Single-cell transcriptional diversity is a hallmark of developmental potential

The landscape of malignant transition: Unraveling cancer cell-of-origin and heterogeneous tissue microenvironment

Understanding disease progression and sophisticated tumor ecosystems is imperative for investigating tumorigenesis mechanisms and developing novel prevention strategies. Here, we dissected heterogeneous microenvironments during malignant transitions by leveraging data from 1396 samples spanning 13 major tissues. Within transitional stem-like subpopulations highly enriched in precancers and cancers, we identified 30 recurring cellular states strongly linked to malignancy, including hypoxia and epithelial senescence, revealing a high degree of plasticity in epithelial stem cells. By characterizing dynamics in stem-cell crosstalk with the microenvironment along the pseudotime axis, we found differential roles of ANXA1 at different stages of tumor development. In precancerous stages, reduced ANXA1 levels promoted monocyte differentiation toward M1 macrophages and inflammatory responses, whereas during malignant progression, upregulated ANXA1 fostered M2 macrophage polarization and cancer-associated fibroblast transformation by increasing TGF-β production. Our spatiotemporal analysis further provided insights into mechanisms responsible for immunosuppression and a potential target to control evolution of precancer and mitigate the risk for cancer development.

Engineering a stem cell-embedded bilayer hydrogel with biomimetic collagen mineralization for tendon-bone interface healing

The tendon-bone interface effectively transfers mechanical stress for movement, yet its regeneration presents significant clinical challenges due to its hierarchical structure and composition. Biomimetic strategies that replicate the distinctive characteristics have demonstrated potential for enhancing the healing process. However, there remains a challenge in developing a composite that replicates the nanostructure of the tendon-bone interface and embeds living cells. Here, we engineered a nanoscale biomimetic bilayer hydrogel embedded with tendon stem cells for tendon-bone interface healing. Specifically, the biomimetic hydrogel incorporates intra- and extrafibrillar mineralized collagen fibrils as well as non-mineralized collagen fibrils resembling the tendon-bone interface at the nanoscale. Furthermore, biomimetic mineralization with the presence of cells realizes living tendon-bone-like tissue constructs. In the in vivo patella-patellar tendon-interface injury model, the tendon stem cell-laden biomimetic hydrogel promoted tendon-bone interface regeneration, demonstrated by increased fibrocartilage formation, improved motor function, and enhanced biomechanical outcomes. This study highlights the potential of the stem cell-laden biomimetic hydrogel as an effective strategy for tendon-bone interface regeneration, offering a novel approach to engineering complex tissue interfaces.

Development and validation of a transcription factor regulatory network-based signature for individualized prognostic risk in lung adenocarcinoma

Despite significant progress in diagnostic and therapeutic modalities, lung adenocarcinoma (LUAD) still exhibits a high recurrence risk and a low 5-year survival rate. Reliable prognostic signatures are imperative for risk stratification in LUAD patients. This study encompassed 2740 patients from 23 LUAD cohorts, including one single-cell RNA sequencing (scRNA-seq) dataset, five bulk RNA-seq datasets, and 17 microarray datasets. Using scRNA-seq dataset, we defined a group of epithelial-specific transcription factors significantly over-represented in the epithelial-to-mesenchymal transition (EMT) gene set (enrichment ratio [ER] = 5.80, Fisher's exact test p < .001), and the corresponding target genes were significantly enriched in the cancer driver gene set (ER = 2.74, p < .001), indicating of their crucial roles in the EMT process and tumor progression. We constructed a single-cell gene pairs (scGPS) signature, composed of 3521 gene pairs derived from the epithelial cell-specific transcription factor regulatory network, to predict overall survival (OS) of LUAD. High-risk patients identified by scGPS in the discovery cohort exhibited significantly worse OS compared to low-risk patients (Hazard ratio [HR] = 1.78, 95% CI: 1.29-2.46, log-rank p = 1.80 × 10-4). The scGPS outperformed other established gene signatures and demonstrated robust prognostic stratification across various independent datasets, including microarray data and even early-stage LUAD patients. It remained an independent prognostic factor after adjusting for clinical and pathologic factors. In addition, combining scGPS with tumor stage further enhanced prognostic accuracy compared to using stage alone. The scGPS signature offers individualized prognosis estimations, showing significant potential for practical application in clinical settings.

Pdia3 deficiency exacerbates intestinal injury by disrupting goblet and Paneth cell function during ischemia/reperfusion

Intestinal ischemia/reperfusion (I/R) injury is a severe medical condition associated with high mortality rates due to its disruption of intestinal homeostasis and impairment of mucosal defenses. The intestinal epithelium, particularly goblet and Paneth cells, plays a critical role in maintaining gut barrier integrity. Protein disulfide isomerase A3 (PDIA3) is involved in protein folding within intestinal epithelial cells (IECs) and has been linked to the stress response during I/R injury. This study aims to explore the role of PDIA3 in preserving intestinal integrity and immune function during I/R injury. Our study employed both human and mouse models to investigate PDIA3's expression and function. The correlation between PDIA3 expression and disease severity was analyzed using statistical tests, including Pearson's correlation coefficient. An intestinal I/R model was established in intestinal epithelium-specific conditional knockout mice lacking the Pdia3 gene. Single-cell RNA sequencing, immunohistochemistry, and transcriptomic analysis were used to assess PDIA3 expression in various intestinal cell types and to evaluate its role in epithelial differentiation and immune responses. PDIA3 was found to be highly expressed in healthy IECs, especially in goblet and Paneth cells. Its expression was reduced in patients with mesenteric artery ischemia and Pdia3-deficient mice, leading to severe intestinal damage, including impaired goblet and Paneth cell function, reduced antimicrobial peptide production, and altered gut microbiota. Treatment with recombinant defensin α1, an antimicrobial peptide secreted by Paneth cells, significantly alleviated the adverse effects of Pdia3 deficiency, restoring gut microbiota balance and reducing inflammation in the intestinal I/R injury mice. Taken together, our findings suggest that Pdia3 plays a vital role in maintaining intestinal barrier function and immune defense. Its deficiency exacerbates I/R-induced intestinal damage by impairing epithelial differentiation, mucus production, and antimicrobial peptide secretion. Targeting Pdia3 and associated pathways offers promising therapeutic strategies for mitigating I/R injury and restoring intestinal homeostasis.

Single-Cell RNA Sequencing Reveals the Immune Landscape of Granulomatous Mastitis

Granulomatous mastitis (GM) is a form of non-lactational breast inflammation that is closely associated with autoimmune processes, however its underlying pathogenesis remains elusive. In this study, we employed single-cell RNA sequencing (scRNA-seq) to conduct a comparative analysis of GM lesion tissues versus normal breast tissues, thereby unveiling the immune profile of GM tissues. Our investigation centered on T and NK cells, macrophages, epithelial cells, and endothelial cells. Notably, we observed a substantial infiltration of immune cells in GM tissues, accompanied by immune disorders, an elevation in Th1 cell counts, enrichment of the toll-like receptor (TLR) pathway, and upregulation of various factors including interferon-γ (IFN-γ), C-C motif chemokine ligand 3 (CCL3), CCL4, chemokine (C-X-C motif) ligand (CXCL) 13, CD69, signal transducer and activator of transcription 1 (STAT1), and heat shock protein family A member 1A (HSPA1A). Furthermore, the macrophage subpopulations in GM tissues exhibited a transition to a pro-inflammatory phenotype, enriched for pathways such as interferon-γ (IFN-γ), IFN-α, interleukin-6/janus kinase/signal transducer and activator of transcription 3 (IL-6/JAK/STAT3), and tumor necrosis factor-α/nuclear factor-κB (TNF-α/NF-κB). Mammary luminal cells demonstrated an impaired estrogenic profile yet displayed upregulation of prolactin downstream signaling pathways, namely the JAK/STAT and mitogen-activated protein kinase (MAPK) pathways. Additionally, vascular endothelial cells were found to recruit immune cells and exhibited a prominent angiogenic profile in GM tissues. Cellular interaction analysis unveiled an intricate network of interactions between mesenchymal and immune cells. This study provides a comprehensive immune landscape of granulomatous mastitis and offers some potential therapeutic targets for the disease.

Metabolic-associated fatty liver disease (MAFLD) promotes the progression of hepatocellular carcinoma by enhancing KIF20A expression

BACKGROUND

Compared to other HCC, those related to MAFLD exhibit distinct prognostic differences. This article aims to elucidate the impact of MAFLD on HCC prognosis through the lens of KIF20A, thereby providing a theoretical foundation for targeted therapies in MAFLD-related HCC.

METHODS

We employed the Weighted gene co-expression network analysis (WGCNA) method alongside the Mime package to identify key genes associated with MAFLD-related HCC. Subsequently, we utilized OCLR and CytoTRACE algorithms to evaluate the relationship between these genes and HCC stemness. The R package was employed to conduct immunological analyses on both mRNA sequencing and single-cell data. We validated the effects of core genes on HCC through experimental approaches, including cell culture, Transwell assays, Western Blot, and proliferation assays. Finally, we predicted potential therapeutic drugs using the OncoPredict software package.

