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Identification and characterization of aging/senescence-induced genes in osteosarcoma and predicting clinical prognosis.
BACKGROUND: Aging is an influential risk factor for progression of both degenerative and oncological diseases of the bone. Osteosarcoma, considered the most common primary mesenchymal tumor of the bone, is a worldwide disease with poor 5-year survival. This study investigated the role of aging-/senescence-induced genes (ASIGs) in contributing to osteosarcoma diagnosis, prognosis, and therapeutic agent prediction. METHODS: Therapeutically Applicable Research to Generate Effective Treatments (TARGET), Gene Expression Omnibus (GEO), and The Cancer Genome Atlas (TCGA) were used to collect relevant gene expression and clinical data of osteosarcoma and paracancerous tissues. Patients were clustered by consensus using prognosis-related ASIGs. ssGSEA, ESTIMATE, and TIMER were used to determine the tumor immune microenvironment (TIME) of subgroups. Functional analysis of differentially expressed genes between subgroups, including Gene Ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG), and gene set variation analyses (GSVAs), was performed to clarify functional status. Prognostic risk models were constructed by univariate Cox regression and least absolute shrinkage and selection operator (LASSO) regression. SCISSOR was used to identify relevant cells in osteosarcoma single-cell data for different risk groups. The effect of immunotherapy was predicted based on TIDE scores and chemotherapy drug sensitivity using CTRP and PRISM. RESULTS: Three molecular subgroups were identified based on prognostic differentially expressed ASIGs. Immunological infiltration levels of the three groups differed significantly. Based on GO and KEGG analyses, differentially expressed genes between the three subgroups mainly relate to immune and aging regulation pathways; GSVA showed substantial variations in multiple Hallmark pathways among the subgroups. The ASIG risk score built based on differentially expressed genes can predict patient survival and immune status. We also developed a nomogram graph to accurately predict prognosis in combination with clinical characteristics. The correlation between the immune activation profile of patients and the risk score is discussed. Through single-cell analysis of the tumor microenvironment, we identified distinct risk-group-associated cells with significant differences in immune signaling pathways. Immunotherapeutic efficacy and chemotherapeutic agent screening were evaluated based on risk score. CONCLUSION: Aging-related prognostic genes can distinguish osteosarcoma molecular subgroups. Our novel aging-associated gene signature risk score can be used to predict the osteosarcoma immune landscape and prognosis. Moreover, the risk score correlates with the TIME and provides a reference for immunotherapy and chemotherapy in terms of osteosarcoma.
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The mechanism of fibronectin 1 promoting papillary thyroid cancer progression by regulating anoikis resistance.
Background: Papillary thyroid cancer is a common head and neck malignancy with a globally rising incidence. While most patients attain favorable prognosis following standard treatment, a subset develops recurrence and metastasis—two key factors that compromise clinical outcomes. Anoikis resistance is a prerequisite for tumor metastasis; however, the role and mechanism of Fibronectin 1 (FN1)—a molecule overexpressed in multiple cancers and linked to tumor progression—in papillary thyroid cancer anoikis resistance remain undefined. Objective: This study therefore investigated the function and regulatory mechanism of FN1 in papillary thyroid cancer anoikis resistance using a combination of bioinformatics analyses and experimental validation. Methods: First, using The Cancer Genome Atlas (TCGA) dataset and anoikis-related genes from GeneCards, we identified FN1 as an anoikis-related hub gene in thyroid cancer through bioinformatics analyses, including consensus clustering, weighted gene co-expression network analysis (WGCNA), and protein-protein interaction (PPI) network analysis. Its clinical relevance was further analyzed from the perspectives of pathological typing, survival prognosis, immune cell infiltration (via xCell) and single-cell expression patterns. Next, we performed validation using papillary thyroid cancer tissues, adjacent normal tissues, and cell lines (8305c, BCPAP, Nthy-ori 3 − 1): FN1 expression and cancer cell anoikis were detected by immunohistochemistry (IHC) and TUNEL staining; FN1 mRNA and protein levels were quantified via qRT-PCR and Western blot. Finally, we modulated FN1 expression through RNA interference (for knockdown). Cell proliferation, migration, and invasion were assessed using CCK-8 and Transwell assays, while Western blot was applied to measure the expression of apoptosis-related proteins. Results: FN1 is highly expressed in papillary thyroid cancer tissues and cell lines and is associated with poor tumor prognosis. Silencing FN1 can inhibit the proliferation, migration and invasion of papillary thyroid cancer cells and increase the anoikis rate. Overexpression of FN1 showed the opposite effect. Mechanistically, FN1 can up-regulate anti-apoptotic proteins BCL2L1 and Caspase-3, and down-regulate pro-apoptotic protein BAD, thereby enhancing anoikis resistance. Conclusions: FN1 is highly expressed in papillary thyroid cancer and correlates with poor prognosis. Mechanistically, FN1 enhances papillary thyroid cancer cell tumorigenic potential by regulating proliferation, migration, invasion and apoptotic progression via the BCL2L1/BAD axis, thus driving tumor development. FN1 may act as a promising therapeutic target for advanced papillary thyroid cancer.
