It is identified that lymph node metastases in high-risk neuroblastomas display distinctive cellular heterogeneity and plasticity, marked by mesenchymal-like and stem-like states and heightened epithelial-to-mesenchymal transition activity compared to primary adrenal tumors.
Abstract
Neuroblastoma, a pediatric cancer derived from sympathetic ganglia of the peripheral nervous system, frequently metastasizes, driving poor outcomes. Primary neuroblastomas are well-characterized, but the mechanisms underlying metastasis remain poorly understood. Here, by using single-cell and spatial multiomics, we identified that lymph node metastases in high-risk neuroblastomas display distinctive cellular heterogeneity and plasticity, marked by mesenchymal-like and stem-like states and heightened epithelial-to-mesenchymal transition activity compared to primary adrenal tumors. In addition, compared to primary adrenal masses, the metastatic niche display increased immunosuppressive myeloid programs, heightened immune checkpoint signaling, and lymphocyte exhaustion, which are indicative of immune evasion and dysfunction. Notably, metastatic neuroblastomas show elevated eIF4F translation machinery and XPO1 levels. Dual inhibition of eIF4A and XPO1 synergistically halted tumor growth and prolonged survival in xenograft models. Together, our multiomics studies reveal the molecular and cellular plasticity that contributes to therapy resistance and highlight exploitable therapeutic vulnerabilities in high-risk metastatic neuroblastomas.
ABSTRACT Metastasis is a major determinant of treatment failure and mortality in thyroid cancer, yet the interplay between malignant evolution and the immune microenvironment remains poorly characterized. Immunotherapy offers promise, but its efficacy requires a deeper understanding of tumor-associated immune infiltration and checkpoint regulation. In this study, we constructed a high-resolution transcriptomic atlas of the thyroid cancer ecosystem by analyzing 55,005 single cells from paired primary tumors and lymph node metastases. By integrating chromosomal copy number variation (CNV) inference with consensus nonnegative matrix factorization (cNMF), we deciphered the intrinsic heterogeneity of malignant epithelial cells, revealing distinct transcriptional programs and developmental trajectories driving the metastatic cascade. The metastatic niche exhibited significant reprogramming of the immunosuppressive landscape, characterized by the enrichment of FOXP3⁺ regulatory T (Treg) cells, LAMP3⁺ dendritic cells (DCs), and CCL18⁺ M2-like macrophages. Notably, while canonical checkpoints PD-1 and PD-L1/2 showed minimal expression, ligand-receptor interaction analysis identified the LAG3-LGALS3 axes as dominant immune evasion pathways mediating the crosstalk between CD8⁺ T cells and the tumor stroma. In conclusion, this study comprehensively maps the coevolution of malignant thyrocyte plasticity and the immunosuppressive metastatic niche. By uncovering the specific role of LAMP3⁺ DCs and identifying LAG3/TIGIT as critical alternative checkpoints, our findings challenge the utility of conventional PD-1 blockade in this context and provide a robust molecular rationale for developing next-generation immunotherapeutic strategies tailored to thyroid cancer. Although limited by a modest sample size, these findings provide a foundation for further investigation of the metastatic immune landscape in thyroid cancer.
Shu-hang Xu, Yaorong Su, Senmin Zhang et al.· Oncoimmunology· 0 citations
Intrahepatic metastasis in multifocal hepatocellular carcinoma is associated with poor prognosis and therapeutic resistance, yet the immune mechanisms driving disease progression remain unclear. Here, we analyzed genetic and immune differences between primary tumors and intrahepatic metastatic lesions using sequencing approaches and spatial validation methods. We found that metastatic lesions shared key genomic features with primary tumors but exhibited a distinct immunosuppressive environment enriched in myeloid and T cell populations. In particular, a subset of macrophages expressing glycoprotein nonmetastatic melanoma protein B (GPNMB) was consistently enriched in metastatic niches across multiple independent cohorts. These macrophages were spatially colocalized with CD8+ T cells exhibiting features of terminal exhaustion. Mechanistically, integrated multiomics and functional analyses revealed that GPNMB overexpression triggers lipid metabolic rewiring via the phosphatidylinositol 3-kinase/AKT-cyclooxygenase-2 cascade, leading to elevated prostaglandin E2 secretion, which directly suppresses CD8+ T cell cytotoxicity. Specific silencing of this subset using a dual-targeted, lipid-polymer nanoparticle (APLsiGpnmb) effectively reversed T cell exhaustion, inhibited metastasis, and synergized with anti-programmed death 1 immunotherapy in mouse models without inducing systemic toxicity. These findings identify GPNMB-positive macrophages as key metabolic and immune regulatory hubs, suggesting that targeting the GPNMB–prostaglandin E2 axis provides a promising precision therapeutic strategy for intrahepatic metastasis in multifocal hepatocellular carcinoma.