RESULTS

WGCNA identified the cyan module associated with MAFLD in GSE135251 and the blue module linked to HCC in TCGA. Further analysis identified KIF20A as the core gene in MAFLD-related HCC. Utilizing the OCLR and CytoTRACE algorithms, KIF20A was found to correlate with mRNA stemness index (mRNAsi). Analysis of public databases revealed that KIF20A promotes immune tolerance through the SPP1-CD44 pathway and drives HCC progression via the G2M checkpoint. Experimental results demonstrated that lipotoxic damage in HCC cells and small extracellular vesicles (sEVs) derived from these cells upregulate KIF20A, thereby accelerating HCC progression. Finally, OncoPredict and AutoDock were employed to predict drugs targeting KIF20A.

CONCLUSION

MAFLD-related HCC can elevate KIF20A levels and promote tumor proliferation and migration.

Characterizing the immune landscape of tumor-infiltrating lymphocytes in non-small cell lung cancer

Tumor-Infiltrating Lymphocytes (TILs) immunotherapy is a highly promising treatment for Non-small Cell Lung Cancer (NSCLC), which is responsible for 18% of all cancer-related deaths. The heterogeneity of TILs remains poorly understood. Here, we utilized combined single-cell RNA (scRNA)/T cell receptor sequencing (scTCR-seq) data from lung adenocarcinoma (LUAD) patients. Naïve CD4+ and effector memory CD8+ T cells were increased in tumor tissue compared with circulating blood samples. Activated signaling pathways were detected, and GZMA was identified as a potential novel diagnostic biomarker. During the transitional phase, macrophages (FTL) and dendritic (AIF1) cells transported the most CD3 TCR clones to T cells, while cytotoxicity CD8+ T (NKG7) cells transported to terminal exhausted CD8+ T cells. In both transition and expansion phases, T helper cells (CXCL13) are transported to regulatory T cells (Tregs). Additionally, we investigated the expression profiles of key cytokines, checkpoint receptors, and their ligands. Cytotoxicity CD8+ T cells (CCL5 and IFNG), T helper cells (FTL, TNFRSF4, and TIGIT), and regulatory T cells (CTLA4, TIGIT and FTL) exhibited functional roles in both primary and metastatic tumor stages. Taken together, our study provides a single-cell resolution of the TIL immune landscape and suggests potential treatment strategies to overcome drug resistance.

A highly resolved integrated transcriptomic atlas of human breast cancers

In this study, we developed an integrated single cell transcriptomic (scRNAseq) atlas of human breast cancer (BC), the largest resource of its kind, totaling > 600,000 cells across 138 patients. Rigorous integration and annotation of publicly available scRNAseq data enabled a highly resolved characterization of epithelial, immune, and stromal heterogeneity within the tumor microenvironment (TME). Within the immune compartment we were able to characterize heterogeneity of CD4, CD8 T cells and macrophage subpopulations. Within the stromal compartment, subpopulations of endothelial cells (ECs) and cancer associated fibroblasts (CAFs) were resolved. Within the cancer epithelial compartment, we characterized the functional heterogeneity of cells across the axes of stemness, epithelial-mesenchymal plasticity, and canonical cancer pathways. Across all subpopulations observed in the TME, we performed a multi-resolution survival analysis to identify epithelial cell states and immune cell types which conferred a survival advantage in both The Cancer Genome Atlas (TCGA) and METABRIC. We also identified robust associations between TME composition and clinical phenotypes such as tumor subtype and grade that were not discernible when the analysis was limited to individual datasets, highlighting the need for atlas-based analyses. This atlas represents a valuable resource for further high-resolution analyses of TME heterogeneity within BC.

Single-cell transcriptomics reveal the effects of chemoimmunotherapy on hypopharyngeal cancer and its tumor microenvironment

Induction chemoimmunotherapy (ICIT) has emerged as a potential treatment option for resectable hypopharyngeal cancer (HPC), while its effectiveness remains limited to a significant portion of HPC cases, and a major challenge behind lies in the lack of reliable molecular markers to identify treatment-resistant patients. In this study, we analyzed biopsy samples of HPC patients collected before and after ICIT, classifying them based on treatment response. By investigating the tumor microenvironment (TME) at the single-cell level, we demonstrated that the heterogeneity within the TME is closely linked to different treatment outcomes. Specially, a strong treatment response correlated with a subpopulation of cancer-associated fibroblasts (CAFs). Additionally, we identified that the S100A2 gene is highly expressed in tumor cells and appears to influence ICIT efficacy. Using bulk RNA sequencing, we estimated cell composition and validated these observations at the protein level. Our research provides a novel approach for identifying genes and cell populations that predict treatment responses in HPC, potentially enabling the timely identification of treatment-resistant patients. This could increase the likelihood of preserving laryngeal function and optimizing treatment strategies.

Single-cell transcriptomic analysis reveals distinct plasma cell populations in chronic thromboembolic pulmonary hypertension

BACKGROUND

Chronic thromboembolic pulmonary hypertension (CTEPH) presents challenges due to its complex pathobiology. Although numerous studies have reported heterogeneous cell types by single-cell RNA sequencing, the atlas and characteristics of plasma cells remain poorly understood.

OBJECTIVES

To identify the altered phenotype and differentiation patterns of plasma cells in CTEPH.

METHODS

We performed single-cell RNA sequencing on pulmonary endarterectomy tissue from 5 patients and 6 normal pulmonary arteries. Serum immunoglobulins (Igs) were measured using protein electrophoresis among 273 CTEPH patients, 259 idiopathic pulmonary arterial hypertension (IPAH) patients, and 251 healthy controls.

RESULTS

The percentage of plasma cells was significantly increased from less than 1% in healthy controls to 15% in CTEPH patients. We identified 1 B cell cluster and 5 distinct mature plasma cell clusters, including IGHG1, HSPA1A, AHNAK, IGLC3, and IGKV4. Notably, the AHNAK and IGLC3 subclusters are newly identified. GeneSwitches analysis indicated early activation of IGHG1 and early deactivation of HLA-DPA1. The trajectory of AHNAK cluster was earlier than that of IGLC3 cluster, with an enrichment for pathways responsive to lipopolysaccharide. The IGLC3 cluster revealed lower differentiation potential and was predominantly associated with Ig production. Furthermore, Igα2 levels in CTEPH patients were lower than in controls but higher than in IPAH patients. Significantly, Igγ levels were markedly elevated in CTEPH patients compared with IPAH patients and controls, better distinguishing CTEPH patients from controls and IPAH patients.

CONCLUSION

Plasma cells of CTEPH had a distinctive landscape and heterogeneity. The newly identified clusters represented excessive Ig production but lacked immune response function. These findings highlight that targeted plasma cells can be used to develop novel CTEPH treatments.

Single-cell sequencing reveals PHLDA1-positive smooth muscle cells promote local invasion in head and neck squamous cell carcinoma

BACKGROUND

Smooth muscle cells within the tumor microenvironment play a crucial role in cancer progression. However, their involvement in the local invasion of head and neck squamous cell carcinoma remains poorly understood. In this research, we aim to investigate the role of smooth muscle cells-mediated cell interactions in facilitating the local invasion of head and neck squamous cell carcinoma.

METHODS

Single-cell sequencing data from the public databases GSE164690 and GSE181919 were utilized to identify a specific smooth muscle cells cluster. Smooth muscle cells were isolated from tumor microenvironment of head and neck squamous cell carcinoma. PHLDA1 expression in smooth muscle cells was assessed through immunofluorescence staining. The role of THBS1 was investigated through in vitro studies.

RESULTS

PHLDA1-positive smooth muscle cells were significantly enriched in head and neck squamous cell carcinoma. PHLDA1 promoted the expression of THBS1 in smooth muscle cells. In vitro, THBS1 facilitated head and neck squamous cell carcinoma migration and invasion through SDC1 receptor.

CONCLUSION

PHLDA1-positive smooth muscle cells play a critical role in head and neck squamous cell carcinoma invasion through THBS1. Targeting PHLDA1-positive smooth muscle cells or THBS1 may offer a promising therapeutic approach for head and neck squamous cell carcinoma treatment.

Single cell analysis reveals that SPP1+ macrophages enhance tumor progression by triggering fibroblast extracellular vesicles

Patients with liver metastatic colorectal cancer (mCRC) have a poor prognosis and are the leading cause of death in colorectal cancer (CRC) patients, but the mechanisms associated with CRC metastasis have not been fully elucidated. In this study, we obtained data from the Gene Expression Omnibus database and characterized the single-cell profiles of CRC, mCRC and healthy samples at single-cell resolution, and explored the cells that influence CRC metastasis. We find that AQP1+ CRC identified as highly malignant tumor cells exhibited proliferative and metastatic characteristics. Immunosuppressive properties are present in the tumor microenvironment (TME), while NOTCH3+ Fib is identified to play a facilitating role in the metastatic colonization of CRC. Importantly, we reveal that tumor-associated macrophages (TAM) characterized by SPP1-specific high expression may be involved in TME remodeling through intercellular communication. Specifically, SPP1+ TAM mediates the generation of Fib-derived extracellular vesicle through the APOE-LRP1 axis, which in turn delivers tumor growth-promoting factors in the TME. This study deepens the understanding of the mechanism of TME in mCRC and lays the scientific foundation for the development of therapeutic regimens for mCRC patients.