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Integrative Analysis of Glycine, Serine, and Threonine Metabolism and the Immune Microenvironment in Endometrial Cancer: A Prognostic Model and Metabolic-Immune Framework for Precision Oncology.
BACKGROUND: Metabolic reprogramming is a hallmark of the pathogenesis and progression of endometrial carcinoma (EC). This study comprehensively analyzed the expression profiles of glycine, serine, and threonine (Gly/Ser/Thr) metabolism-related genes in EC. We also established a robust prognostic model and developed a molecular subtyping framework that integrates metabolic and immune characteristics based on the identified prognostic genes. The aims of this work are to enhance diagnostic precision and improve clinical management strategies for patients with EC. METHODS: Untargeted metabolomic analysis was performed on 35 EC and 15 normal tissues. The Cancer Genome Atlas (TCGA) transcriptomic data were integrated with weighted gene co-expression network analysis (WGCNA) to identify EC-related metabolic genes and construct a prognostic model using Cox proportional hazards and least absolute shrinkage and selection operator (LASSO) regression analyses. The model was validated using an independent proteomic and single-cell dataset from our institution. Consensus clustering classified patients into three molecular subtypes, which were further characterized by gene set variation analysis (GSVA) and profiling of immune infiltration. Finally, key prognostic genes were validated by reverse transcription quantitative polymerase chain reaction (RT-qPCR) in EC and normal endometrial epithelial cells. RESULTS: Metabolomic analysis revealed significant enrichment of the Gly/Ser/Thr metabolic pathways. WGCNA identified a tumor-associated metabolic module among 1741 pathway-related genes. A prognostic model comprising methylenetetrahydrofolate dehydrogenase 2 (MTHFD2), ribosomal protein S6 kinase A1 (RPS6KA1), and cyclin-dependent kinase inhibitor 2A (CDKN2A) was subsequently established. Consensus clustering based on risk scores stratified EC patients into three molecular subtypes: immunometabolic-suppressed (C1), proliferative-immunobalanced (C2), and immune-activated (C3). The C1 subtype had the poorest prognosis and was characterized by metabolic suppression and immune evasion. The C2 subtype showed a favorable prognosis and was defined by a "proliferation-immune balance" in which high proliferative activity coexisted with strong anti-tumor immunity. The C3 subtype was also associated with a favorable outcome, driven by upregulated DNA repair and oxidative phosphorylation pathways alongside infiltration of immune-active cells. RT-qPCR confirmed significant differences in the mRNA expression of MTHFD2, RPS6KA1, and CDKN2A between normal and EC cells (p < 0.05). CONCLUSION: This study developed a Gly/Ser/Thr pathway-based prognostic model for EC, based on the expression of MTHFD2, RPS6KA1, and CDKN2A as novel biomarkers. The resulting patient stratification framework holds significant clinical potential for guiding precise and personalized management of EC.
