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Identification of TNFRSF21 as an inhibitory factor of osteosarcoma based on a necroptosis-related prognostic gene signature and molecular experiments.
BACKGROUND: Osteosarcoma is one of the most common malignant bone tumors with bad prognosis. Necroptosis is a form of programmed cell death. Recent studies showed that targeting necroptosis was a new promising approach for tumor therapy. This study aimed to establish a necroptosis-related gene signature to evaluated prognosis and explore the relationship between necroptosis and osteosarcoma. METHODS: Data from The Cancer Genome Atlas was used for developing the signature and the derived necroptosis score (NS). Data from Gene Expression Omnibus served as validation. Principal component analysis (PCA), Cox regression, receiver operating characteristic (ROC) curves and Kaplan-Meier survival analysis were used to assess the performance of signature. The association between the NS and osteosarcoma was analyzed via gene set enrichment analysis, gene set variation analysis and Pearson test. Single-cell data was used for further exploration. Among the genes that constituted the signature, the role of TNFRSF21 in osteosarcoma was unclear. Molecular experiments were used to explore TNFRSF21 function. RESULTS: Our data revealed that lower NS indicated more active necroptosis in osteosarcoma. Patients with lower NS had a better prognosis. PCA and ROC curves demonstrated NS was effective to predict prognosis. NS was negatively associated with immune infiltration levels and tumor microenvironment scores and positively associated with tumor purity and stemness index. Single-cell data showed necroptosis heterogeneity in osteosarcoma. The cell communication pattern of malignant cells with high NS was positively correlated with tumor progression. The expression of TNFRSF21 was down-regulated in osteosarcoma cell lines. Overexpression of TNFRSF21 inhibited proliferation and motility of osteosarcoma cells. Mechanically, TNFRSF21 upregulated the phosphorylation levels of RIPK1, RIPK3 and MLKL to promote necroptosis in osteosarcoma. CONCLUSIONS: The necroptosis prognostic signature and NS established in this study could be used as an independent prognostic factor, TNFRSF21 may be a necroptosis target in osteosarcoma therapy.
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Ectopic expression of BEX genes in T-cell acute lymphoblastic leukemia.
T-cell acute lymphoblastic leukemia (T-ALL) is a malignant proliferation of T-cell progenitors originating in the thymus. T-ALL is a heterogenous disease involving the dysregulation of various oncogenes/tumor-suppressor (TS) genes. Loss of the TS gene phosphatase and TENsin homolog (PTEN) is a recurrent alteration, which is often associated with a mature T-ALL subgroup expressing a T-cell receptor. Herein, we used a single-cell RNA-sequencing approach to investigate the impact of the absence of PTEN on pathological development of mouse thymocytes. First, our differential gene expression analysis of tumor cells vs physiologic cells uncovers an ectopic expression, in leukemic cells, of the gene encoding Bex1. Then, to determine the relevance of our observation in humans, we queried a public RNA-sequencing database from the TARGET-TCGA (Therapeutically Applicable Research to Generate Effective Treatments-The Cancer Genome Atlas) project. We show that BEX1, BEX2, and BEX5 genes are ectopically expressed in T-ALL samples and we further found that ectopic BEX expression is mainly restricted to the T-ALL subgroup overexpressing TAL1 oncogene. Proximity ligation assays demonstrated the nuclear colocalization of brain-expressed X-linked 1/2 (BEX1/2) proteins with T-cell acute lymphocytic leukemia protein 1 (TAL1) in T-ALL cells. To investigate their functional role, we generated Jurkat cells with a triple knockout of BEX1, BEX2, and BEX5 using CRISPR-CRISPR-associated protein 9. This genetic inactivation led to reduced cell proliferation, a loss of histone H3 lysine 4 monomethylation (H3K4me1) marks notably at genomic regions enriched for E-box motifs, and dysregulation of several TAL1 target genes. Collectively, our findings suggest that BEX1 and BEX2 may contribute to human T-ALL oncogenesis by acting as cofactors within the TAL1 complex.
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Single-cell atlas of tumor cell evolution in response to therapy in hepatocellular carcinoma and intrahepatic cholangiocarcinoma.
