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Despite marked development in cancer therapies during recent decades, the prognosis for advanced cancer remains poor. The conventional tumor–cell‐centric view of cancer can only explain part of cancer progression, and thus a thorough understanding of the tumor microenvironment (TME) is crucial. Among cells within the TME, cancer‐associated fibroblasts (CAFs) are attracting attention as a target for cancer therapy. However, CAFs present a heterogeneous population of cells and more detailed classification of CAFs and investigation of functions of each subset is needed to develop novel CAF‐targeted therapies. In this context, application of newly developed approaches to single‐cell analysis has already made an impact on our understanding of the heterogeneity of CAFs. Here, we review the recent literature on CAF heterogeneity and function, and discuss the possibility of novel therapies targeting CAF subsets. The conventional tumor–cell‐centric view of cancer can only explain a part of cancer progression, thus understanding of the tumor microenvironment (TME) is crucial. Among cells within the TME, cancer‐associated fibroblasts (CAFs) are attracting attention as a target for cancer therapy. Here, we review the recent literature that has improved our understanding of heterogeneity in CAFs and function of each subset, and discuss the possibility of novel therapies targeting CAF subsets.

Cancer-associated fibroblasts (CAFs) are a heterogeneous cell population that plays a crucial role in remodeling the tumor microenvironment (TME). Here, through the integrated analysis of spatial and single-cell transcriptomics data across six common cancer types, we identified four distinct functional subgroups of CAFs and described their spatial distribution characteristics. Additionally, the analysis of single-cell RNA sequencing (scRNA-seq) data from three additional common cancer types and two newly generated scRNA-seq datasets of rare cancer types, namely epithelial-myoepithelial carcinoma (EMC) and mucoepidermoid carcinoma (MEC), expanded our understanding of CAF heterogeneity. Cell–cell interaction analysis conducted within the spatial context highlighted the pivotal roles of matrix CAFs (mCAFs) in tumor angiogenesis and inflammatory CAFs (iCAFs) in shaping the immunosuppressive microenvironment. In patients with breast cancer (BRCA) undergoing anti-PD-1 immunotherapy, iCAFs demonstrated heightened capacity in facilitating cancer cell proliferation, promoting epithelial-mesenchymal transition (EMT), and contributing to the establishment of an immunosuppressive microenvironment. Furthermore, a scoring system based on iCAFs showed a significant correlation with immune therapy response in melanoma patients. Lastly, we provided a web interface ( https://chenxisd.shinyapps.io/pancaf/ ) for the research community to investigate CAFs in the context of pan-cancer.

Integrin‐based focal adhesion is one of the major mechanosensory in osteocytes. The aim of this study was to mine the hub genes associated with focal adhesion and investigate their roles in osteoporosis based on the data of single‐cell RNA sequencing and RNA‐sequencing. Two hub genes (FAM129A and RNF24) with the same expression trend and AUC values greater than 0.7 in both GSE56815 and GSE56116 cohorts were uncovered. The nomogram was created to predict the risk of OP based on two hub genes. Subsequently, the competing endogenous RNA network was established based on two hub genes, 14 microRNAs and five long noncoding RNAs. Meanwhile, transcription factors‐hub gene network was established based on two hub genes and 14 TFs. Finally, 73 drugs were predicted, of which there were 13 drugs targeting FAM129A and 66 drugs targeting RNF24. In both mouse and human blood samples, FAM129A expression was decreased in granulocytes and RNF24 expression was increased in monocytes. In the mouse experiment, FAM129A and anti‐RNF24 were found to partially alleviate the progression of osteoporosis. In conclusion, two hub genes related to focal adhesion were identified by combined scRNA‐seq and RNA‐seq analyses, which might supply a new insight for the treatment and evaluation of OP.

Single-cell RNA sequencing (scRNA-seq), a technology that analyzes transcriptomes of complex tissues at single-cell levels, can identify differential gene expression and epigenetic factors caused by mutations in unicellular genomes, as well as new cell-specific markers and cell types. scRNA-seq plays an important role in various aspects of tumor research. It reveals the heterogeneity of tumor cells and monitors the progress of tumor development, thereby preventing further cellular deterioration. Furthermore, the transcriptome analysis of immune cells in tumor tissue can be used to classify immune cells, their immune escape mechanisms and drug resistance mechanisms, and to develop effective clinical targeted therapies combined with immunotherapy. Moreover, this method enables the study of intercellular communication and the interaction of tumor cells and non-malignant cells to reveal their role in carcinogenesis. scRNA-seq provides new technical means for further development of tumor research and is expected to make significant breakthroughs in this field. This review focuses on the principles of scRNA-seq, with an emphasis on the application of scRNA-seq in tumor heterogeneity, pathogenesis, and treatment.

Female fecundity declines in a nonlinear manner with age during the reproductive years, even as ovulatory cycles continue, which reduces female fertility, disrupts metabolic homeostasis, and eventually induces various chronic diseases. Despite this, the aging‐related cellular and molecular changes in human ovaries that occur during these reproductive years have not been elucidated. Here, single‐cell RNA sequencing (scRNA‐seq) of human ovaries is performed from different childbearing ages and reveals that the activation of the pyroptosis pathway increased with age, mainly in macrophages. The enrichment of pyroptotic macrophages leads to a switch from a tissue‐resident macrophage (TRM)‐involve immunoregulatory microenvironment in young ovaries to a pyroptotic monocyte‐derived macrophage (MDM)‐involved proinflammatory microenvironment in middle‐aged ovaries. This remolded ovarian immuno‐microenvironment further promotes stromal cell senescence and accelerated reproductive decline. This hypothesis is validated in a series of cell and animal experiments using GSDMD‐KO mice. In conclusion, the work expands the current understanding of the ovarian aging process by illustrating a pyroptotic macrophage‐involved immune mechanism, which has important implications for the development of novel strategies to delay senescence and promote reproductive health. ScRNA‐seq analysis of human ovaries identified age‐related changes in cellular interactomes during reproductive years.The immune regulatory mechanisms of ovarian aging are underscored by emphasizing the central role of pyroptotic macrophages in accelerating collagen deposition and stromal cell senescence in elder ovaries, which eventually lead to ovarian function decline.