Human skeletal development and regeneration are shaped by functional diversity of stem cells across skeletal sites

The skeleton is one of the most structurally and compositionally diverse organ systems in the human body, depending on unique cellular dynamisms. Here, we integrate prospective isolation of human skeletal stem cells (hSSCs; CD45-CD235a-TIE2-CD31-CD146-PDPN+CD73+CD164+) from ten skeletal sites with functional assays and single-cell RNA sequencing (scRNA-seq) analysis to identify chondrogenic, osteogenic, stromal, and fibrogenic subtypes of hSSCs during development and their linkage to skeletal phenotypes. We map the distinct composition of hSSC subtypes across multiple skeletal sites and demonstrate their unique in vivo clonal dynamics. We find that age-related changes in bone formation and regeneration disorders stem from a pathological fibroblastic shift in the hSSC pool. Utilizing a Boolean algorithm, we uncover gene regulatory networks that dictate differences in the ability of hSSCs to generate specific skeletal tissues. Importantly, hSSC lineage dynamics are pharmacologically malleable, providing a new strategy to treat aberrant hSSC diversity central to aging and skeletal maladies.

CREB1-BCL2 drives mitochondrial resilience in RAS GAP-dependent breast cancer chemoresistance

Triple-negative breast cancer (TNBC) is an aggressive and heterogenous breast cancer subtype. RASAL2 is a RAS GTPase-activating protein (GAP) that has been associated with platinum resistance in TNBC, but the underlying mechanism is unknown. Here, we show that RASAL2 is enriched following neoadjuvant chemotherapy in TNBC patients. This enrichment is specific to the tumour compartment compared to adjacent normal tissues, suggesting that RASAL2 upregulation is tumour-selective. Analyses based on 2D/3D cultures and patient-derived xenograft models reveal that RASAL2 confers cross-resistance to common DNA-damaging chemotherapies other than platinum. Mechanistically, we found that apoptotic signalling is significantly downregulated upon RASAL2 expression. This feature is characterised by substantial alterations in the expression of anti-versus pro-apoptotic factors, pointing to heterogeneous mechanisms. In particular, RASAL2 upregulates BCL2 via activation of the oncogenic transcription co-factor YAP. CREB1, a YAP-interacting protein, was identified as the common transcription factor that binds to the promoter regions of RASAL2 and BCL2, driving their collective expression. A subset of RASAL2 colocalises with BCL2 subcellularly. Both proteins decorate mitochondria, where the high levels of mitochondrial RASAL2-induced BCL2 expression render the organelles refractory to apoptosis. Accordingly, mitochondrial outer membrane permeabilisation assay using live mitochondria from RASAL2-high/chemoresistant tumour cells demonstrated attenuated release of death signal, cytochrome c, when exposed to pro-apoptotic factors BAX and tBID. Similarly, these cells were more resilient towards chemotherapy-induced mitochondrial depolarisation. Together, this work reveals a previously undocumented molecular link between RAS GAP and apoptosis regulation, providing a new mechanistic framework for targeting a subset of chemorefractory tumours.

Multiomic spatial atlas shows deleted in malignant brain tumors 1 (DMBT1) glycoprotein is lost in colonic dysplasia

Colorectal cancer (CRC) is responsible for over 900,000 annual deaths worldwide. Emerging evidence supports pro-carcinogenic bacteria in the colonic microbiome are at least promotional in CRC development and may be causal. We previously showed toxigenic C. difficile from human CRC-associated bacterial biofilms accelerates tumorigenesis in ApcMin/+ mice, both in specific pathogen-free mice and in gnotobiotic mice colonized with a defined consortium of bacteria. To further understand host-microbe interactions during colonic tumorigenesis, we combined single-cell RNA-sequencing (scRNA-seq), spatial transcriptomics, and immunofluorescence to define the molecular spatial organization of colonic dysplasia in our consortium model with or without C. difficile. Our data show a striking bipartite regulation of Deleted in Malignant Brain Tumors 1 (DMBT1) in the inflamed versus dysplastic colon. From scRNA-seq, differential gene expression analysis of normal absorptive colonocytes at 2 weeks postinoculation showed DMBT1 upregulated by C. difficile compared to colonocytes from mice without C. difficile exposure. In contrast, our spatial transcriptomic analysis showed DMBT1 dramatically downregulated in dysplastic foci compared with normal-adjacent tissue. We further integrated our datasets to generate custom colonic dysplasia scores and ligand-receptor mapping. Validation with immunofluorescence showed DMBT1 protein downregulated in dysplastic foci from three mouse models of colonic tumorigenesis and in adenomatous dysplasia from human samples. Finally, we used mouse and human organoids to implicate WNT signaling in the downregulation of DMBT1 mRNA and protein. Together, our data reveal cell type-specific regulation of DMBT1, a potential mechanistic link between bacteria and colonic tumorigenesis. Published 2025. This article is a U.S. Government work and is in the public domain in the USA. The Journal of Pathology published by John Wiley & Sons Ltd on behalf of The Pathological Society of Great Britain and Ireland.

Single-Cell Profiling Reveals Conserved Differentiation and Partial EMT Programs Orchestrating Ecosystem-Level Antagonisms in Head and Neck Cancer

Head and neck squamous cell carcinoma (HNSC) exhibits profound intratumoral heterogeneity, driven by dynamic interactions between malignant cells and the tumour microenvironment (TME). Using consensus non-negative matrix factorisation (cNMF) on multi-site HNSC single-cell transcriptomes, we resolving conserved meta-programs define cellular ecosystems. Six major epithelial programmes emerged, including a differentiation-associated programme (Epi_Diff) correlated with SPDEF activity and favourable patient prognosis, and an invasive programme (Epi_pEMT) potentially controlled by TEAD4-mediated ECM remodelling, exhibiting partial EMT markers (VIM, TGFB1). Compartment-specific crosstalk analysis revealed Epi_pEMT cells may coordinate with mCAF1 fibroblasts and TAM(SPP1) through COL1A1-CD44 and SPP1-CD44 signalling, suggesting potential formation of a pro-invasive niche. Conversely, Epi_Diff cells may interact with NK/T cells through CEACAM5-CD8A and CCL5-ACKR2, and may contribute to inhibit immune infiltration. Multi-compartment correlation analysis revealed three ecosystem-level patterns: (1) Inverse association between Epi_Diff and Epi_pEMT (Spearman R = -0.43); (2) Negative correlation between mCAF1 abundance and cCAF frequency (R = -0.48); (3) TAM(SPP1) dominance inversely correlating with both TAM(C1Q) (R = -0.43) and NK/T infiltration (R = -0.36). These axes suggest a potential hierarchical ecology framework where lineage-specific polarisation and inter-compartment synergies may collectively govern disease progression.

Single-cell RNA sequencing and functional analysis reveal the role of altered glycosylation levels of hepatic macrophages in liver cirrhosis

BACKGROUND

Liver cirrhosis represents a critical stage of chronic liver disease, characterized by progressive liver damage, cellular dysfunction, and disrupted cell-to-cell interactions. Glycosylation, an essential post-translational modification, significantly influences cellular behavior and disease progression. Its role in cirrhosis at the single-cell level remains unclear, despite its importance.

METHODS

This study, based on single-cell glycosylation and transcriptome data, compared the expression of differentially expressed genes in liver tissues from cirrhotic and healthy control samples, identifying changes in glycosylation-related genes and their functional pathway enrichment characteristics. Additionally, it analyzed the composition of immune cells and intercellular interaction features, with a focus on the interaction between macrophages and other immune cells and their potential role in immune regulation.

RESULTS

The analysis revealed significant changes in immune cell composition and glycosylation patterns in cirrhotic livers. Specifically, the number of macrophages increased substantially, while overall glycosylation levels decreased. Enhanced interactions between macrophages and other cell types were observed, highlighting the central role of macrophages in reshaping the immune microenvironment during cirrhosis progression. Gene expression analysis showed a marked upregulation of FUCA1, a gene encoding a glycosylation-related hydrolase. This change was strongly associated with the observed reduction in glycosylation levels. Functional enrichment analysis further revealed that glycosylation-related genes were primarily involved in immune pathways, including antigen processing and presentation, cytokine signaling, and immune activation.

CONCLUSIONS

Single-cell glycosylation analysis provides crucial insights into immune cell interactions in cirrhosis. Targeting glycosylation pathways in macrophages may offer new treatment strategies for cirrhosis.

NAALAD2 mutations disrupt the fate of photoreceptor cells and retinal pigment epithelial cells during early retinal development

In recent years, the global incidence of myopia has steadily increased, highlighting the importance of prevention and early intervention, particularly in the absence of effective treatments. Here, we identified a previously unreported mutation in the human N-acetylated alpha-linked acidic dipeptidase 2 (NAALAD2) gene (c.2109 T > G, p.F703L) considered in a Chinese family with pathological myopia (PM). We explored the potential link between NAALAD2 mutation and the development of PM by using the Naalad2 point mutation knock-in mouse models. Through single-cell RNA sequencing, we analyzed the retinal cell composition and transcriptional profiles both in Naalad2+/+ and Naalad2+/- mice, especially the changes in Cone photoreceptor cells, Rod photoreceptor cells and retinal pigment epithelial (RPE) cells. We found that the Naalad2 mutation led to a reduction in the abundance of Cone and Rod photoreceptor cells, along with upregulation of immediate early genes and abnormal differentiation of certain cell subpopulations. Additionally, RPE cell subpopulations exhibited a fibrotic tendency, disrupting their interactions with photoreceptor cells. Moreover, this study suggests that NAALAD2 mutation may accelerate retinal degeneration by influencing photoreceptor cell apoptosis, stress responses, and the epithelial-mesenchymal transition process in RPE cells. These findings provide new insights into the pathogenic mechanisms of NAALAD2 mutations in PM and offer potential therapeutic targets for future PM research.

