptors (LHCGR, PTGFR, PRLR) significantly increased, while CYP17A1 expression decreased. Cloprostenol treatment resulted in reduction of steroidogenic activity, proving its suitability for functional studies. Persian and Clouded leopards' cell cultures exhibited similar patterns in progestagen secretion and gene expression, compared to domestic cats. This model, with its defined luteinization, as well as high and stable progestagen production, allows future investigation of factors regulating CL life cycle and function.

Specialized pericyte subtypes in the pulmonary capillaries

Pericytes are essential for capillary stability and homeostasis, with impaired pericyte function linked to diseases like pulmonary arterial hypertension. Investigating pericyte biology has been challenging due to the lack of specific markers, making it difficult to distinguish pericytes from other stromal cells. Using bioinformatic analysis and RNAscope, we identified Higd1b as a unique gene marker for pericytes and subsequently generated a knock-in mouse line, Higd1b-CreERT2, that accurately labels pericytes in the lung and heart. Single-cell RNA sequencing revealed two distinct Higd1b+ pericyte subtypes: while Type 1 pericytes support capillary homeostasis, Type 2 pericytes accumulate in arterioles, and co-express smooth muscle markers and higher levels of vimentin under hypoxic conditions. Lastly, healthy human lung pericytes with upregulation of vimentin exhibited increased adhesion, migration, and higher expression levels of the smooth muscle marker SM22 in vitro. These findings highlight the specialization of pulmonary pericytes and their contribution to vascular remodeling during hypoxia-induced pulmonary hypertension.

Single-cell RNA Sequencing Analysis Reveals Cancer-associated Fibroblast Signature for Prediction of Clinical Outcomes and Immunotherapy in Gastric Cancer

Gastric cancer (GC) is a significant worldwide health concern and is a leading cause of cancer-related mortality. Immunotherapy has arisen as a promising strategy to stimulate the patient's immune system in combating cancer cells. Nevertheless, the effectiveness of immunotherapy in individuals with gastric cancer (GC) is not yet optimal. Thus, it is crucial to discover biomarkers capable appof predicting the advantages of immunotherapy for tailored treatment. The tumor microenvironment (TME) and its constituents, including cancer-associated fibroblasts (CAFs), exert a substantial influence on immune responses and treatment outcomes. In this investigation, we utilized single-cell RNA sequencing to profile CAFs in GC and established a scoring method, referred to as the CAF score (CAFS), for the prediction of patient prognosis and response to immunotherapy. Through our analysis, we successfully identified distinct subgroups within CAFs based on CAF score (CAFS), namely CAFS-high and CAFS-low subgroups. Notably, we noted that individuals within the CAFS-high subgroup experienced a lessF favorable prognosis and displayed diminished responsiveness to immunotherapy in contrast to the CAFS low subgroup. Furthermore, we analyzed the mutation and immune characteristics of these subgroups, identifying differentially mutated genes and immune cell compositions. We established that CAFS could forecast treatment advantages in patients with gastric cancer, both for chemotherapy and immunotherapy. Its efficacy was additionally confirmed in contrast to other biomarkers, including Tumor Immune Dysfunction and Exclusion (TIDE) and Immunophenotypic Score (IPS). These findings emphasize the clinical relevance and potential utility of CAFS in guiding personalized treatment strategies for gastric cancer.

Heterogeneous Cardiac-Derived and Neural Crest-Derived Aortic Smooth Muscle Cells Exhibit Similar Transcriptional Changes After TGFβ Signaling Disruption

BACKGROUND

Smooth muscle cells (SMCs) of cardiac and neural crest origin contribute to the developing proximal aorta and are linked to disease propensity in adults.

METHODS

We analyzed single-cell transcriptomes of aortic SMCs from adult mice to determine basal states and changes after disrupting TGFβ (transforming growth factor-β) signaling necessary for aortic homeostasis.

RESULTS

A minority of Myh11 lineage-marked SMCs differentially expressed genes suggestive of embryological origin. Additional analyses in Nkx2-5 and Wnt1 lineage-marked SMCs derived from cardiac and neural crest progenitors, respectively, showed both lineages contributed to a major common cluster and each lineage to a minor distinct cluster. Common cluster SMCs extended from root to arch, cardiac subset cluster SMCs from root to ascending, and neural crest subset cluster SMCs were restricted to the arch. The neural crest subset cluster had greater expression of a subgroup of TGFβ-dependent genes. Nonetheless, conditional deletion of TGFβ receptors resulted in similar transcriptional changes among all SMC clusters. Several disease-associated transcriptional responses were comparable among SMC clusters in a mouse model of Marfan syndrome aortopathy, while many embryological markers of murine aortic SMCs were not detected in adult human aortas.