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Colorectal Cancer Cell's Weapon: RNF32 Engages SPP1+ Macrophages to Foster Liver Metastasis, Targeted by Indole-3-Acetic Acid.
Colorectal cancer liver metastasis (CRLM) involves complex molecular mechanisms. By integrating The Cancer Genome Atlas (TCGA) data and employing Cox regression, Weighted Gene Co-expression Network Analysis (WGCNA), and single-cell RNA sequencing, this study identifies RNF32 as a key gene linking poor prognosis to metastasis. Functional assays demonstrate that RNF32 promotes tumor cell proliferation, invasion, and epithelial-mesenchymal transition (EMT) in vitro, and drives tumor growth and liver metastasis in vivo. Mechanistically, RNF32 catalyzes K48-linked ubiquitination at the K60 site of GSK3β, stabilizing β-catenin and activating the Wnt signaling pathway, thereby upregulating CCL2. Mass cytometry and other experiments further reveal that RNF32 recruits SPP1+ macrophages via CCL2 to remodel the metastatic niche, a process dependent on the CCR2/FABP1/PPARG axis. Macrophage depletion abrogates metastasis, while the FABP1 inhibitor orlistat reverses SPP1 upregulation in macrophages. Moreover, SPP1+ macrophages interact with tumor cell CD44, synergizing with RNF32 to enhance cancer stemness via Wnt signaling. Importantly, virtual screening identifies indole-3-acetic acid (IAA) as an RNF32 inhibitor that suppresses liver metastasis and reverses immunosuppression in vivo. This study establishes RNF32 as a dual-functional driver of metastasis and proposes IAA as a promising therapeutic agent, offering new hope for targeting both tumor-intrinsic EMT and the immune microenvironment in CRC liver metastasis.
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Notch1 supports proliferation and bioenergetic activity in a pancreatic neuroendocrine neoplasm cell line.
BACKGROUND: Pancreatic neuroendocrine neoplasms (PNENs) arise from neuroendocrine cells of the pancreas. Therapeutic options are limited for patients with advanced disease and the molecular mechanisms that drive PNEN progression remain elusive. The Notch pathway regulates cell fate, proliferation, cell-cell communication, and survival in multicellular organisms. Dysregulation of one pathway member, Notch1, has been linked to the development and growth of several cancers; however, the role of Notch1 signaling in PNENs is not defined. METHODS: Notch1 expression was evaluated in normal adult pancreas and PNENs using publicly available single-cell RNA sequencing data from the Human Protein Atlas and immunohistochemistry on PNEN tissue microarrays. A CRISPR/Cas9-mediated knockout of Notch1 was generated in a PNEN cell line ('BON'). The functional impact of Notch1 loss was assessed through proliferation assays, cell cycle analysis, bulk transcriptomics, and Seahorse metabolic flux assays. In vivo tumor growth was evaluated using subcutaneous xenografts, and global proteomic profiling was performed on resected tumors. RESULTS: Notch1 was found to be absent in normal adult pancreatic neuroendocrine cells but was re-expressed in 39-45% of primary and metastatic PNENs. Genetic deletion of Notch1 significantly reduced PNEN cell proliferation in both 2D and 3D conditions, induced G1 cell cycle arrest, and slowed xenograft tumor growth. We also found that Notch1 regulates proliferation and cellular bioenergetic pathways in PNEN cells. CONCLUSIONS: Our findings reveal a role for Notch1 in supporting proliferation and bioenergetics in a PNEN cell line, providing new insights into its potential oncogenic function and contribution to PNEN pathobiology.
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Transcriptomics Analysis Identifies the Decline in the Alveolar Type II Stem Cell Niche in Aged Human Lungs.