Single-cell transcriptome profiling of the human endometrium of patients with intrauterine adhesions

Intrauterine adhesions (IUAs) are a complex condition that frequently results in menstrual disturbances, infertility, and obstetric complications. Unfortunately, the underlying pathophysiology of IUAs remains poorly understood, and current treatments often exhibit limited efficacy. We performed the single-cell RNA-sequencing (scRNA-Seq) comparison of 5 endometrial tissues, including patients with confirmed intrauterine adhesions and healthy controls(HCs). We profiled the transcriptomes of 55,308 primary human endometrial cells isolated from healthy controls and intrauterine adhesions patients at single-cell resolution. Compared with those in HCs, the number of fibroblasts derived from IUAs significantly decreased. Further analysis found that fibroblasts subcluster 3 were enriched in the IUAs, whereas opposite in HCs. GO enrichment analysis revealed that specific genes of fibroblasts subcluster 3 were markedly involved in the positive regulation of embryonic placenta development, the response to reactive oxygen species and female pregnancy, and the positive regulation of the mitotic DNA damage checkpoint and DNA damage response. In addition, the proportion of proliferating endothelial cells was significantly lower in IUAs. GO enrichment analysis revealed that the specific genes were markedly involved in the positive regulation of cell cycle arrest, the cellular response to interferon - gamma and the negative regulation of the mitotic cell cycle. According to the number of intercellular receptor-ligand pairs, we identified endothelial cells as the core cell population. Our study provides deeper insights into the endometrial microenvironment disorders that are potentially applicable to improving therapeutics for IUAs.

Single-cell spatial transcriptomics of tertiary lymphoid organ-like structures in human atherosclerotic plaques

Tertiary lymphoid organs have been identified in the arterial adventitia in both mouse models of atherosclerosis and patients with atherosclerosis, yet their role in the disease remains insufficiently explored. Here we present a spatially resolved single-cell transcriptome atlas of human atherosclerotic plaques, identifying 14 distinct cell types and providing evidence of plaque tertiary lymphoid organs (PTLOs). The development of PTLOs was associated with the expression of lymphangiogenic chemokine genes and the adhesion molecule gene in fibroblast-like smooth muscle cells. PTLOs harbor abundant B cells with expanded and diversified B cell receptors, suggesting substantial immune involvement. We also observed that B cells may be exchanged between PTLOs and perivascular adipose tissues. The presence of PTLO-like structures correlates with cerebrovascular events, which may be mediated by PTLO-derived IgG antibodies enhancing macrophage functional activity. Our findings suggest the existence and characteristics of PTLOs in human atherosclerosis, elucidating their cellular functions and clinical implications and offering avenues for understanding, diagnosing and treating this condition.

Resistance to anti-LAG-3 plus anti-PD-1 therapy in head and neck cancer is mediated by Sox9+ tumor cells interaction with Fpr1+ neutrophils

Relatlimab and nivolumab combination therapy shows significant efficacy in treating various types of cancer. Current research on the molecular mechanisms of this treatment is abundant, but in-depth investigations into post-treatment resistance remain notably lacking. In this study, we identify significant enrichment of SRY (sex determining region Y)-box 9 (Sox9)+ tumor cells in resistant samples using single cell RNA sequencing (scRNAseq) in a head and neck squamous cell carcinoma (HNSCC) mouse model. In addition, Sox9 directly regulates the expression of annexin A1 (Anxa1), mediating apoptosis of formyl peptide receptor 1 (Fpr1)+ neutrophils through the Anxa1-Fpr1 axis, which promotes mitochondrial fission, inhibits mitophagy by downregulating BCL2/adenovirus E1B interacting protein 3 (Bnip3) expression and ultimately prevents the accumulation of neutrophils in tumor tissues. The reduction of Fpr1+ neutrophils impairs the infiltration and tumor cell-killing ability of cytotoxic Cd8 T and γδT cells within the tumor microenvironment, thereby leading to the development of resistance to the combination therapy. We further validate these findings using various transgenic mouse models. Overall, this study comprehensively explains the mechanisms underlying resistance to the anti-LAG-3 plus anti-PD-1 combination therapy and identifies potential therapeutic targets to overcome this resistance.

Comprehensive single-cell transcriptome analysis of autologous platelet-rich plasma therapy on human thin endometrium

Therapeutics for thin endometrium (TE) have emerged, with autologous platelet-rich plasma (PRP) therapy gaining significant attention. In the present study, ten eligible TE patients were recruited for PRP infusion. Endometrial tissue biopsies collected before and after PRP therapy (paired samples) were subjected to single-cell RNA sequencing (scRNA-seq). Additionally, haematoxylin and eosin (HE) and immunohistochemistry (IHC) were employed to validate changes in protein markers. The results demonstrated PRP therapy increased the average endometrial thickness in these patients. Cellular trajectory reconstruction analysis using gene counts and expression (CytoTRACE) scores indicated that high-stemness cells were more enriched in proliferating stromal cells (pStr) or stromal cells (Str) in post-PRP samples, while greater stemness was observed in glandular epithelial cells (GE) and luminal epithelial cells (LE). Gene set variation analysis (GSVA) revealed significant differences in mesenchymal‒epithelial transition (MET)-related gene signature scores between paired samples. Furthermore, an increased number of macrophages, particularly M1-type macrophages, was detected in post-PRP samples. As the first study to investigate the effects of PRP therapy via transcriptomic analysis, our findings suggest PRP therapy may enhance high-stemness, stimulate MET, and boost macrophage function. These insights contribute to a better understanding of the mechanisms underlying PRP therapy and its potential in treating TE patients.

Distinct adipose progenitor cells emerging with age drive active adipogenesis

Starting at middle age, adults often suffer from visceral adiposity and associated adverse metabolic disorders. Lineage tracing in mice revealed that adipose progenitor cells (APCs) in visceral fat undergo extensive adipogenesis during middle age. Thus, despite the low turnover rate of adipocytes in young adults, adipogenesis is unlocked during middle age. Transplantations quantitatively showed that APCs in middle-aged mice exhibited high adipogenic capacity cell-autonomously. Single-cell RNA sequencing identified a distinct APC population, the committed preadipocyte, age-enriched (CP-A), emerging at this age. CP-As demonstrated elevated proliferation and adipogenesis activity. Pharmacological and genetic manipulations indicated that leukemia inhibitory factor receptor signaling was indispensable for CP-A adipogenesis and visceral fat expansion. These findings uncover a fundamental mechanism of age-dependent adipose remodeling, offering critical insights into age-related metabolic diseases.

The dynamic immune behavior of primary and metastatic ovarian carcinoma

Patients with high-grade serous ovarian carcinoma (HGSC) are usually diagnosed with advanced-stage disease, and the tumors often have immunosuppressive characteristics. Together, these factors are important for disease progression, drug resistance, and mortality. In this study, we used a combination of single-cell sequencing and spatial transcriptomics to identify the molecular mechanisms that lead to immunosuppression in HGSC. Primary tumors consistently showed a more active immune microenvironment than did omental tumors. In addition, we found that untreated primary tumors were mostly populated by dysfunctional CD4 and CD8 T cells in later stages of differentiation; this, in turn, was correlated with expression changes in the interferon α and γ pathways in epithelial cells, showing that cross-communication between the epithelial and immune compartments is important for immune suppression in HGSC. These findings could have implications for the design of clinical trials with immune-modulating drugs.

Tumor-infiltrated double-negative regulatory T cells predict outcome of T cell-based immunotherapy in nasopharyngeal carcinoma

Adoptive cell therapy (ACT) using tumor-infiltrating lymphocytes (TILs) has demonstrated clinical success in solid tumors. We analyze 47 TIL infusion products and 62 pretreatment tumor microenvironments (TMEs) from a randomized phase 2 clinical study of concurrent chemoradiotherapy plus TIL-ACT (NCT02421640). Using single-cell and bulk RNA sequencing along with flow cytometry, we identify 14 CD3+ T cell clusters within 26 TIL infusion products: 11 CD3+CD8+ TILs, 2 CD3+CD4+ TILs, and 1 CD3+CD8-CD4- double-negative (DN) TIL. (DN) TILs, significantly associated with poor TIL-ACT outcomes, exhibit an activated regulatory T cell-like phenotype and include two CD56+ and four CD56- subsets. Among them, CD56-KZF2+ (DN) TILs are predominantly suppressive. (DN) TILs inhibit CD8+ TIL expansion via Fas-FasL, transforming growth factor β (TGF-β), and interleukin (IL)-10 signaling. Distinct CD8+ T subsets differentially impact on TIL-ACT outcomes, while 9 baseline TME gene signatures and 14 intracellular T cell genes hold prognostic value. Our findings identify predictive TIL subsets and biomarkers for TIL-ACT outcomes.