CONCLUSIONS

There are multiple subtypes of cardiac-derived and neural crest-derived SMCs with shared or distinctive transcriptional profiles; neural crest subset cluster SMCs with increased expression of certain TGFβ-inducible genes are not spatially linked to the aortic root predisposed to aneurysms from aberrant TGFβ signaling; and loss of TGFβ responses after receptor deletion is uniform among SMC clusters.

Transcriptional profile of the rat cardiovascular system at single-cell resolution

We sought to characterize cellular composition across the cardiovascular system of the healthy Wistar rat, an important model in preclinical cardiovascular research. We performed single-nucleus RNA sequencing (snRNA-seq) in 78 samples in 10 distinct regions, including the four chambers of the heart, ventricular septum, sinoatrial node, atrioventricular node, aorta, pulmonary artery, and pulmonary veins, which produced 505,835 nuclei. We identified 26 distinct cell types and additional subtypes, with different cellular composition across cardiac regions and tissue-specific transcription for each cell type. Several cell subtypes were region specific, including a subtype of vascular smooth muscle cells enriched in the large vasculature. We observed tissue-enriched cellular communication networks, including heightened Nppa-Npr1/2/3 signaling in the sinoatrial node. The existence of tissue-restricted cell types suggests regional regulation of cardiovascular physiology. Our detailed transcriptional characterization of each cell type offers the potential to identify novel therapeutic targets and improve preclinical models of cardiovascular disease.

Telocytes in inflammatory bowel diseases: contributions to pathology and therapeutic potentials

Telocytes, a novel mesenchymal cell population, are characterized by their distinctive long and slender projections known as telopodes and have garnered significant interest since their formal introduction to the literature in 2010. These cells have been identified in various tissues, including the gastrointestinal (GI) tract, where they are suggested to play important roles in maintaining structural integrity, immune modulation, and barrier function. Inflammatory bowel diseases (IBD), which include Crohn's disease (CD) and ulcerative colitis (UC), are characterized by chronic inflammation and fibrosis. While limited information is available on the fate of telocytes in this group of diseases, it has been suggested that loss/plasticity of telocytes can be among the key factors contributing to their pathogenesis. This review focuses on the current understanding of telocytes, their structural features, and their distribution within the GI tract under gut homeostasis and IBD. We also discuss the roles of these cells in immune regulation and intestinal repair. We highlight evidence implicating telocytes in the pathogenesis of IBD and other chronic inflammatory diseases that share similar pathophysiological processes with IBD. Lastly, we discuss the current challenges in gut telocyte biology and the potential therapeutic implications of telocytes in IBD.

Integrated single-cell RNA sequencing reveals the tumor heterogeneity and microenvironment landscape during liver metastasis in adenocarcinoma of esophagogastric junction

Background

Adenocarcinoma of the esophagogastric junction (AEGJ) is a highly aggressive tumor that frequently metastasizes to the liver. Understanding the cellular and molecular mechanisms that drive this process is essential for developing effective therapies.

Methods

We employed single-cell RNA sequencing to analyze the tumor heterogeneity and microenvironmental landscape in patients with AEGJ liver metastases. This approach enabled us to characterize the diverse cell populations involved in the liver metastatic process.

Results

Our analysis revealed a significant involvement of fibroblasts and mural cells in AEGJ liver metastasis. We identified a specific fibroblast type in AEGJ liver metastasis and observed distinct gene expression patterns between adenocarcinoma of the esophagogastric junction and other stomach adenocarcinomas. Our study demonstrated high expression of the SFRP2 gene in pericyte cells during the liver metastasis of AEGJ. The incorporation of GEO, TCGA, and immunofluorescence staining of SFRP2 expression enhanced our study. High expression of SFRP2 in pericytes may influence vascular stability and angiogenesis through the Wnt pathway.

Conclusion

Our study provides novel insights into the cellular interactions and molecular mechanisms that underlie AEGJ liver metastasis. Targeting the identified subtype of fibroblasts or influencing SFRP2 gene expression in pericytes may offer new therapeutic strategies for combating this aggressive tumor.

Transcription Factor 21 Regulates Cardiac Myofibroblast Formation and Fibrosis

BACKGROUND

TCF21 (transcription factor 21) is a bHLH (basic helix-loop-helix) protein required for the developmental specification of cardiac fibroblasts (CFs) from epicardial progenitor cells that surround the embryonic heart. In the adult heart, TCF21 is expressed in tissue-resident fibroblasts and is downregulated in response to injury or stimuli leading to myofibroblast differentiation. These findings led to the hypothesis that TCF21 regulates fibroblast differentiation in the adult mammalian heart to affect fibrosis.

