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Single-cell RNA sequencing reveals hemocyte heterogeneity, differentiation trajectories, and viral tropism in shrimp (Macrobrachium rosenbergii) infected with decapodiridovirus litopenaeus1.
Decapodiridovirus litopenaeus1 (DIV1) is a highly pathogenic virus threatening crustacean aquaculture. Hemocytes, the primary immune cells in shrimp, play crucial roles in host defense, yet their transcriptional heterogeneity and differentiation dynamics under viral infection remain poorly understood. Here, we characterize hemocyte subpopulations in Macrobrachium rosenbergii before and after DIV1 infection at single-cell resolution. We identified 12 distinct hemocyte clusters with unique molecular signatures. DIV1 infection induced significant shifts in hemocyte composition, with clusters 0, 5, 6, and 8 expanding, while clusters 9 and 10 exhibited resistance. Clusters 0, 5, and 8 were highly susceptible, showing elevated viral gene expression. Pseudo-time analysis revealed that DIV1 accelerates hemocyte differentiation, driving prohemocytes and semi-granulocytes toward terminally differentiated granulocytes and hyalinocytes, particularly the immune-active HC4 subpopulation. Functional enrichment analysis showed that susceptible hemocytes were associated with viral processes, oxidative stress, and phagocytosis, while resistant clusters exhibited distinct immune signatures. Furthermore, knockdown experiments confirmed the antiviral roles of PPO2, RAB11B, LAMP1, and Dorsal, as their silencing led to increased viral loads, higher major capsid protein (MCP) levels, and reduced shrimp survival. Taken together, our study provides the first single-cell resolution atlas of shrimp hemocytes under DIV1 infection, revealing their transcriptional heterogeneity, differentiation trajectories, and immune responses. These findings offer novel insights into shrimp antiviral immunity and lay the foundation for disease-resistant breeding and immunostimulatory strategies in aquaculture.IMPORTANCEDIV1 is a highly pathogenic virus threatening crustacean aquaculture, causing severe economic losses. Hemocytes in shrimp play crucial roles in antiviral defense, yet their diversity, differentiation, and responses to viral infection remain poorly understood. In this study, we employed single-cell RNA sequencing to comprehensively characterize hemocyte subpopulations in Macrobrachium rosenbergii before and after DIV1 infection. We identified 12 transcriptionally distinct hemocyte clusters and revealed significant changes in hemocyte composition following infection. Notably, we discovered that specific clusters (0, 5, and 8) were highly susceptible to DIV1, while others (9 and 10) exhibited resistance. Additionally, we reconstructed hemocyte differentiation trajectories and found that DIV1 infection drives hematopoiesis, accelerating the transition of progenitor cells into terminally differentiated immune-active hemocytes. Functional analysis highlighted key antiviral effectors, including PPO2, RAB11B, LAMP1, and Dorsal. These findings provide novel insights into shrimp antiviral immunity and viral pathogenesis, offering potential targets for disease-resistant breeding and immunostimulatory interventions.
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Integrative analyses identify CD73 as a prognostic biomarker and immunotherapeutic target in intrahepatic cholangiocarcinoma.
BACKGROUND: CD73 promotes progression in several malignancies and is considered as a novel immune checkpoint. However, the function of CD73 in intrahepatic cholangiocarcinoma (ICC) remains uncertain. In this study, we aim to investigate the role of CD73 in ICC. METHODS: Multi-omics data of 262 ICC patients from the FU-iCCA cohort were analyzed. Two single-cell datasets were downloaded to examine the expression of CD73 at baseline and in response to immunotherapy. Functional experiments were performed to explore the biological functions of CD73 in ICC. The expression of CD73 and HHLA2 and infiltrations of CD8 + , Foxp3 + , CD68 + , and CD163 + immune cells were evaluated by immunohistochemistry in 259 resected ICC samples from Zhongshan Hospital. The prognostic value of CD73 was assessed by Cox regression analysis. RESULTS: CD73 correlated with poor prognosis in two ICC cohorts. Single-cell atlas of ICC indicated high expression of CD73 on malignant cells. TP53 and KRAS gene mutations were more frequent in patients with high CD73 expression. CD73 promoted ICC proliferation, migration, invasion, and epithelial-mesenchymal transition. High CD73 expression was associated with a higher ratio of Foxp3 + /CD8 + tumor-infiltrating lymphocytes (TILs) and CD163 + /CD68 + tumor-associated macrophages (TAMs). A positive correlation between CD73 and CD44 was observed, and patients with high CD73 expression showed elevated expression of HHLA2. CD73 expression in malignant cells was significantly upregulated in response to immunotherapy. CONCLUSIONS: High expression of CD73 is associated with poor prognosis and a suppressive tumor immune microenvironment in ICC. CD73 could potentially be a novel biomarker for prognosis and immunotherapy in ICC.