Aging poses a global public health challenge, which is linked to the rise of age-related lung diseases. The precise understanding of the molecular and genetic changes in the aging lung that elevate the risk of acute and chronic lung diseases remains incomplete. Alveolar type II (AT2) cells are stem cells that maintain epithelial homeostasis and repair the lung after injury. AT2 progenitor function decreases with aging. The maintenance of AT2 function requires niche support from other cell types, but little has been done to characterize alveolar alterations with aging in the AT2 niche. To systematically profile the genetic changes associated with age, we present a single-cell transcriptional atlas comprising nearly half a million cells from the healthy lungs of human subjects spanning various ages, sexes, and smoking statuses. Most annotated cell lineages in aged lungs exhibit dysregulated genetic programs. Specifically, the aged AT2 cells demonstrate loss of epithelial identities, heightened inflammaging characterized by increased expression of AP-1 (Activator Protein-1) transcription factor and chemokine genes, and significantly increased cellular senescence. Furthermore, the aged mesenchymal cells display a remarkable decrease in collagen and elastin transcription and a loss of support to epithelial cell stemness. The decline of the AT2 niche is further exacerbated by a dysregulated genetic program in macrophages and dysregulated communications between AT2 and macrophages in aged human lungs. These findings highlight the dysregulations observed in both AT2 stem cells and their supportive niche cells, potentially contributing to the increased susceptibility of aged populations to lung diseases.
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HDAC5 modulates PD-L1 expression and cancer immunity via p65 deacetylation in pancreatic cancer.
Rationale: Pancreatic ductal adenocarcinoma (PDAC) is a lethal disease with a dismal 5-year survival less than 10%. Most patients with PDAC exhibit poor response to single-agent immunotherapy. Multimodal therapies targeting mechanisms of resistance to immunotherapy are urgently needed. We found that the class IIa histone deacetylase (HDAC) member, HDAC5 is downregulated in multiple solid tumors and its level were associated with favorable prognosis in PDAC patients. Upregulated genes in patients harboring HDAC5 deletions were enriched in adaptive immune responses and lymphocyte-mediated immunity in The Cancer Genome Atlas (TCGA) pancreatic cancer dataset. Methods: Tissue microarray of pancreatic cancer were used to analysis the correlation between HDAC5 and PD-L1. RNA-seq, transcription factor motif analysis, drug screening and molecular biology assays were performed to identify the mechanism of HDAC5's repression on PD-L1. Allografts of pancreatic cancer in mouse were applied to test the efficiency of HDAC5 inhibition and anti-PD1 co-treatment. Results: HDAC5 regulated PD-L1 expression by directly interacting with NF-κB p65; this interaction was suppressed by p65 phosphorylation at serine-311. Additionally, HDAC5 diminished p65 acetylation at lysine-310, which is essential for the transcriptional activity of p65. Importantly, we demonstrated that HDAC5 silencing or inhibition sensitized PDAC tumors to immune checkpoint blockade (ICB) therapy in syngeneic mouse model and KPC mouse derived PDAC model. Conclusion: Our findings revealed a previously unknown role of HDAC5 in regulating the NF-κB signaling pathway and antitumor immune responses. These findings provide a strong rationale for augment the antitumor effects of ICB in immunotherapy-resistant PDAC by inhibiting HDAC5.
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Single-cell RNA sequencing highlights the immunosuppression of IDO1+ macrophages in the malignant transformation of oral leukoplakia.