METHODS

Tamoxifen-inducible Cre genetic mouse models were used to permit either Tcf21 gene deletion or its enforced expression in adult CFs. Histological and echocardiographic analyses were used, as well as transcriptomic analysis to determine the consequences of TCF21 gain-of-function and loss-of-function in vivo. Genomic Tcf21 occupancy was identified by chromatin immunoprecipitation and sequencing in CFs. Myocardial infarction and AngII (angiotensin II)/phenylephrine served as models of cardiac fibrosis.

RESULTS

Acute and long-term deletion of Tcf21 in CFs of the adult mouse heart does not alter fibroblast numbers, myofibroblast differentiation, or fibrosis. Fibroblast-specific Tcf21 gene-deleted mice demonstrate no significant alterations in cardiac function or scar formation in response to cardiac injury compared with control mice. In contrast, enforced expression of TCF21 in CFs inhibits myofibroblast differentiation and significantly reduces cardiac fibrosis and hypertrophy in response to 1 week of Ang II/phenylephrine infusion. Mechanistically, sustained TCF21 expression prevents the induction of genes associated with fibrosis and ECM (extracellular matrix) organization.

CONCLUSIONS

TCF21 expression is not required to maintain the cell state of CFs in the adult heart. However, preventing the normal downregulation of TCF21 expression with injury reduces myofibroblast formation, cardiac fibrosis, and the acute cardiac hypertrophic response following 1 week of Ang II/phenylephrine stimulation.

A cell atlas of the human fallopian tube throughout the menstrual cycle and menopause

The fallopian tube undergoes extensive molecular changes during the menstrual cycle and menopause. We use single-cell RNA and ATAC sequencing to construct a comprehensive cell atlas of healthy human fallopian tubes during the menstrual cycle and menopause. Our scRNA-seq comparison of 85,107 pre- and 46,111 post-menopausal fallopian tube cells reveals substantial shifts in cell type frequencies, gene expression, transcription factor activity, and cell-to-cell communications during menopause and menstrual cycle. Menstrual cycle dependent hormonal changes regulate distinct molecular states in fallopian tube secretory epithelial cells. Postmenopausal fallopian tubes show high chromatin accessibility in transcription factors associated with aging such as Jun, Fos, and BACH1/2, while hormone receptors were generally downregulated, a small proportion of secretory epithelial cells had high expression of ESR2, IGF1R, and LEPR. While a pre-menopausal secretory epithelial gene cluster is enriched in the immunoreactive molecular subtype, a subset of genes expressed in post-menopausal secretory epithelial cells show enrichment in the mesenchymal molecular type of high-grade serous ovarian cancer.

TNFR2 signaling in oligodendrocyte precursor cells suppresses their immune-inflammatory function and detrimental microglia activation in CNS demyelinating disease

Multiple Sclerosis (MS) is a chronic degenerative disease of the central nervous system (CNS) characterized by inflammation, demyelination, and progressive neurodegeneration. These processes, combined with the failure of reparative remyelination initiated by oligodendrocyte precursor cells (OPCs), lead to irreversible neurological impairment. The cytokine tumor necrosis factor (TNF) has been implicated in CNS repair via activation of its cognate receptor TNFR2 in glia. Here, we demonstrate the important role of TNFR2 in regulating OPC function in vivo during demyelinating disease, and that TNFR2 expressed in OPCs modulates OPC-microglia interactions. In PdgfrαCreERT:Tnfrsf1bfl/fl:Eyfp mice with selective TNFR2 ablation in OPCs, we observed an earlier onset and disease peak in experimental autoimmune encephalomyelitis (EAE). This was associated with accelerated immune cell infiltration and increased microglia activation in the spinal cord. Similarly, PdgfrαCreERT:Tnfrsf1bfl/fl:Eyfp mice showed rapid and increased microglia reactivity compared to control mice in the corpus callosum after cuprizone-induced demyelination, followed by chronic reduction in the number of mature myelinating oligodendrocytes (OLs). With EAE and cuprizone models combined, we uncovered that TNFR2 does not have a cell autonomous role in OPC differentiation, but may be important for survival of newly formed mature OLs. Finally, using an in vitro approach, we demonstrated that factors released by Tnfrsf1b ablated OPCs drove microglia to develop an exacerbated "foamy" phenotype when incubated with myelin-rich spinal cord homogenate, aberrantly increasing lysosomal lipid accumulation. Together, our data indicate that TNFR2 signaling in OPCs is protective by dampening their immune-inflammatory activation and by suppressing neurotoxic microglia reactivity. This suggests that boosting TNFR2 activation or its downstream cascades could be an effective strategy to restore OPC reparative capacity in neuroimmune and demyelinating disease.