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CXCR4 expression is associated with proneural-to-mesenchymal transition in glioblastoma.
Glioblastoma (GBM) is the most common primary intracranial malignant tumor and consists of three molecular subtypes: proneural (PN), mesenchymal (MES) and classical (CL). Transition between PN to MES subtypes (PMT) is the glioma analog of the epithelial-mesenchymal transition (EMT) in carcinomas and is associated with resistance to therapy. CXCR4 signaling increases the expression of MES genes in glioma cell lines and promotes EMT in other cancers. RNA sequencing (RNAseq) data of PN GBMs in The Cancer Genome Atlas (TCGA) and secondary high-grade gliomas (HGGs) from an internal cohort were examined for correlation between CXCR4 expression and survival as well as expression of MES markers. Publicly available single-cell RNA sequencing (scRNAseq) data was analyzed for cell type specific CXCR4 expression. These results were validated in a genetic mouse model of PN GBM. Higher CXCR4 expression was associated with significantly reduced survival and increased expression of MES markers in TCGA and internal cohorts. CXCR4 was expressed in immune and tumor cells based on scRNAseq analysis. Higher CXCR4 expression within tumor cells on scRNAseq was associated with increased MES phenotype, suggesting a cell-autonomous effect. In a genetically engineered mouse model, tumors induced with CXCR4 exhibited a mesenchymal phenotype and shortened survival. These results suggest that CXCR4 signaling promotes PMT and shortens survival in GBM and highlights its inhibition as a potential therapeutic strategy.
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WT1-AS acts as a tumor suppressor in cervical cancer via OSR2-mediated transcriptional activation.
BACKGROUND: Cervical cancer (CESC) remains a major global health burden, and its molecular mechanisms are not fully understood. Long non-coding RNAs (lncRNAs) have emerged as critical regulators in tumor biology. Among them, Wilms tumor 1 antisense RNA (WT1-AS) has been implicated in several cancers, but its role in CESC is largely unknown. Therefore, this study aimed to investigate the expression pattern, prognostic significance, biological function, and upstream transcriptional regulation of WT1-AS in CESC. METHODS: We performed a comprehensive analysis integrating The Cancer Genome Atlas (TCGA) pan-cancer and CESC datasets to examine the expression profile and prognostic relevance of WT1-AS. Gene Ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment, and single-cell RNA sequencing analyses were conducted to explore its biological functions. Functional assays, including Western blotting, flow cytometry, and xenograft mouse models, were performed to validate the effects of WT1-AS on apoptosis and tumor growth. Upstream transcriptional regulation was investigated using transcription factor prediction, co-expression analysis, and luciferase reporter assays. RESULTS: WT1-AS was significantly dysregulated across multiple cancers and correlated with poor prognosis in several tumor types. In CESC, WT1-AS was primarily expressed in malignant epithelial cells and fibroblasts and was functionally enriched in apoptosis- and extracellular matrix-related pathways. Overexpression of WT1-AS promoted apoptosis, as evidenced by increased cleaved-caspase3 and cleaved-PARP expression, and suppressed tumor growth in vivo. Mechanistically, odd-skipped related transcription factor 2 (OSR2) was identified as a direct transcriptional regulator of WT1-AS. Overexpression of OSR2 enhanced apoptosis, and co-overexpression with WT1-AS further amplified pro-apoptotic effects. CONCLUSIONS: Our findings reveal that WT1-AS functions as a tumor suppressor in CESC by promoting apoptosis and identify OSR2 as a novel upstream regulator. The WT1-AS/OSR2 axis may have biological and potential prognostic relevance in CESC, although its clinical applicability requires further validation.