THBS2-producing matrix CAFs promote colorectal cancer progression and link to poor prognosis via the CD47-MAPK axis

Cancer-associated fibroblasts (CAFs) display significant functional and molecular heterogeneity within the tumor microenvironment, playing diverse roles in cancer progression. Employing single-cell RNA sequencing data of colorectal cancer (CRC), we identified a subset of matrix CAFs (mCAFs) as a critical subtype that secretes THBS2, a molecule linked to advanced cancer stages and poor prognosis. Spatial transcriptomics and multiplex immunohistochemistry revealed clear spatial colocalization between THBS2-producing mCAFs and tumor cells. Mechanically, CAF-secreted THBS2 binds to CD47 on tumor cells, triggering the MAPK/ERK5 signaling pathway, which enhances tumor progression. The tumor-promoting role of THBS2 was further validated using fibroblast-specific THBS2 knockout mice, patient-derived organoids, and xenografts. Moreover, the transcription factor CREB3L1 was identified as a regulator of the transformation of normal fibroblasts into THBS2-producing mCAFs. These findings underscore the pivotal role of THBS2 in CRC progression and highlight the therapeutic potential of targeting the THBS2-CD47 axis and CREB3L1 in CRC.

Unravelling NK cell subset dynamics and specific gene signatures post-ibrutinib therapy in chronic lymphocytic leukaemia via single-cell transcriptomics

BACKGROUND

As part of the innate immune system, NK cells contribute to optimizing cancer immunotherapy strategies and are becoming a focal point in cancer research. However, limited research has been conducted to further investigate changes in NK cell subsets and their critical genes following ibrutinib treatment in CLL patients.

METHODS

Peripheral blood samples from patients clinically and pathologically diagnosed with monoclonal B-cell lymphocytosis (MBL), newly diagnosed with CLL (ND-CLL), postibrutinib-treated patients who achieved a complete response (CR) or partial response (PR), and those with Richter's syndrome (RS) were collected. Single-cell transcriptome sequencing was performed, followed by pseudotemporal analysis and functional enrichment to characterize the NK cell subsets. Mendelian randomization analysis and colocalization analysis were employed to identify key genes. Multiple algorithms were used for immune infiltration analysis, and drug sensitivity analysis was conducted to pinpoint potential therapeutic agents.

RESULTS

Three distinct NK cell subsets were identified: CD56bright_NK cells, CD56dim_NK cells, and a highly cytotoxic CLL_NK subset. The core genes of the CLL_NK subset were elucidated through Mendelian randomization and colocalization analyses. A cell subset-specific novel index (CNI) was constructed based on these core genes and was shown to be capable of predicting responses to immunotherapy. Oncopredictive algorithms and molecular docking screenings further identified semaxanib and ulixertinib as potential therapeutic candidates for CLL.

CONCLUSION

The CLL_NK subset plays a crucial role in the development and progression of CLL. The CNI, derived from its key genes, holds promise as a predictor of immune therapeutic responses, highlighting the significance of CLL_NK subset dynamics and their genetic underpinnings in CLL management.

NR2F2 and its contribution to lymph node metastasis in oral squamous cell carcinoma

OBJECTIVES

To investigate the role of cancer stem cells (CSCs) in lymph node metastasis (LNM) of oral squamous cell carcinoma (OSCC), focusing on the expression and biological significance of nuclear receptor subfamily 2 group F member 2 (NR2F2).

METHODS

Single-cell RNA sequencing data from OSCC patients were analyzed using the CytoTRACE algorithm to assess stemness. Gene set scores were calculated with the irGSEA and GSVA R packages. GO and KEGG analyses identified enriched pathways. NR2F2 and CD44 expression in OSCC and lymph nodes (LNs) were validated via immunohistochemistry and immunofluorescence. NR2F2/Nr2f2 overexpression and knockdown cell lines were established, with stemness markers confirmed by Western blot. Functional assays evaluated stemness, proliferation, migration, and invasion capabilities of OSCC cells. In vivo experiments evaluated the ability of NR2F2 to promote tumor growth and metastasis. Bulk RNA sequencing and drug sensitivity analyses explored NR2F2-related mechanisms and drug responses.

RESULTS

CSCs in OSCC were divided into five subgroups, with NR2F2 identified as the key gene in CSC4, the subgroup with the highest stemness, and found to be overexpressed in metastatic LNs. Immunohistochemistry showed NR2F2 overexpression in OSCC, associated with LNM. Immunofluorescence confirmed co-expression of NR2F2 and CD44 in metastatic OSCC and LNs. Overexpression of NR2F2 enhanced stemness, proliferation, and migration of OSCC cells. In vivo experiments showed that NR2F2 promoted the growth and LNM of OSCC. Bulk RNA sequencing revealed that NR2F2 is involved in multiple pathways and plays a role in LNM. Trametinib was identified as a sensitive drug.

CONCLUSION

NR2F2 is associated with the maintenance of tumor stemness and may influence LNM in OSCC by promoting tumor cell proliferation and migration.

Single cell transcriptome profiling of immune tissues from germ-free and specific pathogen-free piglet

The commensal microbiota provides immunomodulatory signals during the development, differentiation and activation of immune cells, and is crucial for maintaining host immune homeostasis. However, the systematic effects of commensal microbiota on host immunity based on large animal model at the single-cell level remain to be resolved. Here, we utilized single-cell RNA sequencing (scRNA-seq) to analyze the transcriptome profiling containing 57,720 cells from three important immune tissues [Peyer's patches (PP), mesenteric lymph node (MLN), and spleen] of germ-free (GF) and specific pathogen-free (SPF) piglet. We presented detailed description of the dataset and preliminarily identified the major cell types including immune and non-immune cells, and further annotated the immune cell subsets. This dataset provides a data mining resource for researchers involved in microbe-host interactions, and enables in-depth analysis of cell map alterations caused by the microbiota colonization during early immune development. As the first single-cell transcriptomics dataset for immune tissue of GF and SPF piglet, this provides a valuable data resource for the study of commensal microbe-host immunity regulation.

Hypoxia-induced Wnt5a-secreting fibroblasts promote colon cancer progression

Wnt5a, a representative Wnt ligand that activates the β-catenin-independent pathway, has been shown to promote tumorigenesis. However, it is unclear where Wnt5a is produced and how it affects colon cancer aggressiveness. In this study, we demonstrate that Wnt5a is expressed in fibroblasts near the luminal side of the tumor, and its depletion suppresses mouse colon cancer formation. To characterize the specific fibroblast subtype, a meta-analysis of human and mouse colon fibroblast single-cell RNA-seq data is performed. The results show that Wnt5a is expressed in hypoxia-induced inflammatory fibroblast (InfFib), accompanied by the activation of HIF2. Moreover, Wnt5a maintains InfFib through the suppression of angiogenesis mediated by soluble VEGF receptor1 (Flt1) secretion from endothelial cells, thereby inducing further hypoxia. InfFib also produces epiregulin, which promotes colon cancer growth. Here, we show that Wnt5a acts on endothelial cells, inducing a hypoxic environment that maintains InfFib, thereby contributing to colon cancer progression through InfFib.

Peripheral nervous system microglia-like cells regulate neuronal soma size throughout evolution

Microglia, essential in the central nervous system (CNS), were historically considered absent from the peripheral nervous system (PNS). Here, we show a PNS-resident macrophage population that shares transcriptomic and epigenetic profiles as well as an ontogenetic trajectory with CNS microglia. This population (termed PNS microglia-like cells) enwraps the neuronal soma inside the satellite glial cell envelope, preferentially associates with larger neurons during PNS development, and is required for neuronal functions by regulating soma enlargement and axon growth. A phylogenetic survey of 24 vertebrates revealed an early origin of PNS microglia-like cells, whose presence is correlated with neuronal soma size (and body size) rather than evolutionary distance. Consistent with their requirement for soma enlargement, PNS microglia-like cells are maintained in vertebrates with large peripheral neuronal soma but absent when neurons evolve to have smaller soma. Our study thus reveals a PNS counterpart of CNS microglia that regulates neuronal soma size during both evolution and ontogeny.

A cohort of highly activated CD99- CD72+ B cells promoting autoimmune progression in juvenile systemic lupus erythematosus

CD72 inhibits the development of systemic lupus erythematosus (SLE) by suppressing TLR7-dependent B cell responses to self-nucleic acids (NAs). The absence of CD72 promotes the progression of lupus disease. Here, we find a highly activated subset of CD99- CD72+ B cells (CD72+ BCs) expressing elevated levels of TLR7 in juvenile SLE, which contributes to autoimmunity. Through multi-omics integrated analysis of single-cell RNA sequencing(scRNA-seq) data and bulk RNA sequencing (RNA-seq) data, we demonstrate that CD72+ BCs possess characteristics of both activated naïve B cells (aN) and age-associated B cells (ABCs). Concurrently, CD72+ BCs exhibit pronounced plasmablast-like features compared to other cellular subpopulations. We propose a plausible conclusion that CD72+ BCs represent a critical transitional cell population involved in the activation and subsequent plasma cell differentiation of naïve B cells and age-related B cells following exposure to self-antigens in SLE. This finding offers novel opportunities for elucidating the genesis of autoantibody-secreting cells involved in the autoimmune response processes in lupus.

Dual states of murine Bmi1-expressing intestinal stem cells drive epithelial development utilizing non-canonical Wnt signaling

Intestinal epithelial development and homeostasis critically rely upon balanced stem cell proliferation, involving slow-cycling/label-retaining and active-cycling/canonical Wnt-dependent intestinal stem cell (ISC) subtypes. ISC regulation during development remains poorly understood but has important implications for establishing key mechanisms governing tissue maintenance. Herein, we identify Bmi1+ cells as functional stem cells present in early murine intestinal development, prior to Lgr5-expressing ISCs. Lineage tracing and single-cell RNA sequencing identify that Bmi1+ ISCs can trace to Lgr5+ ISCs and other differentiated lineages. Initially highly proliferative, Bmi1+ ISCs transition to slow-cycling states as Lgr5+ ISCs emerge. Non-canonical Wnt signaling regulates the proliferative Bmi1+ cell state. These findings highlight the dynamic interplay between stem cell populations and the opposing Wnt pathways that govern proliferation-ultimately having implications for tissue development, homeostasis, regeneration, and tumorigenesis. Understanding these fundamental developmental mechanisms is critical for understanding adult intestinal maintenance.