Novel Therapeutic Strategies Targeting Fibroblasts to Improve Heart Disease

Cardiac fibrosis represents the terminal pathological manifestation of various heart diseases, with the formation of fibroblasts playing a pivotal role in this process. Consequently, targeting the formation and function of fibroblasts holds significant potential for improving outcomes in heart disease. Recent research reveals the considerable potential of fibroblasts in ameliorating cardiac conditions, demonstrating different functional characteristics at various time points and spatial locations. Therefore, precise modulation of fibroblast activity may offer an effective approach for treating cardiac fibrosis and achieving targeted therapeutic outcomes. In this review, we focus on the fate and inhibition of fibroblasts, analyze their dynamic changes in cardiac diseases, and propose a framework for identifying markers of fibroblast activation mechanisms and selecting optimal time windows for therapeutic intervention. By synthesizing research findings in these areas, we aim to provide new strategies and directions for the precise treatment of fibroblasts in cardiac diseases.

Surface Molecular Markers for the Isolation of Viable Fibroblast Subpopulations in the Female Reproductive Tract: A Comprehensive Review

Advancements in single-cell analyzis technologies, particularly single-cell RNA sequencing (scRNA-seq) and Fluorescence-Activated Cell Sorting (FACS), have enabled the analyzis of cellular diversity by providing resolutions that were not available previously. These methods enable the simultaneous analyzis of thousands of individual transcriptomes, facilitating the classification of cells into distinct subpopulations, based on transcriptomic differences, adding a new level of complexity to biomolecular and medical research. Fibroblasts, despite being one of the most abundant cell types in the human body and forming the structural backbone of tissues and organs, remained poorly characterized for a long time. This is largely due to the high morphological similarity between different types of fibroblasts and the lack of specific markers to identify distinct subpopulations. Once thought to be cells responsible solely for the synthesis of extracellular matrix (ECM) components, fibroblasts are now recognized as active participants in diverse physiological processes, including inflammation and antimicrobial responses. However, defining the molecular profile of fibroblast subpopulations remains a significant challenge. In this comprehensive review, which is based on over two thousand research articles, we focus on the identification and characterization of fibroblast subpopulations and their specific surface markers, with an emphasis on their potential as molecular targets for selective cell isolation. By analyzing surface markers, alongside intra- and extracellular protein profiles, we identified multiple fibroblast subtypes within the female reproductive system. These subtypes exhibit distinct molecular signatures and functional attributes, shaped by their anatomical localization and the surrounding physiological or pathological conditions. Our findings underscore the heterogeneity of fibroblasts and their diverse roles in various biological contexts. This improved understanding of fibroblast subpopulations paves the way for innovative diagnostic and therapeutic strategies, offering the potential for precision targeting of specific fibroblast subsets in clinical applications.

Myoblast-derived ADAMTS-like 2 promotes skeletal muscle regeneration after injury

Skeletal muscle regeneration and functional recovery after minor injuries requires the activation of muscle-resident myogenic muscle stem cells (i.e. satellite cells) and their subsequent differentiation into myoblasts, myocytes, and ultimately myofibers. We recently identified secreted ADAMTS-like 2 (ADAMTSL2) as a pro-myogenic regulator of muscle development, where it promoted myoblast differentiation. Since myoblast differentiation is a key process in skeletal muscle regeneration, we here examined the role of ADAMTSL2 during muscle regeneration after BaCl2 injury. Specifically, we found that muscle regeneration was delayed after ablation of ADAMTSL2 in myogenic precursor cells and accelerated following injection of pro-myogenic ADAMTSL2 protein domains. Mechanistically, ADAMTSL2 regulated the number of committed myoblasts, which are the precursors for myocytes and regenerating myofibers. Collectively, our data support a role for myoblast-derived ADAMTSL2 as a positive regulator of muscle regeneration and provide a proof-of-concept for potential therapeutic applications.

Breast pericytes: a newly identified driver of tumor cell proliferation

Introduction

Effective treatment of breast cancer remains a formidable challenge, partly due to our limited understanding of the complex microenvironmental factors that contribute to disease pathology. Among these factors are tissue-resident perivascular cells, which play crucial roles in shaping vascular basement membranes, maintaining vessel integrity, and communicating with adjacent endothelial cells. Despite their essential functions, perivascular cells have been relatively overlooked. Identifying them by immunostaining has been challenging due to their low abundance, inherent heterogeneity, and shared marker expression with other cell types. These challenges have hindered efforts to purify pericytes and generate primary cell models for studying their biology.

Methods

Using a recently developed FACS method, we successfully identified and purified each cell type from breast tissues, allowing us to deep-sequence their transcriptomes and generate primary cell models of each cell type-including pericytes. Here, we used these data to analyze cell-type-specific gene expression in tumors, which revealed a strong association between pericyte-specific genes and breast cancer patient mortality. To explore this association, we defined the heterogeneity of breast pericytes using single-cell RNA sequencing and identified a broad marker for visualizing perivascular cells in breast tumors.