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SCALPEL: A pipeline for processing large-scale spatial transcriptomics data.
Spatial transcriptomics enables the precise mapping of gene expression patterns within tissue architecture, offering unprecedented insights into cellular interactions, tissue heterogeneity, and disease pathology that are unattainable with traditional transcriptomic approaches. We present a tool for processing spatial transcriptomics data, SCALPEL (Spatial Cell Analysis, Labeling, Processing, and Expression Linking). SCALPEL is specifically designed to support the analysis of large, atlas-level datasets. Our new workflow features advanced 3D segmentation optimized for dense and heterogeneous tissues, refined filtering criteria, and transcriptome-based doublet detection to remove low-quality or artifactual cells. Cell type label transfer from existing taxonomies is further improved through updated filtering thresholds. Spatial domain detection is incorporated to capture local transcriptomic organization, and tissue sections are registered to the Allen Mouse Brain Common Coordinate Framework version 3 (CCFv3) for precise anatomical alignment. Genome-wide expression imputation from single-cell RNA-sequencing (scRNAseq) further enriches the dataset. Crucially, we benchmark the performance of this updated pipeline against a previously published version of our whole-mouse-brain (WMB) dataset (Yao et al., 2023b), demonstrating substantial improvements in cell number, expression profile clarity, and spatial registration. These advances provide a robust foundation for downstream spatial analyses and set a new standard for large-scale spatial transcriptomics studies.
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Thyroid hormone deprivation creates an immunological signature in the mouse liver, involving Kupffer cell presentation as the mouse ages.
PURPOSE: Aging is associated with an increased prevalence of chronic liver diseases suggesting impaired immune and metabolic function. In addition, thyroid hormone (TH) impacts liver physiology and TH deprivation or excess negatively affect organ maintenance. However, whether age-dependent consequences of TH alterations are reflected in a liver-specific adaptation is unknown so far. The present study aimed to characterize the impact of TH deprivation or excess on the liver transcriptome during aging. METHODS: Five- and 21-month-old male C57BL/6 mice were exposed either to chronic TH deprivation or to chronic TH excess and compared to control treatment by microarray-based liver transcriptome analysis. RESULTS: Significant roles of both TH state and age became obvious: Bioinformatic analysis of the liver transcriptome data revealed an age-dependent immune signature by chronic TH deprivation, an age-dependent immune and metabolic signature independent of exogenous TH modulation, as well as an age-dependent metabolic signature by chronic TH excess. Published data of single cell transcriptomic atlas characterizing aging tissues in the mouse were compared with our data and revealed Kupffer cell presentation in the immunological signature by TH deprivation during aging. Literature data for four prominent differentially expressed genes, namely C1qb, C3ar1, Ctss, and Msr1, revealed that the complement system, extracellular matrix remodelling, as well as the proinflammatory phenotype of Kupffer cells are altered by TH deprivation during aging. CONCLUSION: In conclusion, our study illuminates the interplay between TH deprivation, aging, and liver transcriptome signatures, highlighting potential implications for immune function and tissue maintenance, particularly through the modulation of Kupffer cell presentation.
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Spatiotemporal Evolution of Malignant Hepatocyte Clones Unveils Immune Evasion Features and Therapeutic Vulnerabilities in Hepatocellular Carcinoma.
Hepatocellular carcinoma (HCC), a highly lethal disease often developing in the context of chronic liver disease, is marked by high relapse rates and low 5-year survival. To investigate the multicellular ecosystem and molecular features of hepatocarcinogenesis and progression, a comprehensive analysis integrating single-cell and spatial transcriptomics was conducted. Significant alterations were observed in various cell types, notably an increase in liver parenchymal and endothelial cells, which play critical roles in tissue repair and angiogenesis. Scissor+ cells, predominantly hepatocytes, were identified as potentially evolving into malignant cells with poor prognosis and enhanced immune evasion capabilities. Key genes associated with Scissor+ cells exhibited potential as cancer prognostic markers. Additionally, the disruption of cellular communication networks during malignant progression revealed the evolution of hepatocytes into cancerous phenotypes. The enhanced signaling pathways, such as MDK-SDC4 and COL4A-SDC, were identified as pivotal in driving the malignant transformation of hepatocytes. This transformative process, wherein Scissor+ cells acquire malignant features, highlights novel mechanisms of cancer progression. These findings provide deeper insights into hepatocarcinogenesis and offer potential avenues for targeted and personalized therapeutic strategies.