Targeting the poliovirus receptor to activate T cells and induce myeloid-derived suppressor cells to differentiate to pro-inflammatory macrophages via the IFN-γ-p-STAT1-IRF8 axis in cancer therapy

T cell immunoglobulin and ITIM domain (TIGIT) is one of the most important immune checkpoints expressed on lymphocytes, and poliovirus receptor (PVR, also CD155) serves as the most crucial ligand for TIGIT, harboring an important function in cancer cells and influencing the tumor microenvironment (TME). While it's well-established that TIGIT blockade could reverse immunosuppression, the question of whether direct inhibition of PVR yields comparable results remains to be fully elucidated. This study investigated the role of PVR within the TME on the LLC, CT26 and MC38 tumor models and found that direct blockade of PVR on tumor cells could trigger T cell activation, enhance the production of immunostimulatory cytokine IFN-γ, and drive the differentiation of intratumoral myeloid-derived suppressor cells (MDSCs) into pro-inflammatory macrophages through the IFN-γ-p-STAT1-IRF8 axis. Furthermore, this study found that the anti-PVR nanobody monotherapy reduced tumor volume in the CT26 and MC38 tumor models. Combination of anti-PVR nanobody and anti-PD-1 antibody was effective in the LLC, CT26 and MC38 tumor models and had acceptable toxicity. These findings collectively suggest that PVR exhibits considerable promise as a therapeutic target in the development of immunotherapies aimed at augmenting the anti-tumor immune response.

Single-nucleus RNA sequencing and spatial transcriptomics reveal an immunosuppressive tumor microenvironment related to metastatic dissemination during pancreatic cancer liver metastasis

Background: Pancreatic ductal adenocarcinoma (PDAC) is a highly aggressive malignancy characterized by early liver metastasis and high mortality. The tumor microenvironment plays a pivotal role in tumor progression; however, the immune microenvironment's involvement in PDAC liver metastasis remains poorly understood. Methods: This study investigates cellular heterogeneity in primary tumor (PT) and liver metastasis (LM) tissues of PDAC using single-nucleus RNA sequencing and spatial transcriptomics. Intra-tumor heterogeneity and cell interactions were elucidated through deconvolution, intercellular signalling, pseudotime analysis, and immune infiltration profiling. The spatial distribution of immune cells was assessed by multiplexed immunofluorescence staining, and prognostic models were developed and validated through immunohistochemistry (IHC). Analyzing the regulatory role of CITED4 in the invasion and metastasis of pancreatic cancer cells through transwell assay and scratch wound healing assay. Results: A total of 62,326 cells were sequenced, with metastatic dissemination cells showing significant upregulation of epithelial-mesenchymal transition (EMT)-related genes during liver metastasis. Spatial transcriptomics revealed the enrichment of metastatic dissemination cells and FOXP3-related Treg cells at the tumor front in PT tissues. In comparison to LM tissues, the tumor front in PT tissues fosters an immunosuppressive microenvironment through the accumulation of Treg cells. Interaction analysis identified the SPP1 pathway as a key promoter of this immunosuppressive environment. Furthermore, prognostic models highlighted CITED4 as critical biomarkers in PDAC. Elevated CITED4 expression is correlated with liver metastasis and poor prognosis in patients with PDAC. siRNA-mediated knockdown of CITED4 suppresses the invasion and metastasis of pancreatic cancer cells. Conclusions: In summary, this study revealed that Treg cell alterations, mediated by metastatic dissemination cells within the immune microenvironment, significantly contribute to PDAC liver metastasis, and that CITED4 enhances the metastatic potential of metastatic dissemination cells.

Natural killer cells' functional impairment drives the immune escape of pre-malignant clones in early-stage myelodysplastic syndromes

Dissecting the preneoplastic disease states' biological mechanisms that precede tumorigenesis can lead to interventions that can slow down disease progression and/or mitigate disease-related comorbidities. Myelodysplastic syndromes (MDS) cannot be cured by currently available pharmacological therapies, which fail to eradicate aberrant hematopoietic stem cells (HSCs), most of which are mutated by the time of diagnosis. Here, we sought to elucidate how MDS HSCs evade immune surveillance and expand in patients with clonal cytopenias of undetermined significance (CCUS), the pre-malignant stage of MDS. We used multi-omic single-cell approaches and functional in vitro studies to show that immune escape at disease initiation is mainly mediated by mutant, dysfunctional natural killer (NK) cells with impaired cytotoxic capability against cancer cells. Preclinical in vivo studies demonstrated that injecting NK cells from healthy donors efficiently depleted CCUS mutant cells while allowing normal cells to regenerate hematopoiesis. Our findings suggest that early intervention with adoptive cell therapy can prevent or delay the development of MDS.

Prediction of radiosensitivity in non-small cell lung cancer based on computed tomography and tumor genomics: a multiple real world cohort study

BACKGROUND

The varying degrees of radiotherapy sensitivity of tumors limit the efficacy of tumor radiotherapy. In this research, based on single cell sequence data we used radiomics to help identify and screen feature signatures to distinguish varying radiosensitivity in different regions of the target area of non-small cell lung cancer can provide a new pattern to assess sensitivity of radiotherapy and assist in clinical decision-making.

METHODS

This retrospective study included CT radiology data from 454 patients diagnosed with non-small cell lung cancer in multiple real-world cohorts prior to radiotherapy. The tumor primary target area was delineated on a training set (n = 154) and segmented to obtain a radiogenomic single signature. The radiogenomic signature LCDigital-RT, which can predict radiosensitivity, was developed by combining transcriptome sequencing signature radiosensitivity index and validated on two independent external validation sets (n = 74) and (n = 160). Besides, we also described the single-cell landscape of non-small cell lung cancer with different radiosensitivity, attempting to explain the potential biological mechanism at the single-cell level.

RESULTS

By constructing solely from the single radiomics feature signature, pre LCDigital-RT can effectively identify populations with differences in radiation sensitivity in non-small cell lung cancer, with AUCs of 0.759, 0.728 and 0.745 for the training and two external validation sets, respectively. However, LCDigital-RT has a greater advantage, with a training set AUC of 0.837, which has been well validated in the JXCH cohort (AUC = 0.789) and GDPH cohort (AUC = 0.791). With the help of LCDigital-RT, patients can be divided into radiation sensitive and radiation resistant groups, and there is a significant difference in the characteristics of primary tumor lesions between the two groups. We have also enriched the interpretability of our radiogenomic features in biology at the single-cell level, demonstrating their enormous value in clinical translational research.

CONCLUSIONS

We have developed an LCDigital RT prediction tool that will help predict populations at risk of radiation sensitivity differences. By visualizing the thermal map of the primary tumor area, we can assist in the development of radiotherapy plans, reduce the occurrence of radiation toxicity events, and improve radiotherapy efficacy. At the same time, it provides a reference basis for evaluating radiation sensitivity from imaging, genetics, and other aspects.

Identification of novel metabolism-related biomarkers of Kawasaki disease by integrating single-cell RNA sequencing analysis and machine learning algorithms

Background

The bile acid metabolism (BAM) and fatty acid metabolism (FAM) have been implicated in Kawasaki disease (KD), but their precise mechanisms remain unclear. Identifying signature cells and genes related to BAM and FAM could offer a deeper understanding of their role in the pathogenesis of KD.

Method

We analyzed the public single-cell RNA sequencing (scRNA-seq) dataset GSE1687323 to characterize the immune cell-type landscape in KD. Gene sets related to BAM and FAM were collected from the Gene Set Enrichment Analysis (GSEA) database and previous literature. We analyzed the cellular heterogeneity of BAM and FAM at the single-cell level using R packages. Through differential expressed genes (DEG) analysis, high-dimensional Weighted Correlation Network Analysis (hdWGCNA) and machine learning algorithms, we identified signature genes associated with both BAM and FAM. The cellular expression patterns of signature genes were further validated using our own scRNA-seq dataset. Finally, quantitative real-time PCR (qRT-PCR) was performed to validate the expression levels of signature genes in KD, and Receiver Operating Characteristic (ROC) curve analysis was conducted to evaluate their diagnostic potential.

Results

Enhanced BAM and FAM were detected in monocytes and natural killer (NK) cells from KD in the public scRNA-seq dataset. Our scRNA-seq data confirmed the signature genes identified by machine learning algorithms: Vimentin (VIM) and chloride intracellular channel 1 (CLIC1) were upregulated in monocytes, while integrin subunit beta 2 (ITGB2) was elevated in NK cells of KD. qRT-PCR results also validated the bioinformatic analysis. Moreover, these genes demonstrated significant diagnostic potential. In the training dataset (GSE68004), the area under the curve (AUC) values and 95% CI were as follows: VIM: 0.914 (0.863-0.966), ITGB2: 0.958 (0.925-0.991), and CLIC1: 0.985 (0.969-1). The validation dataset (GSE73461) yielded similarly robust results, with AUC values and 95% CI: VIM: 0.872 (0.811-0.934), ITGB2: 0.861 (0.795-0.928), and CLIC1: 0.893 (0.837-0.948).