BACKGROUND & AIMS: Intratumor molecular heterogeneity is a key feature of tumorigenesis and is linked to treatment failure and patient prognosis. Herein, we aimed to determine what drives tumor cell evolution by performing single-cell transcriptomic analysis. METHODS: We analyzed 46 hepatocellular carcinoma (HCC) and intrahepatic cholangiocarcinoma (iCCA) biopsies from 37 patients enrolled in interventional studies at the NIH Clinical Center, with 16 biopsies collected before and after treatment from 7 patients. We developed a novel machine learning-based consensus clustering approach to track cellular states of 57,000 malignant and non-malignant cells including tumor cell transcriptome-based functional clonality analysis. We determined tumor cell relationships using RNA velocity and reverse graph embedding. We also studied longitudinal samples from 4 patients to determine tumor cellular state and its evolution. We validated our findings in bulk transcriptomic data from 488 patients with HCC and 277 patients with iCCA. RESULTS: Using transcriptomic clusters as a surrogate for functional clonality, we observed an increase in tumor cell state heterogeneity which was tightly linked to patient prognosis. Furthermore, increased functional clonality was accompanied by a polarized immune cell landscape which included an increase in pre-exhausted T cells. We found that SPP1 expression was tightly associated with tumor cell evolution and microenvironmental reprogramming. Finally, we developed a user-friendly online interface as a knowledge base for a single-cell atlas of liver cancer. CONCLUSIONS: Our study offers insight into the collective behavior of tumor cell communities in liver cancer as well as potential drivers of tumor evolution in response to therapy. LAY SUMMARY: Intratumor molecular heterogeneity is a key feature of tumorigenesis that is linked to treatment failure and patient prognosis. In this study, we present a single-cell atlas of liver tumors from patients treated with immunotherapy and describe intratumoral cell states and their hierarchical relationship. We suggest osteopontin, encoded by the gene SPP1, as a candidate regulator of tumor evolution in response to treatment.
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PPP1R14B Promotes Lung Adenocarcinoma Tumorigenesis and Paclitaxel Resistance by Increasing ARPC1A Expression.
To investigate the biological functions of PPP1R14B in lung adenocarcinoma and further elucidate its underlying regulatory mechanisms. The Cancer Genome Atlas clinical cohorts, single-cell sequencing, Kaplan-Meier survival analysis, immunohistochemistry, qRT-PCR, and Western blot were performed to assess the expression and prognostic value of PPP1R14B in lung adenocarcinoma. Then, PPP1R14B-silenced A549 cells and PPP1R14B-overexpressing H1650 cells were constructed. Colony formation, CCK-8, EdU assay, flow cytometry, scratch, and Transwell chamber assays were utilized to evaluate cell proliferation, apoptosis, migration, invasion, and paclitaxel (PTX) resistance. To elucidate the molecular mechanism of PPP1R14B, transcriptome sequencing (RNA-seq) and co-immunoprecipitation assays were conducted. Additionally, a xenograft tumor mouse model was established to explore the in vivo role of PPP1R14B. PPP1R14B exhibited high expression in lung adenocarcinoma and correlated with an unfavorable prognosis. Silencing of PPP1R14B markedly suppressed the proliferation, migration, and invasion of A549 cells, while concurrently promoting apoptosis and sensitizing cells to PTX. Nevertheless, overexpression of PPP1R14B in H1650 cells displayed an opposite trend. PPP1R14B directly interacted with ARPC1A and promoted its expression. Overexpression of ARPC1A reversed the inhibitory effects of PPP1R14B silencing on the malignant biological behaviors of A549 cells. In vivo, silencing of PPP1R14B repressed tumor growth, as evidenced by smaller tumor volume, lower tumor weight, fewer Ki67-positive cells, and more TUNEL-positive cells. PPP1R14B directly binds ARPC1A and increases its expression to facilitate lung adenocarcinoma tumorigenesis and PTX resistance.
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Cellular dynamics across aged human brains uncover a multicellular cascade leading to Alzheimer's disease.
Alzheimer's Disease (AD) is a progressive neurodegenerative disease seen with advancing age. Recent studies have revealed diverse AD-associated cell states, yet when and how they impact the causal chain leading to AD remains unknown. To reconstruct the dynamics of the brain's cellular environment along the disease cascade and to distinguish between AD and aging effects, we built a comprehensive cell atlas of the aged prefrontal cortex from 1.64 million single-nucleus RNA-seq profiles. We associated glial, vascular and neuronal subpopulations with AD-related traits for 424 aging individuals, and aligned them along the disease cascade using causal modeling. We identified two distinct lipid-associated microglial subpopulations, one contributed to amyloid-β proteinopathy while the other mediated the effect of amyloid-β in accelerating tau proteinopathy, as well as an astrocyte subpopulation that mediated the effect of tau on cognitive decline. To model the coordinated dynamics of the entire cellular environment we devised the BEYOND methodology which uncovered two distinct trajectories of brain aging that are defined by distinct sequences of changes in cellular communities. Older individuals are engaged in one of two possible trajectories, each associated with progressive changes in specific cellular communities that end with: (1) AD dementia or (2) alternative brain aging. Thus, we provide a cellular foundation for a new perspective of AD pathophysiology that could inform the development of new therapeutic interventions targeting cellular communities, while designing a different clinical management for those individuals on the path to AD or to alternative brain aging.