Results

Remarkably, we discovered perivascular cells dissociated from vessels and emerged as a dominant mesenchymal cell type in a subset of breast tumors that contrasted with their normal perivascular location. Moreover, when we purified pericytes from the breast and cultured them alongside breast tumor cells, we discovered that they induced rapid tumor cell growth significantly greater than isogenic fibroblast controls.

Discussion

These findings identify perivascular cells as a key microenvironmental factor in breast cancer, highlighting the critical need for further research to explore their biology and identify specific stimulatory mechanisms that could be targeted therapeutically.

FAPs orchestrate homeostasis of muscle physiology and pathophysiology

As a common clinical manifestation, muscle weakness is prevalent in people with mobility disorders. Further studies of muscle weakness have found that patients with muscle weakness present with persistent muscle inflammation, loss of muscle fibers, fat infiltration, and interstitial fibrosis. Therefore, we propose the concept of muscle microenvironment homeostasis, which explains the abnormal pathological changes in muscles through the imbalance of muscle microenvironment homeostasis. And we identified an interstitial progenitor cell FAP during the transition from normal muscle microenvironment homeostasis to muscle microenvironment imbalance caused by muscle damage diseases. As a kind of pluripotent stem cell, FAPs do not participate in myogenic differentiation, but can differentiate into fibroblasts, adipocytes, osteoblasts, and chondrocytes. As a kind of mesenchymal progenitor cell, it is involved in the generation of extracellular matrix, regulate muscle regeneration, and maintain neuromuscular junction. However, the muscle microenvironment is disrupted by the causative factors, and the abnormal activities of FAPs eventually contribute to the complex pathological changes in muscles. Targeting the mechanisms of these muscle pathological changes, we have identified appropriate signaling targets for FAPs to improve and even treat muscle damage diseases. In this review, we propose the construction of muscle microenvironmental homeostasis and find the key cells that cause pathological changes in muscle after homeostasis is broken. By studying the mechanism of abnormal differentiation and apoptosis of FAPs, we found a strategy to inhibit the abnormal pathological changes in muscle damage diseases and improve muscle regeneration.

Enter the Matrix: Fibroblast-immune cell interactions shape extracellular matrix deposition in health and disease

Fibroblasts, non-hematopoietic cells of mesenchymal origin, are tissue architects which regulate the topography of tissues, dictate tissue resident cell types, and drive fibrotic disease. Fibroblasts regulate the composition of the extracellular matrix (ECM), a 3-dimensional network of macromolecules that comprise the acellular milieu of tissues. Fibroblasts can directly and indirectly regulate immune responses by secreting ECM and ECM-bound molecules to shape tissue structure and influence organ function. In this review, we will highlight recent studies which elucidate the mechanisms by which fibroblast-derived ECM factors (e.g., collagens, fibrillar proteins) regulate ECM architecture and subsequent immune responses, with a focus on macrophages. As examples of fibroblast-derived ECM proteins, we examine Collagen Triple Helix Repeat Containing 1 (CTHRC1) and Transforming Growth Factor-β-inducible protein (TGFBI), also known as BIGH3. We address the need for investigation into how diverse fibroblast populations coordinate immune responses by modulating ECM, including the fibroblast-ECM-immune axis and the precise molecular mediators and pathways which regulate these processes. Finally, we will outline how novel research identifying key regulators of ECM deposition is critical for therapeutic development for fibrotic diseases and cancer.

Cross-species single-cell RNA-seq analysis reveals disparate and conserved cardiac and extracardiac inflammatory responses upon heart injury

The immune system coordinates the response to cardiac injury and controls regenerative and fibrotic scar outcomes in the heart and subsequent chronic low-grade inflammation associated with heart failure. Adult mice and humans lack the ability to fully recover while adult zebrafish spontaneously regenerate after heart injury. Here we profile the inflammatory response to heart cryoinjury in zebrafish and coronary artery ligation in mouse using single cell transcriptomics. We interrogate the extracardiac reaction to cardiomyocyte necrosis to assess the specific peripheral tissue and immune cell reaction to chronic stress. Cardiac macrophages play a critical role in determining tissue homeostasis by healing versus scarring. We identify distinct transcriptional clusters of monocytes/macrophages (mono/Mϕ) in each species and find analogous pairs in zebrafish and mice. However, the reaction to myocardial injury is largely disparate between mice and zebrafish. The dichotomous response to heart damage between the murine and zebrafish mono/Mϕ and/or the presence of distinct zebrafish mono/Mϕ subtypes may underlie the impaired regenerative process in adult mammals and humans. Our study furnishes a direct cross-species comparison of immune responses between regenerative and profibrotic myocardial injury models, providing a useful resource to the fields of regenerative biology and cardiovascular research.