Conclusion

This study successfully identified and validated VIM and CLIC1 in monocytes, as well as ITGB2 in NK cells, as novel metabolism-related genes in KD. These findings suggest that BAM and FAM may play crucial roles in KD pathogenesis. Furthermore, these signature genes hold promising potential as diagnostic biomarkers for KD.

Tff2 marks gastric corpus progenitors that give rise to pyloric metaplasia/SPEM following injury

In Brief

Tu et al. show that Tff2 + corpus isthmus cells are TA progenitors, and they, not chief cells, are the primary source of SPEM following injury. Upon Kras mutation, these progenitors directly progress to dysplasia, bypassing metaplasia, highlighting them as a potential origin of gastric cancer.

Highlights

Tff2 + corpus cells are TA progenitors that give rise to secretory cells. Tff2 + progenitors, not chief cells, are the primary source of SPEM after injury. Kras-mutant Tff2 + progenitors progress directly to dysplasia, bypassing metaplasia. Multi-omics analysis reveals distinct trajectories for SPEM and gastric cancer.

Abstract Figure

Pyloric metaplasia, also known as spasmolytic polypeptide-expressing metaplasia (SPEM), arises in the corpus in response to oxyntic atrophy, but its origin and role in gastric cancer remain poorly understood. Using Tff2-CreERT knockin mice, we identified highly proliferative Tff2 + progenitors in the corpus isthmus that give rise to multiple secretory lineages, including chief cells. While lacking long-term self-renewal ability, Tff2 + corpus progenitors rapidly expand to form short-term SPEM following acute injury or loss of chief cells. Genetic ablation of Tff2 + progenitors abrogated SPEM formation, while genetic ablation of GIF + chief cells enhanced SPEM formation from Tff2 + progenitors. In response to H. pylori infection, Tff2 + progenitors progressed first to metaplasia and then later to dysplasia. Interestingly, induction of Kras G12D mutations in Tff2 + progenitors facilitated direct progression to dysplasia in part through the acquisition of stem cell-like properties. In contrast, Kras-mutated SPEM and chief cells were not able to progress to dysplasia. Tff2 mRNA was downregulated in isthmus cells during progression to dysplasia. Single-cell RNA sequencing and spatial transcriptomics of human tissues revealed distinct differentiation trajectories for SPEM and gastric cancer. These findings challenge the conventional interpretation of the stepwise progression through metaplasia and instead identify Tff2 + progenitor cells as potential cells of origin for SPEM and possibly for gastric cancer.

Single-cell RNA sequencing reveals the intra-tumoral heterogeneity and immune microenvironment of small cell carcinoma of the ovary, hypercalcemic type

PURPOSE

Small cell carcinoma of the ovary, hypercalcemic type (SCCOHT) is a rare and lethal cancer lacking effective treatment. Its genomic mutations and tumor microenvironment need further exploration.

METHODS

We performed whole-exome sequencing or gene panel test to explore the SMARCA4 mutation spectrum in SCCOHT (15 samples). Single-cell RNA sequencing was conducted on one primary lesion with matched normal ovarian tissue and one recurrent lesion to investigate the intra-tumoral heterogeneity and immune microenvironment. Multiplex immunofluorescence staining validated T cell infiltration and PD-1 expression.

RESULTS

13/15 (86.7%) patients harbored SMARCA4 mutations. The loss of heterozygosity (LOH) occurred in 10/15 (66.7%) patients. Cancer cells and immune cells were observed in SCCOHT tumors. Cancer cells were further divided into seven subtypes and one from recurrent lesion exhibited the highest stemness accompanied by high expression of genes related to cell mitosis (AURKB, CHEK2, CCNB1, WEE1), DNA repair (BRCA1, RAD51) and epigenetic (EZH2, DNMT1). Immune cells mainly included macrophages and T cells. Lipid-associated tumor-associated macrophages (TAMs) was mainly in primary lesion while inflammatory cytokine-enriched TAMs in recurrent lesion. CD4+/ CD8+ T cell infiltration was observed in SCCOHT tumor and a certain proportion of T cells expressed PD-1.

CONCLUSIONS

SCCOHT exhibits universal SMARCA4 LOH and significant intra-tumoral heterogeneity, suggesting potential therapeutic targets, including CHEK2, CCNB1, and WEE1. Exhausted T cells and distinct TAM subsets infiltrate tumors. Targeting macrophage polarization or cytokine signaling may also be promising. These findings provide insights for developing novel therapies to improve outcomes in SCCOHT.

CLINICAL TRIAL NUMBER

Not applicable.

Combination of anlotinib with immunotherapy enhanced both anti-angiogenesis and immune response in high-grade serous ovarian cancer

Background

High-grade serous ovarian cancer (HGSOC) poses significant treatment challenges due to frequent recurrence and resistance to conventional therapies. Combination of anlotinib with immunotherapy have showed promise in various cancers, but its impact on HGSOC remains to be fully elucidated.

Methods

A retrospective analysis was performed on 36 HGSOC patients treated with anlotinib-based therapies, including both monotherapy and combination treatment with anti-PD-L1/anti-PD-1 antibody (aPD-L1/aPD-1). Peripheral blood mononuclear cell-derived patient-derived xenograft (PBMC-PDX) model was established from drug-resistant recurrent HGSOC patient-derived tumor cells, and single-cell RNA sequencing (scRNA-seq) was conducted to dissect the TME following treatment with anlotinib, anlotinib + aPD-L1 and anlotinib + aPD-1.

Results

Clinical analysis revealed a disease control rate (DCR) of 71.43% for anlotinib monotherapy, which improved to 100% when combined with aPD-L1/aPD-1. In PBMC-PDX models, treatment evaluation showed that anlotinib decreased tumor volume, an effect further enhanced by its combination with aPD-L1. scRNA-seq analysis demonstrated that anlotinib reduced the proportions of myofibroblastic cancer-associated fibroblasts and ESM1+ endothelial cells, resulting in decreased angiogenesis. The combination of anlotinib and aPD-L1 further amplified these effects, promoting CD8+ T cell infiltration and reversing T cell exhaustion, whereas anlotinib + aPD-1 showed limited efficacy in this regard. Additionally, anlotinib + immunotherapy induced a shift toward M1 polarization of myeloid cells, enhanced anti-tumor activity, and inhibited immune escape. Cell-cell communication analysis revealed reduced APP-CD74 signaling and increased CD99-CD99 signaling, which might contribute to immune activation.

Conclusion

The combination of anlotinib and aPD-L1 effectively modulates the HGSOC tumor microenvironment by inhibiting angiogenesis, enhancing immune infiltration, and reversing T cell exhaustion.

HMOX1-LDHB interaction promotes ferroptosis by inducing mitochondrial dysfunction in foamy macrophages during advanced atherosclerosis

Advanced atherosclerosis is the pathological basis for acute cardiovascular events, with significant residual risk of recurrent clinical events despite contemporary treatment. The death of foamy macrophages is a main contributor to plaque progression, but the underlying mechanisms remain unclear. Bulk and single-cell RNA sequencing demonstrated that massive iron accumulation in advanced atherosclerosis promoted foamy macrophage ferroptosis, particularly in low expression of triggering receptor expressed on myeloid cells 2 (TREM2low) foamy macrophages. This cluster exhibits metabolic characteristics with low oxidative phosphorylation (OXPHOS), increasing ferroptosis sensitivity. Mechanically, upregulated heme oxygenase 1 (HMOX1)-lactate dehydrogenase B (LDHB) interaction enables Lon peptidase 1 (LONP1) to degrade mitochondrial transcription factor A (TFAM), leading to mitochondrial dysfunction and ferroptosis. Administration of the mitochondria-targeted reactive oxygen species (ROS) scavenger MitoTEMPO (mitochondrial-targeted TEMPO) or LONP1 inhibitor bortezomib restored mitochondrial homeostasis in foamy macrophages and alleviated atherosclerosis. Collectively, our study elucidates the cellular and molecular mechanism of foamy macrophage ferroptosis, offering potential therapeutic strategies for advanced atherosclerosis.

Multiomics Analysis Reveals Neuroblastoma Molecular Signature Predicting Risk Stratification and Tumor Microenvironment Differences

Neuroblastoma (NB) remains associated with high mortality and low initial response rate, especially for high-risk patients, thus warranting exploration of molecular markers for precision risk classifiers. Through integrating multiomics profiling, we identified a range of hub genes involved in cell cycle and associated with dismal prognosis and malignant cells. Single-cell transcriptome sequencing revealed that a subset of malignant cells, subcluster 1, characterized by high proliferation and dedifferentiation, was strongly correlated with the hub gene signature and orchestrated an immunosuppressive tumor microenvironment (TME). Furthermore, we constructed a robust malignant subcluster 1 related signature (MSRS), which was an independent prognostic factor and superior to other clinical characteristics and published signatures. Besides, TME differences conferred remarkably distinct therapeutic responses between high and low MSRS groups. Notably, polo-like kinase-1 (PLK1) was one of the most crucial contributors to MSRS and remarkably correlated with malignant subcluster 1, and PLK1 inhibition was effective for NB treatment as demonstrated by in silico analysis and in vitro experiments. Overall, our study constructs a novel molecular model to further guide the clinical classification and individualized treatment of NB.