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Construction and experimental validation of a B cell senescence-related gene signature to evaluate prognosis and immunotherapeutic sensitivity in bladder cancer.
Senescent B cells exhibit reduced antibody production and enhanced proinflammatory cytokine and chemokine secretion, exerting non-negligible functions in antitumor immunity. This study aims to clarify the prognosis value of B cell senescence-related genes in bladder cancer (BLCA). Twelve B cell senescence-related genes were identified based on previous studies and the single-cell RNA sequencing of a BLCA sample from Gene Expression Omnibus (GEO). The Cancer Genome Atlas BLCA cohort was used as the training dataset. Three cohorts from GEO, 35 clinical samples from the local hospital, and in vitro cell experiments were used for validation. The unsupervised clustering based on the 12 genes was associated with the prognosis and the tumor immunity. Through least absolute shrinkage and selection operator regression and random forest algorithm, G protein subunit gamma 11 (GNG11) and inhibitor of DNA binding 1 (ID1) of the 12 genes were determined as significant prognosis predictors and then included in the multivariate Cox regression model. The model was a reliable and robust prognosis biomarker across multiple large-scale cohorts (pooled HR = 1.76, 95% CI = 1.41-2.20). The tight association between the model and BLCA malignant degree was demonstrated in the local cohort (P < 0.01). The model could also predict the immunotherapeutic sensitivity, which was confirmed by the tumor immune dysfunction and exclusion algorithm (P < 0.0001) and IMvigor210 cohort (P < 0.0001). At last, in vitro cell experiments in IM-9 and GM12878 B cells indicated that GNG11 and ID1 were involved in the cellular aging process. Collectively, a B cell senescence-related gene signature was constructed to evaluate the prognosis and immunotherapeutic response in BLCA, providing novel insights into the biological mechanisms.
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Cardio-oncology-relevant programmes in the cervical cancer tumour microenvironment: an exploratory multi-omics and endothelial-cell study.
BACKGROUND: Bevacizumab and immune-checkpoint inhibitors (ICIs) improve outcomes in advanced cervical cancer but may cause cardiovascular toxicity (CVT). Public cervical-cancer transcriptomic datasets do not contain cardiac tissue or adjudicated CVT outcomes; consequently, tumour-microenvironment (TME) expression cannot by itself establish a cardiac susceptibility mechanism. We reanalysed the available data to ask the narrower question of whether cervical tissues contain angiogenic, endothelial, inflammatory, T-cell-exhaustion, and TGF-β/fibrotic programmes that are biologically relevant to cardio-oncology. METHODS: All nine single-cell RNA-sequencing specimens in GSE208653 were analysed: two HPV-negative healthy cervix, two HPV-positive histologically normal cervix, two high-grade squamous intraepithelial lesions, two squamous-cell carcinomas, and one adenocarcinoma. After prespecified quality control, 74,457 cells were integrated with Harmony and annotated into broad lineages. Prespecified module scores and four ligand-receptor expression-product scores were aggregated by biological specimen; malignant versus non-malignant differences were evaluated with exact specimen-label permutation tests and Benjamini-Hochberg correction. Four GSE208654 Visium count matrices were analysed descriptively at spot level. Coexpression among the five programmes was assessed in 304 TCGA-CESC primary tumours. qRT-PCR summary data from HUVEC (ATCC PCS-100-010) and primary human aortic endothelial cells (HAEC; ATCC PCS-100-011) were reinterpreted as endothelial pharmacology, not cardiac validation. RESULTS: The scRNA-seq atlas contained 32 clusters spanning epithelial, immune, endothelial, and stromal lineages. None of the five specimen-level programmes differed significantly between malignant and non-malignant specimens after multiple-testing correction (all