Ovariectomy drives increase of an ECM transcription signature in the posterior eye and retina

Increased risk of developing glaucoma has recently been associated with early age of menopause. Here, we examined how age and surgically-induced menopause via ovariectomy (OVX) impacted gene expression in gene pathways previously linked to glaucoma, such as extracellular matrix (ECM) remodeling and TGF-β signaling. Using bulk RNA sequencing, we analyzed changes in young (3-4 months) and middle-aged (9-10 months) Long-Evans rats. We focused on posterior pole tissues (sclera and optic nerve head) but also examined the retina to compare observed changes across different tissue regions. Our results demonstrated that aging and OVX significantly alter gene expression in the sclera and optic nerve head. Generally, OVX triggered the enrichment of immune-related processes. However, OVX in young rats also led to significant enrichment of ECM and TGF-β gene sets. At the same time, these effects were diminished in middle-aged rats, indicating an age dependency of the effects of OVX on matrix-related pathways. Notably, the transcriptional factor Fos was downregulated in the posterior eye and retina in aged and OVX animals. Fos is a major regulator of cell proliferation and survival, and its dysregulation may play an important role in aging and menopause for women. These findings underscore the important role of menopause timing in modulating molecular pathways associated with glaucoma, which is consistent with clinical studies showing that early menopause may heighten the risk of developing this condition. This study also highlights the importance of considering women's health factors, such as menopause, in understanding and managing glaucoma risk.

PRDM16 determines specification of ventricular cardiomyocytes by suppressing alternative cell fates

PRDM16 is a transcription factor with histone methyltransferase activity expressed at the earliest stages of cardiac development. Pathogenic mutations in humans lead to cardiomyopathy, conduction abnormalities, and heart failure. PRDM16 is specifically expressed in ventricular but not atrial cardiomyocytes, and its expression declines postnatally. Because in other tissues PRDM16 is best known for its role in binary cell fate decisions, we hypothesized a similar decision-making function in cardiomyocytes. Here, we demonstrated that cardiomyocyte-specific deletion of Prdm16 during cardiac development results in contractile dysfunction and abnormal electrophysiology of the postnatal heart, resulting in premature death. By combined RNA+ATAC single-cell sequencing, we found that PRDM16 favors ventricular working cardiomyocyte identity, by opposing the activity of master regulators of ventricular conduction and atrial fate. Myocardial loss of PRDM16 during development resulted in hyperplasia of the (distal) ventricular conduction system. Hence, PRDM16 plays an indispensable role during cardiac development by driving ventricular working cardiomyocyte identity.

Different gene expression patterns between mouse and human brain pericytes revealed by single-cell/nucleus RNA sequencing

AIMS

Pericytes in the brain play important roles for microvascular physiology and pathology and are affected in neurological disorders and neurodegenerative diseases. Mouse models are often utilized for pathophysiology studies of the role of pericytes in disease; however, the translatability is unclear as brain pericytes from mouse and human have not been systematically compared. In this study, we investigate the similarities and differences of brain pericyte gene expression between mouse and human. Our analysis provides a comprehensive resource for translational studies of brain pericytes.

METHODS

We integrated and compared four mouse and human adult brain pericyte single-cell/nucleus RNA-sequencing datasets derived using two single-cell RNA sequencing platforms: Smart-seq and 10x. Gene expression abundance and specificity were analyzed. Pericyte-specific/enriched genes were assigned by comparison with endothelial cells present in the same datasets, and mouse and human pericyte transcriptomes were subsequently compared to identify species-specific genes.

RESULTS

An overall concordance between pericyte transcriptomes was found in both Smart-seq and 10x data. 206 orthologous genes were consistently differentially expressed between human and mouse from both platforms, 91 genes were specific/up-regulated in human and 115 in mouse. Gene ontology analysis revealed differences in transporter categories in mouse and human brain pericytes. Importantly, several genes implicated in human disease were expressed in human but not in mouse brain pericytes, including SLC6A1, CACNA2D3, and SLC20A2.

CONCLUSIONS

This study provides a systematic illustration of the similarities and differences between mouse and human adult brain pericytes.