Zn‐DHM Nanozymes Enhance Muscle Regeneration Through ROS Scavenging and Macrophage Polarization in Volumetric Muscle Loss Revealed by Single‐Cell Profiling

Volumetric muscle loss (VML) is a severe condition in which the loss of skeletal muscle surpasses the body's intrinsic repair capabilities, leading to irreversible functional deficits and potential disability, with persistent inflammation and impaired myogenic differentiation. To address these challenges, a novel zinc‐dihydromyricetin (Zn‐DHM) nanozyme with superoxide dismutase (SOD)‐like activity is developed, designed to neutralize excessive reactive oxygen species (ROS) and restore oxidative balance. Zn‐DHM mitigates oxidative stress and promotes polarization of macrophages from the proinflammatory M1 phenotype to the anti‐inflammatory M2 phenotype, thereby reducing chronic inflammation and creating a conducive environment for muscle repair. Further, Zn‐DHM significantly enhances the myogenic differentiation of C2C12 cells, accelerating wound healing processes. These studies confirm the biosafety and low toxicity of Zn‐DHM. As per a murine tibialis anterior VML model, Zn‐DHM effectively suppresses inflammation and markedly improves skeletal muscle repair outcomes. Single‐cell RNA sequencing reveals that Zn‐DHM treatment increases the expression of M2 macrophage markers and enhances the proliferation and differentiation capacity of muscle stem cells (MuSCs). In addition, intercellular communication analysis reveals interactions between MuSCs and macrophages in the Zn‐DHM treatment group, suggesting that these interactions may drive tissue regeneration through the activation of the GAS and Notch signaling pathways.

Amino Acid Metabolism Subtypes in Neuroblastoma Identifying Distinct Prognosis and Therapeutic Vulnerabilities

Although amino acid (AA) metabolism is linked to tumor progression and could serve as an attractive intervention target, its association with neuroblastoma (NB) is unknown. Based on AA metabolism-related genes, we established three NB subtypes associated with distinct prognoses and specific functions, with C1 and C2 having better outcomes. The C1 displayed enhanced metabolic activity and recruited metabolism-associated cells. The C2 exhibited an activated immune microenvironment and was more vulnerable to immunotherapy. The C3, characterized by cell cycle peculiarity, possessed a dismal prognosis and high frequency of gene mutations and was susceptible to chemotherapy. Furthermore, single-cell RNA sequencing analysis revealed that the C3-associated Scissor+ cell subpopulation was characterized by notorious functional states and orchestrated an immunosuppressive microenvironment. Additionally, we identified that ALK and BIRC5 contributed to the shorter lifespan of C3 and their corresponding inhibitors were potential interventions. In conclusion, we identified three distinct subtypes of NB, which help us foster individualized therapeutic strategies to improve the prognosis of NB.

Fibroblast atlas: Shared and specific cell types across tissues

Understanding the heterogeneity of fibroblasts depends on decoding the complexity of cell subtypes, their origin, distribution, and interactions with other cells. Here, we integrated 249,156 fibroblasts from 73 studies across 10 tissues to present a single-cell atlas of fibroblasts. We provided a high-resolution classification of 18 fibroblast subtypes. In particular, we revealed a previously undescribed cell population, TSPAN8+ chromatin remodeling fibroblasts, characterized by high expression of genes with functions related to histone modification and chromatin remodeling. Moreover, TSPAN8+ chromatin remodeling fibroblasts were detectable in spatial transcriptome data and multiplexed immunofluorescence assays. Compared with other fibroblast subtypes, TSPAN8+ chromatin remodeling fibroblasts exhibited higher scores in cell differentiation and resident fibroblast, mainly interacting with endothelial cells and T cells through ligand VEGFA and receptor F2R, and their presence was associated with poor prognosis. Our analyses comprehensively defined the shared and specific characteristics of fibroblast subtypes across tissues and provided a user-friendly data portal, Fibroblast Atlas.

Tracing the Shared Foundations of Gene Expression and Chromatin Structure

The three-dimensional organization of chromatin into topologically associating domains (TADs) may impact gene regulation by bringing distant genes into contact. However, many questions about TADs' function and their influence on transcription remain unresolved due to technical limitations in defining TAD boundaries and measuring the direct effect that TADs have on gene expression. Here, we develop consensus TAD maps for human and mouse with a novel "bag-of-genes" approach for defining the gene composition within TADs. This approach enables new functional interpretations of TADs by providing a way to capture species-level differences in chromatin organization. We also leverage a generative AI foundation model computed from 33 million transcriptomes to define contextual similarity, an embedding-based metric that is more powerful than co-expression at representing functional gene relationships. Our analytical framework directly leads to testable hypotheses about chromatin organization across cellular states. We find that TADs play an active role in facilitating gene co-regulation, possibly through a mechanism involving transcriptional condensates. We also discover that the TAD-linked enhancement of transcriptional context is strongest in early developmental stages and systematically declines with aging. Investigation of cancer cells show distinct patterns of TAD usage that shift with chemotherapy treatment, suggesting specific roles for TAD-mediated regulation in cellular development and plasticity. Finally, we develop "TAD signatures" to improve statistical analysis of single-cell transcriptomic data sets in predicting cancer cell-line drug response. These findings reshape our understanding of cellular plasticity in development and disease, indicating that chromatin organization acts through probabilistic mechanisms rather than deterministic rules.

Software availability

https://singhlab.net/tadmap.

Single-Cell Multiomics Reveals TCR Clonotype-Specific Phenotype and Stemness Heterogeneity of T-ALL Cells

T-cell acute lymphoblastic leukaemia (T-ALL) is a heterogeneous malignant disease with high relapse and mortality rates. To characterise the multiomics features of T-ALL, we conducted integrative analyses using single-cell RNA, TCR and chromatin accessibility sequencing on pre- and post-treatment peripheral blood and bone marrow samples of the same patients. We found that there is transcriptional rewiring of gene regulatory networks in T-ALL cells. Some transcription factors, such as TCF3 and KLF3, showed differences in activity and expression levels between T-ALL and normal T cells and were associated with the prognosis of T-ALL patients. Furthermore, we identified multiple malignant TCR clonotypes among the T-ALL cells, where the clonotypes consisted of distinct combinations of the same TCR α and β chain per patient. The T-ALL cells displayed clonotype-specific immature thymocyte cellular characteristics and response to chemotherapy. Remarkably, T-ALL cells with an orphan TCRβ chain displayed the strongest stemness and resistance to chemotherapy. Our study provided transcriptome and epigenome characterisation of T-ALL cells categorised by TCR clonotypes, which may be helpful for the development of novel predictive markers to evaluate treatment effectiveness for T-ALL.

Evolutionary fingerprints of epithelial-to-mesenchymal transition

Mesenchymal plasticity has been extensively described in advanced epithelial cancers; however, its functional role in malignant progression is controversial1-5. The function of epithelial-to-mesenchymal transition (EMT) and cell plasticity in tumour heterogeneity and clonal evolution is poorly understood. Here we clarify the contribution of EMT to malignant progression in pancreatic cancer. We used somatic mosaic genome engineering technologies to trace and ablate malignant mesenchymal lineages along the EMT continuum. The experimental evidence clarifies the essential contribution of mesenchymal lineages to pancreatic cancer evolution. Spatial genomic analysis, single-cell transcriptomic and epigenomic profiling of EMT clarifies its contribution to the emergence of genomic instability, including events of chromothripsis. Genetic ablation of mesenchymal lineages robustly abolished these mutational processes and evolutionary patterns, as confirmed by cross-species analysis of pancreatic and other human solid tumours. Mechanistically, we identified that malignant cells with mesenchymal features display increased chromatin accessibility, particularly in the pericentromeric and centromeric regions, in turn resulting in delayed mitosis and catastrophic cell division. Thus, EMT favours the emergence of genomic-unstable, highly fit tumour cells, which strongly supports the concept of cell-state-restricted patterns of evolution, whereby cancer cell speciation is propagated to progeny within restricted functional compartments. Restraining the evolutionary routes through ablation of clones capable of mesenchymal plasticity, and extinction of the derived lineages, halts the malignant potential of one of the most aggressive forms of human cancer.

Single-Nucleus RNA Sequencing Reveals Enduring Signatures of Acute Stress and Chronic Exercise in Striatal Microglia

Acute stress has enduring effects on the brain and motivated behavior across species. For example, acute stress produces persisting decreases in voluntary physical activity as well as molecular changes in the striatum, a brain region that regulates voluntary physical activity and other motivated behaviors. Microglia, the primary immune cells of the central nervous system, are positioned at the interface between neural responses to stress and neural coordination of voluntary activity in that they respond to stress, sense molecular changes in the striatum, and modulate neuronal activity. However, the role of striatal microglia in stress-induced long-term suppression of voluntary activity is unknown. Here, we employ single-nucleus RNA sequencing to investigate how stress and exercise impact the biology of microglia in the striatum. We find that striatal microglia display altered activation profiles 6 weeks after an acute stressor. Furthermore, we show that access to a running wheel is associated with an additional and distinct microglial activation profile characterized by upregulation of genes related to complement components and phagocytosis pathways. Finally, we find that distinct gene sets show expression changes associated with general access to a running wheel versus variation in running levels. Taken together, our results deepen our understanding of the diverse molecular states that striatal microglia assume in response to stress and exercise and suggest that microglia exhibit a broader range of functional states than previously thought.