Rationale: Immunosuppressive tumor microenvironment (iTME) plays an important role in carcinogenesis, and some macrophage subsets are associated with iTME generation. However, the sub-population characterization of macrophages in oral carcinogenesis remains largely unclear. Here, we investigated the immunosuppressive status with focus on function of a macrophage subset that expressed indoleamine 2,3 dioxygenase 1 (Macro-IDO1) in oral carcinogenesis. Methods: We built a single cell transcriptome atlas from 3 patients simultaneously containing oral squamous cell carcinoma (OSCC), precancerous oral leukoplakia (preca-OLK) and paracancerous tissue (PCA). Through single-cell RNA sequencing and further validation using multicolor immunofluorescence staining and the in vitro/in vivo experiments, the immunosuppressive cell profiles were built and the role of a macrophage subset that expressed indoleamine 2,3 dioxygenase 1 (Macro-IDO1) in the malignant transformation of oral leukoplakia was evaluated. Results: The iTME formed at preca-OLK stage, as evidenced by increased exhausted T cells, Tregs and some special subsets of macrophages and fibroblasts. Macro-IDO1 was predominantly enriched in preca-OLK and OSCC, distributed near exhausted T cells and possessed tumor associated macrophage transformation potentials. Functional analysis revealed the established immunosuppressive role of Macro-IDO1 in preca-OLK and OSCC: enriching the immunosuppression related genes; having an established level of immune checkpoint score; exerting strong immunosuppressive interaction with T cells; positively correlating with the CD8-exhausted. The immunosuppression related gene expression of macrophages also increased in preca-OLK/OSCC compared to PCA. The use of the IDO1 inhibitor reduced 4NQO induced oral carcinogenesis in mice. Mechanistically, IFN-γ-JAK-STAT pathway was associated with IDO1 upregulation in OLK and OSCC. Conclusions: These results highlight that Macro-IDO1-enriched in preca-OLK possesses a strong immunosuppressive role and contributes to oral carcinogenesis, providing a potential target for preventing precancerous legions from transformation into OSCC.
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Identification of prognosis and therapy related intratumoral microbiome and immune signatures in gastric cancer.
The impact of the intratumoral microbiome (ITM) on the treatment and prognosis of gastric cancer (GC) remains controversial. Our study analyzed the differential ITM in GC tissues and identified nine bacterial genera significantly associated with overall survival (OS), with seven as risk factors and two as protective factors. Three distinct clusters with varying survival outcomes were defined, demonstrating correlations with pathological stage and immune features. An immune-related gene-based RiskScore model incorporating genes such as Apolipoprotein D (APOD), Stanniocalcin 1 (STC1), Coagulation Factor II Thrombin Receptor (F2R), Angiotensinogen (AGT), Fatty Acid Binding Protein 4 (FABP4), Inhibin Subunit Beta A (INHBA), Caspase Recruitment Domain Family Member 11 (CARD11), and Dickkopf WNT Signaling Pathway Inhibitor 1 (DKK1) was established and validated in The Cancer Genome Atlas (TCGA) and Gene Expression Omnibus (GEO) datasets. When combined with clinical factors, this RiskScore model formed a Nomogram model achieving Areas Under the Curve (AUCs) of 0.72, 0.76, and 0.79 for 1, 3, and 5-year OS predictions, respectively. This model exhibited robust predictive accuracy over time and correlated with mutation frequency, drug sensitivity, and immunotherapy response. Furthermore, single-cell analysis revealed that tumor-associated fibroblasts may play a pivotal role in immune-microbial interactions. The results were confirmed using quantitative real-time polymerase chain reaction (qPCR) and immunohistochemistry (IHC). In conclusion, the prognostic model incorporating ITM and immune-related genes aids in risk stratification and provides valuable insights and targets for GC treatment.
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A spatiotemporal atlas of cholestatic injury and repair in mice.
Cholestatic liver injuries, characterized by regional damage around the bile ductular region, lack curative therapies and cause considerable mortality. Here we generated a high-definition spatiotemporal atlas of gene expression during cholestatic injury and repair in mice by integrating spatial enhanced resolution omics sequencing and single-cell transcriptomics. Spatiotemporal analyses revealed a key role of cholangiocyte-driven signaling correlating with the periportal damage-repair response. Cholangiocytes express genes related to recruitment and differentiation of lipid-associated macrophages, which generate feedback signals enhancing ductular reaction. Moreover, cholangiocytes express high TGFβ in association with the conversion of liver progenitor-like cells into cholangiocytes during injury and the dampened proliferation of periportal hepatocytes during recovery. Notably, Atoh8 restricts hepatocyte proliferation during 3,5-diethoxycarbonyl-1,4-dihydro-collidin damage and is quickly downregulated after injury withdrawal, allowing hepatocytes to respond to growth signals. Our findings lay a keystone for in-depth studies of cellular dynamics and molecular mechanisms of cholestatic injuries, which may further develop into therapies for cholangiopathies.