Single-nucleus RNA sequencing reveals cell types, genes, and regulatory factors influencing melanogenesis in the breast muscle of Xuefeng black-bone chicken

The black-bone chicken, known for its high melanin content, holds significant economic value due to this unique trait. Particularly notable is the prominent melanin deposition observed in its breast muscle. However, the molecular mechanisms governing melanin synthesis and deposition in the breast muscle of black-bone chickens remain largely unknown. This study employed a single-nucleus transcriptome assay to identify genes associated with melanin deposition in the breast muscle of black-bone chickens, which are presumed to influence pigmentation levels. A comprehensive analysis of the nuclear transcriptome was conducted on the breast muscle of Xuefeng black-bone chickens, encompassing 18 distinct cell types, including melanocytes. Our findings revealed that STIMATE, LRRC7, ENSGALG00000049990, and GLDC play pivotal regulatory roles in melanin deposition within the breast muscle. Further exploration into the molecular mechanisms unveiled transcription factors and protein interactions suggesting that RARB, KLF15, and PRDM4 may be crucial regulators of melanin accumulation in the breast muscle. Additionally, HPGDS, GSTO1, and CYP1B1 may modulate melanin production and deposition in the breast muscle by influencing melanocyte metabolism. Our findings also suggest that melanocyte function in the breast muscle may be intertwined with intercellular signaling pathways such as PTPRK-WNT5A, NOTCH1-JAG1, IGF1R-IGF1, IDE-GCG, and ROR2-WNT5A. Leveraging advanced snRNA-seq technology, we generated a comprehensive single-cell nuclear transcriptome atlas of the breast muscle of Xuefeng black-bone chickens. This facilitated the identification of candidate genes, regulatory factors, and cellular signals potentially influencing melanin deposition and melanocyte function. Overall, our study provides crucial insights into the molecular basis of melanin deposition in chicken breast muscle, laying the groundwork for future breeding programs aimed at enhancing black-bone chicken cultivation.

Single-cell atlas of healthy vocal folds and cellular function in the endothelial-to-mesenchymal transition

The vocal fold is an architecturally complex organ comprising a heterogeneous mixture of various layers of individual epithelial and mesenchymal cell lineages. Here we performed single-cell RNA sequencing profiling of 5836 cells from the vocal folds of adult Sprague-Dawley rats. Combined with immunostaining, we generated a spatial and transcriptional map of the vocal fold cells and characterized the subpopulations of epithelial cells, mesenchymal cells, endothelial cells, and immune cells. We also identified a novel epithelial-to-mesenchymal transition-associated epithelial cell subset that was mainly found in the basal epithelial layers. We further confirmed that this subset acts as intermediate cells with similar genetic features to epithelial-to-mesenchymal transition in head and neck squamous cell carcinoma. Finally, we present the complex intracellular communication network involved homeostasis using CellChat analysis. These studies define the cellular and molecular framework of the biology and pathology of the VF mucosa and reveal the functional importance of developmental pathways in pathological states in cancer.

Single-cell transcriptomics reveal distinctive patterns of fibroblast activation in heart failure with preserved ejection fraction

Inflammation, fibrosis and metabolic stress critically promote heart failure with preserved ejection fraction (HFpEF). Exposure to high-fat diet and nitric oxide synthase inhibitor N[w]-nitro-l-arginine methyl ester (L-NAME) recapitulate features of HFpEF in mice. To identify disease-specific traits during adverse remodeling, we profiled interstitial cells in early murine HFpEF using single-cell RNAseq (scRNAseq). Diastolic dysfunction and perivascular fibrosis were accompanied by an activation of cardiac fibroblast and macrophage subsets. Integration of fibroblasts from HFpEF with two murine models for heart failure with reduced ejection fraction (HFrEF) identified a catalog of conserved fibroblast phenotypes across mouse models. Moreover, HFpEF-specific characteristics included induced metabolic, hypoxic and inflammatory transcription factors and pathways, including enhanced expression of Angiopoietin-like 4 (Angptl4) next to basement membrane compounds, such as collagen IV (Col4a1). Fibroblast activation was further dissected into transcriptional and compositional shifts and thereby highly responsive cell states for each HF model were identified. In contrast to HFrEF, where myofibroblast and matrifibrocyte activation were crucial features, we found that these cell states played a subsidiary role in early HFpEF. These disease-specific fibroblast signatures were corroborated in human myocardial bulk transcriptomes. Furthermore, we identified a potential cross-talk between macrophages and fibroblasts via SPP1 and TNFɑ with estimated fibroblast target genes including Col4a1 and Angptl4. Treatment with recombinant ANGPTL4 ameliorated the murine HFpEF phenotype and diastolic dysfunction by reducing collagen IV deposition from fibroblasts in vivo and in vitro. In line, ANGPTL4, was elevated in plasma samples of HFpEF patients and particularly high levels associated with a preserved global-longitudinal strain. Taken together, our study provides a comprehensive characterization of molecular fibroblast activation patterns in murine HFpEF, as well as the identification of Angiopoietin-like 4 as central mechanistic regulator with protective effects.