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METTL2B m3C RNA transferase: oncogenic role in ovarian cancer progression via regulation of the mTOR/AKT pathway and its link to the tumor immune microenvironment.
BACKGROUND: Aberrant expression of N3-methylcytidine methyltransferase 2B (METTL2B) has been observed in various human malignancies, including those of the prostate, liver, breasts, and bladder. However, its role in ovarian cancer (OC) remains largely unexplored. This research preliminarily investigated METTL2B expression in OC and elucidated the associated molecular mechanisms. METHODS: We utilized three publicly available cancer-related databases (Genotype-Tissue Expression, Gene Expression Omnibus, and The Cancer Genome Atlas) to identify gene signatures in patients with OC and normal individuals with a specific focus on METTL2B. The role of METTL2B in OC was evaluated using patient survival data, and its impact on oncogenic behaviors in both cell and animal models, including growth potential, migration, invasion, and the tumor microenvironment, was examined. This assessment was conducted using bioinformatics tools such as Gene Set Cancer Analysis, GeneMANIA, and Tumor Immune Single-cell Hub 2. Additionally, the association between drug sensitivity and METTL2B expression was analyzed using CellMiner. RESULTS: METTL2B expression was significantly elevated in OC, highlighting its potential clinical value in the diagnosis and prognosis of OC. Patients with lower METTL2B expression exhibited favorable survival. Furthermore, METTL2B knockdown significantly disrupted oncogenic behaviors in OC cell lines by suppressing the mTOR/AKT signaling pathway. Additionally, bioinformatics-based Gene Ontology and Kyoto Encyclopedia of Genes and Genomes analyses suggested a close correlation between METTL2B and immune responses. CONCLUSIONS: Our research confirmed the upregulation of METTL2B in OC, suggesting its oncogenic function. However, METTL2B expression was negatively correlated with the infiltration scores of multiple immune cells, including cytotoxic cells and T cells, indicating its complex role in the tumor immune microenvironment. These findings highlight the significant clinical value of METTL2B in the diagnosis and prognosis of OC.
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Multi-Omics and Single-Cell Dissection of Exostosin Glycosyltransferases (EXT1/EXT2) Reveals Divergent Oncogenic Roles and Therapeutic Vulnerabilities in Gliomas.
Exostosin glycosyltransferase 1 (EXT1) and exostosin glycosyltransferase 2 (EXT2) catalyze heparan sulfate chain elongation and are increasingly implicated in cancer biology, but their roles in gliomas remain incompletely defined. Here, we performed an integrative multi-omics analysis to dissect the transcriptional, epigenetic, and microenvironmental landscape of EXT1 and EXT2 across gliomas. Bulk transcriptomic data from The Cancer Genome Atlas (TCGA) and the Chinese Glioma Genome Atlas (CGGA) revealed that both EXT1 and EXT2 are upregulated in high-grade gliomas and associate with adverse survival, with EXT1 showing the strongest and most consistent prognostic impact. Gene set enrichment analysis (GSEA) and gene set variation analysis (GSVA) indicated that EXT1-high tumors are enriched for DNA damage and replication stress programs, cell cycle progression, inflammatory response, and stromal activation pathways, whereas EXT2 expression is preferentially linked to extracellular matrix remodeling, cytoskeletal organization and angiogenesis-related signaling. Single-cell RNA sequencing and Immune deconvolution using Cell-type Identification By Estimating Relative Subsets Of RNA Transcripts (CIBERSORT) and Estimation of STromal and Immune cells in MAlignant Tumor tissues using Expression data (ESTIMATE) showed that EXT1 correlates with increased stromal and immune scores, and reduced cytotoxic T cell signatures, consistent with an immunosuppressive tumor microenvironment. EXT2 expression is enriched in gliomas with pronounced vascular and mesenchymal features, supporting a complementary role in invasive growth and tissue remodeling. Immunohistochemistry on a glioma tissue microarray validated the upregulation of EXT1 protein in high-grade tumors. The study findings identified EXT1 as a central glycosylation-linked regulator of replication stress tolerance and immune remodeling in gliomas, and suggest that EXT2 contributes to extracellular matrix and cytoskeletal reprogramming. The exostosin axis represents a promising source of prognostic biomarkers and potential therapeutic targets in glioma.
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A single-cell type transcriptomics map of human tissues.