q ≥ 0.119). Likewise, none of the VEGFA-KDR, IL1B-IL1R1, TGFB1-TGFBR2, or LGALS9-HAVCR2 expression-product scores was significant (all q ≥ 0.143). The four spatial specimens showed heterogeneous spot-level expression but, with one specimen per histology and no slide coordinates in the supplied matrices, did not support group-level spatial inference. TCGA tumours showed coordinated intratumoural expression, strongest between angiogenesis and TGF-β/fibrosis (Spearman ρ=0.707; q = 2.24 × 10⁻46), but TCGA-CESC contained no CVT endpoint. VEGFA increased KDR, ICAM1, VCAM1, and EDN1 mRNA in HUVEC, and bevacizumab attenuated these changes; IL-1β induced inflammatory transcripts in HAEC, and anakinra attenuated IL6, TNF, and CXCL8. CONCLUSIONS: Cervical tissues contain cardio-oncology-relevant transcriptional programmes, but the available data neither demonstrate cardiac expression nor identify bevacizumab- or ICI-induced CVT susceptibility. The endothelial experiments show expected pathway responsiveness and pharmacological blockade, not treatment-induced cardiotoxicity. Prospective analyses must compare CVT-positive and CVT-negative treated patients using matched clinical outcomes and, ideally, blood or cardiac-relevant biospecimens.
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Identification and Validation of Epithelial Cell Centre Regulatory Transcription Factors in the Gastric Cancer Microenvironment.
PURPOSE: To identify the epithelial cell centre regulatory transcription factors in the gastric cancer (GC) microenvironment and provide a new strategy for the diagnosis and treatment of GC. METHODS: The GC single-cell dataset was downloaded from the Gene Expression Omnibus (GEO) database. The regulatory mechanisms of transcription factors in both pan-cancer and GC microenvironments were analysed using the Cancer Genome Atlas (TGCA) database. Real-time quantitative PCR (RT-qPCR) was used to determine the mRNA expression levels of Prospero homeobox gene 1 (PROX1) and Endothelial PAS domain-containing protein 1 (EPAS1) in the human gastric mucosal normal epithelial cell line (GES-1) and the GC cell line (AGS). Immunohistochemistry (IHC) was used to determine the amounts of PROX1 and EPAS1 protein expression in GC and adjacent tissues. GC patients' overall survival (OS) was tracked through outpatient, Inpatient case inquiry, or phone follow-up. RESULTS: The single-cell data from GSE184198 was re-annotated, resulting in nine cell subsets: T cells (13364), NK cells (606), B cells (2525), Epithelial cells (2497), DC cells (1167), Fibroblast cells (372), Endothelial cells (271), Neutrophils cells (246) and Macrophage cells (420). Analysis of cell subgroup signalling pathways revealed that communication intensity between epithelial cells and smooth muscle cells was highest. Transcription factors PROX1 and EPAS1 were notably active in epithelial cells. Cell communication analysis indicated that IFNG may interact with IFNGR1/2 and LIF with IL6ST and LIFR to regulate the downstream PROX1 and EPAS1. PROX1 and EPAS1 were upregulated and negatively correlated with tumour mutation burden (TMB). They also exhibited high positive correlations with immune checkpoints CTLA4 and PDCD1LG2, as well as with chemokines CCL24 and CXCL12 and their receptors CCR3 and CCR4. Additionally, PROX1 and EPAS1 were positively correlated with immunosuppressive factors ADORA2A, CD160, IL10, TGFBR1, KDR and CSF1R, as well as with immunostimulators CD276, PVR, TNFRSF25, ULBP1, CXCL12 and ENTPD1. In GC tissues and AGS, PROX1 and EPAS1 were both substantially expressed. In the meantime, they showed a positive correlation with clinicopathological features such TNM stage and degree of differentiation. In GC patients, the up-regulated group's PROX1 and EPAS1 prognosis was noticeably poorer than the down-regulated group's. CONCLUSION: PROX1 and EPAS1 are likely central regulatory transcription factors in the epithelial cells of the GC environment, regulated by IFNG and LIF. They may contribute to GC progression by modulating the tumour's immune microenvironment.