Extracting dynamical information from single‐cell transcriptomics is a novel task with the promise to advance our understanding of cell state transition and interactions between genes. Yet, theory‐oriented, bottom‐up approaches that consider differences among cell states are largely lacking. Here, we present spliceJAC, a method to quantify the multivariate mRNA splicing from single‐cell RNA sequencing (scRNA‐seq). spliceJAC utilizes the unspliced and spliced mRNA count matrices to constructs cell state‐specific gene–gene regulatory interactions and applies stability analysis to predict putative driver genes critical to the transitions between cell states. By applying spliceJAC to biological systems including pancreas endothelium development and epithelial–mesenchymal transition (EMT) in A549 lung cancer cells, we predict genes that serve specific signaling roles in different cell states, recover important differentially expressed genes in agreement with pre‐existing analysis, and predict new transition genes that are either exclusive or shared between different cell state transitions. Synopsis spliceJAC builds a multivariate mRNA splicing model from single‐cell transcriptome data to infer the context‐specific gene regulation and the key driver genes that guide the transition between cell states. spliceJAC constructs cell state‐specific gene regulatory networks and quantifies changes in signaling roles between cell states. spliceJAC employs stability analysis to identify driver genes that guide transitions between cell states. Context‐specific gene regulation and transition genes are identified using spliceJAC during pancreas endothelium development and epithelial–mesenchymal transition (EMT) in A549 lung cancer cells. Graphical Abstract spliceJAC builds a multivariate mRNA splicing model from single‐cell transcriptome data to infer the context‐specific gene regulation and the key driver genes that guide the transition between cell states.

Osteonecrosis of the femoral head (ONFH) is a progressive orthopedic disorder that often culminates in femoral head collapse and joint failure. Dysfunction of bone marrow mesenchymal stem cells (BMSCs), including impaired osteogenesis, enhanced adipogenesis, and mitochondrial dysfunction, has been increasingly recognized as a central driver of ONFH pathogenesis. However, the molecular mechanisms linking metabolic stress to lineage imbalance remain poorly defined. Paired BMSCs were isolated from necrotic femoral head regions (fhBMSCs) and the iliac crest (iBMSCs) of ONFH patients. Functional assays, RNA sequencing, and molecular analyses were performed to evaluate the effects of the hypoxia mimetic dimethyloxalylglycine (DMOG) on osteogenic-adipogenic balance, mitochondrial function, and senescence. Loss-of-function experiments targeting hypoxia-inducible factor-1[alpha] (HIF-1[alpha]) and Homer3 were conducted to elucidate mechanistic pathways. Compared with iBMSCs, fhBMSCs exhibited impaired osteogenesis, enhanced adipogenesis, mitochondrial dysfunction, and increased senescence. DMOG pretreatment restored osteogenic differentiation, suppressed adipogenesis, improved mitochondrial dynamics, reduced oxidative stress, and enhanced bioenergetic metabolism. These protective effects were dependent on HIF-1[alpha] stabilization. Transcriptomic profiling identified Homer3 as a downstream negative regulator of HIF-1[alpha]. Homer3 was aberrantly upregulated in fhBMSCs but suppressed by DMOG, and its knockdown mimicked the effects of DMOG by promoting osteogenesis, inhibiting adipogenesis, enhancing mitophagy, and restoring mitochondrial function. Conversely, silencing HIF-1[alpha] abolished DMOG-mediated benefits and reinstated Homer3 expression. This study identifies the HIF-1[alpha]/Homer3 axis as a central regulator of lineage balance and mitochondrial homeostasis in ONFH-derived BMSCs. Pharmacological targeting of this pathway with DMOG or related prolyl hydroxylase inhibitors may provide a promising joint-preserving therapeutic strategy for ONFH.

[This corrects the article DOI: 10.1371/journal.pgen.1008367.].[This corrects the article DOI: 10.1371/journal.pgen.1008367.].

N .sup.6-methyladenosine (m.sup.6A) is the most prevalent mRNA internal modification and has been shown to regulate the development, physiology, and pathology of various tissues. However, the functions of the m.sup.6A epitranscriptome in the visual system remain unclear. In this study, using a retina-specific conditional knockout mouse model, we show that retinas deficient in Mettl3, the core component of the m.sup.6A methyltransferase complex, exhibit structural and functional abnormalities beginning at the end of retinogenesis. Immunohistological and single-cell RNA sequencing (scRNA-seq) analyses of retinogenesis processes reveal that retinal progenitor cells (RPCs) and Müller glial cells are the two cell types primarily affected by Mettl3 deficiency. Integrative analyses of scRNA-seq and MeRIP-seq data suggest that m.sup.6A fine-tunes the transcriptomic transition from RPCs to Müller cells by promoting the degradation of RPC transcripts, the disruption of which leads to abnormalities in late retinogenesis and likely compromises the glial functions of Müller cells. Overexpression of m.sup.6A-regulated RPC transcripts in late RPCs partially recapitulates the Mettl3-deficient retinal phenotype. Collectively, our study reveals an epitranscriptomic mechanism governing progenitor-to-glial cell transition during late retinogenesis, which is essential for the homeostasis of the mature retina. The mechanism revealed in this study might also apply to other nervous systems.

In the original publication [...]