Advances in molecular profiling have opened up the possibility to map the expression of genes in cells, tissues, and organs in the human body. Here, we combined single-cell transcriptomics analysis with spatial antibody-based protein profiling to create a high-resolution single-cell type map of human tissues. An open access atlas has been launched to allow researchers to explore the expression of human protein-coding genes in 192 individual cell type clusters. An expression specificity classification was performed to determine the number of genes elevated in each cell type, allowing comparisons with bulk transcriptomics data. The analysis highlights distinct expression clusters corresponding to cell types sharing similar functions, both within the same organs and between organs.
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Comprehensive bioinformatics analysis of EXOSC family genes in lung adenocarcinoma.
The RNA exosome complex (EXOSC1-10) orchestrates 3'-5' RNA processing and decay, yet its family-wide landscape and clinical relevance in lung adenocarcinoma (LUAD) remain incompletely defined. Here, we conducted an integrative multi-omics analysis of EXOSC family members in LUAD using public transcriptomic and proteomic resources, external validation cohorts, and single-cell data. Across TCGA (59 normal vs. 515 tumors), all EXOSC genes were significantly upregulated in tumors, with concordant increases for most proteins in CPTAC and immunohistochemistry evidence from the Human Protein Atlas. Survival analyses identified EXOSC2, EXOSC3 and EXOSC5 as prognostically informative, with elevated EXOSC2/EXOSC5 also associated with inferior disease-specific survival. Receiver operating characteristic analyses indicated moderate-to-high diagnostic performance for several EXOSC genes, supported by qRT-PCR validation in LUAD cell lines and confirmation in GSE31210. Clinicopathological correlations linked EXOSC1-5 and EXOSC8-10 to advanced stage and metastatic features, whereas EXOSC6 and EXOSC7 showed comparatively limited or context-dependent associations, suggesting functional heterogeneity within the family. Genomic profiling revealed recurrent alterations in 11.83% of patients, with EXOSC4 exhibiting the highest alteration frequency (predominantly amplifications), and network analyses identified core interacting partners centered on RNA surveillance machinery. EXOSC expression was broadly correlated with RNA modification regulators (m1A/m5C/m6A) and displayed heterogeneous relationships with immune checkpoint genes and immune infiltration, while higher EXOSC expression consistently associated with lower ESTIMATE-derived microenvironment scores and an immune profile characterized by Th2/T helper enrichment with reduced cytotoxic and antigen-presenting populations. Gene set enrichment analyses implicated cell-cycle regulation, senescence, chromatin-related programs and extracellular matrix pathways, and EXOSC-high tumors were associated with increased tumor mutational burden and homologous recombination deficiency, together with enrichment of DNA damage response pathways. Single-cell analysis (GSE146100) localized highest EXOSC expression to proliferating monocytes/macrophages and suggested TGF-β-linked communication with endothelial and T-cell compartments. Exploratory translational analyses further indicated an association between EXOSC9 and predicted cisplatin sensitivity. Collectively, these findings position the EXOSC family as a clinically and biologically relevant axis in LUAD, linking RNA surveillance dysregulation to immune contexture and genomic instability, and highlight subunit-specific heterogeneity that warrants mechanistic validation.
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Effect of aging on rat testicular interstitial compartment: functional losses in endothelial and mesenchymal cells and activation of immune cells.
Human aging is associated with testosterone decline and spermatogenic defects, impacting fertility and health, yet the underlying cellular mechanisms remain poorly understood. This study aimed to establish a regulatory cell atlas of Leydig cells in aging rat testes and characterize intercellular interactions. Using single-cell RNA sequencing and immunohistochemistry, interstitial cells from young (3-month) and aged (21-month) BN rat testes were analyzed. Among 8 identified interstitial cell types, aging was not synchronous, but with remarkable heterogeneity and stochasticity. Mesenchymal cells exhibited reduced expression of genes involved in detoxification and extracellular matrix maintenance, alongside increased immune regulation genes. Endothelial cells, the most communicatively active population, showed decreased angiogenesis and cell adhesion/migration but enhanced immune responses and leukocyte chemotaxis. In immune populations, dendritic cells decreased while lymphocytes increased, with no significant change in macrophages. Transcriptomic shifts indicated a transition from innate to adaptive immunity. The loss of dendritic cells and gain of lymphocytes may be linked to CCL7 and CXCL9-12, as receptors Ccr1/Ccr5 and Cxcr3 were upregulated in lymphocytes but downregulated in dendritic cells. Overall, inflammatory activation and functional losses occurred in both immune and non-immune cells during testicular aging. This innate-to-adaptive immune shift may further compromise non-immune cell functions, accelerating testicular aging.