Development and use of two Xenopus laevis spleen stromal cell lines to study the role of splenic stromal cells in anuran immune processes

The spleen is an important immune organ in adult Xenopus laevis, supporting the differentiation of B cells and acting as the main peripheral lymphoid organ. Key to these processes are the supporting non-hematopoietic cells, or stromal cells, within the spleen tissue. Despite the importance of the spleen to frog immunity, few frog cell lines originating from spleen tissue have been reported. In this study, we report on the establishment and characterization of two cell lines originating from X. laevis spleen tissue, Xela S5F and Xela S5E. Morphological observations and gene expression profiling suggest that Xela S5F is fibroblast-like and Xela S5E is epithelial-like. Both cell lines express transcripts corresponding to a variety of hematopoietic growth factors, suggesting their potential utility as a feeder cell line to support ex vivo myelopoietic cell differentiation. Xela S5F and Xela S5E produce transcripts for a diversity of pattern recognition receptors including toll-like receptors, scavenger receptors, and cytosolic nucleic acid sensors, suggesting anuran spleen stromal cells may be important cellular sensors of pathogens filtered through the spleen. This idea is supported by the increase in transcript levels for antiviral and proinflammatory genes in both cell lines in response to treatment with the commercially available toll-like receptor ligands, flagellin and poly(I:C). However, despite the ability to sense extracellular synthetic analogues of viral nucleic acids [i.e. poly(I:C)] and susceptibility and permissibility of both cell lines to frog virus 3 (FV3), a large double-stranded DNA virus that infects amphibians, neither cell line upregulates key antiviral or proinflammatory transcripts when challenged with FV3. The establishment of Xela S5F and S5E cell lines expands the current X. laevis invitrome and provides new in vitro cell model systems to investigate the role of splenic stromal cells in anuran immune functions.

Wound healing: insights into autoimmunity, ageing, and cancer ecosystems through inflammation and IL-6 modulation

Wound healing represents a complex and evolutionarily conserved process across vertebrates, encompassing a series of life-rescuing events. The healing process runs in three main phases: inflammation, proliferation, and maturation/remodelling. While acute inflammation is indispensable for cleansing the wound, removing infection, and eliminating dead tissue characterised by the prevalence of neutrophils, the proliferation phase is characterised by transition into the inflammatory cell profile, shifting towards the prevalence of macrophages. The proliferation phase involves development of granulation tissue, comprising fibroblasts, activated myofibroblasts, and inflammatory and endothelial cells. Communication among these cellular components occurs through intercellular contacts, extracellular matrix secretion, as well as paracrine production of bioactive factors and proteolytic enzymes. The proliferation phase of healing is intricately regulated by inflammation, particularly interleukin-6. Prolonged inflammation results in dysregulations during the granulation tissue formation and may lead to the development of chronic wounds or hypertrophic/keloid scars. Notably, pathological processes such as autoimmune chronic inflammation, organ fibrosis, the tumour microenvironment, and impaired repair following viral infections notably share morphological and functional similarities with granulation tissue. Consequently, wound healing emerges as a prototype for understanding these diverse pathological processes. The prospect of gaining a comprehensive understanding of wound healing holds the potential to furnish fundamental insights into modulation of the intricate dialogue between cancer cells and non-cancer cells within the cancer ecosystem. This knowledge may pave the way for innovative approaches to cancer diagnostics, disease monitoring, and anticancer therapy.

Cancer-associated fibroblasts reveal aberrant DNA methylation across different types of cancer

BACKGROUND

Cancer-associated fibroblasts (CAFs) are essential components of the tumor microenvironment and play a critical role in cancer progression. Numerous studies have identified significant molecular differences between CAFs and normal tissue-associated fibroblasts (NAFs). In this study, we isolated CAFs and NAFs from liver tumors and conducted a comprehensive analysis of their DNA methylation profiles, integrating our finding with data from studies on other cancer types.

RESULTS

Our analysis revealed that several CAF samples exhibited aberrant DNA methylation patterns, which corresponded with altered gene expression levels. Notably, DNA methylation at liver CAF-specific CpG sites was linked to survival outcomes in liver cancer datasets. An integrative analysis using publicly available datasets from various cancer types, including lung, prostate, esophageal, and gastric cancers, uncovered common epigenetic abnormalities across these cancers. Among the consistently altered CpGs were cg09809672 (EDARADD), cg07134930 (HDAC4), and cg05935904 (intergenic). These methylation changes were associated with prognosis across multiple cancer types.

CONCLUSION

The activation of CAFs by the tumor microenvironment seems to be associated with distinct epigenetic modifications. Remarkably, similar genomic regions tend to undergo hypomethylation in CAFs across different studies and cancer types. Our findings suggest that CAF-associated DNA methylation changes hold potential as prognostic biomarkers. However, further research and validation are necessary to develop and apply such signatures in a clinical setting.