Yuyan Xu, Cheng Zhang, Zhuocheng Ji et al.· Research· 0 citations
ABSTRACT Pancreatic ductal adenocarcinoma (PDAC) is among the most aggressive human malignancies and has an extremely poor prognosis. Its progression is largely driven by a highly complex and immunosuppressive tumor microenvironment (TME), highlighting the urgent need for a deeper understanding of its molecular mechanisms. Recent advances in single-cell RNA sequencing (scRNA-seq) and spatial transcriptomics (ST) have provided unprecedented opportunities to dissect cellular heterogeneity, spatial organization, and gene expression dynamics within the TME. In this review, we summarize the major scRNA-seq and ST technologies and their unique strengths in cancer research and highlight their integrated applications in revealing PDAC heterogeneity, stromal–immune interactions, and mechanisms of therapeutic resistance. We further discuss how these approaches can inform biomarker discovery and guide the development of novel therapeutic strategies. Together, these findings suggest that integrated single-cell and spatial transcriptomics offers transformative potential to advance precision oncology and improve outcomes for patients with pancreatic cancer.
Mengting Luo, Feng Shen, Wanli Xu et al.· Cancer Biology & Therapy· 0 citations
Triple-negative breast cancer (TNBC) is an aggressive subtype associated with high metastatic potential and poor outcomes, with lung metastasis representing one of the most frequent and life-threatening events. However, the mechanism how cellular plasticity and reprogramming that enable TNBC cells to colonize in the lung remain incompletely understood. Here, we integrated single-cell RNA sequencing and spatial transcriptomics on paired MMTV-PyMT primary mammary tumors and lung metastatic tumors, complemented by functional assays in 4T1 mouse models, to delineate the cellular heterogeneity and molecular mechanisms driving TNBC lung metastasis. We identified three metastasis-associated subtypes-C12-Cd, Cdh5-like, and Wfdc12-each enriched in metastatic lesions and exhibiting distinct biological programs. The C12-Cd subcluster was characterized by the upregulation of Exoc4, a vesicle-trafficking regulator associated with a poor prognosis in patients with TNBC. The Cdh5-like cluster displayed a hypoxia-driven vascular phenotype, in which Hif-2α-mediated Cd36 expression promoted vasculogenic mimicry and metastatic colonization. The Wfdc12 cluster secreted Cxcr2 ligands (Cxcl1/2) and Cxcr2 blockade significantly reduced lung metastasis in vivo, underscoring therapeutic potential. Notably, cross-subtypes of lung metastatic TNBC analysis revealed Sftpc upregulation, reflecting organ-adaptive transcriptional reprogramming that may facilitate tumor cell survival in the pulmonary niche. Collectively, our findings provide a comprehensive cellular and molecular atlas of TNBC lung metastasis. We establish Exoc4, the Hif-2α-Cd36 vasculogenic mimicry axis, Cxcrl1/2-Cxcr2 signaling, and Sftpc as critical mediators of metastatic adaptation. These results not only bridge key knowledge gaps in metastatic heterogeneity and organ-specific adaptation but also highlight novel prognostic markers and therapeutic vulnerabilities with translational potential for treating TNBC lung metastasis.
Hsiao-Chen Lee, C. Kuo, Fang-Ming Chen et al.· Cell Death and Disease· 0 citations
Non-small cell lung cancer (NSCLC) is often presented as a success story for precision oncology, but that success remains uneven. Targeted agents and immune checkpoint inhibitors have changed treatment for molecularly defined or immune-responsive tumors, yet many patients relapse as resistant clones emerge, tumor cells shift state, and local immune pressure changes across the lesion. Bulk genomic and transcriptomic assays have been useful for clinical stratification, but they average signals across mixed cell populations and therefore miss rare resistant cells, transient drug-tolerant states, and spatially restricted tumor–immune interactions. Single-cell and spatial omics now provide a more direct way to examine these problems. In NSCLC, single-cell RNA sequencing, single-cell chromatin profiling, spatial transcriptomics, and multiplex imaging have begun to map malignant epithelial plasticity, persister-like states, dysfunctional immune compartments, stromal remodeling, and metabolically distinct niches. These approaches do not simply add resolution; they help connect cell state, metabolic activity, tissue location, and treatment response. This mini review discusses how single-cell and spatial omics are reshaping our understanding of metabolic reprogramming and tumor–immune ecosystems in NSCLC, and how these findings may inform biomarker discovery, patient stratification, resistance monitoring, and rational combination therapy.
Zhenzhen Lian, Xu Wu, Yangyang Zhou et al.· Frontiers in Immunology· 0 citations
Ewing sarcoma (EwS) is an aggressive pediatric malignancy with poor outcomes for patients with metastatic or relapsed disease. Effective immunotherapeutic approaches, including CAR T-cell therapy, are limited by intratumoral heterogeneity, an incompletely characterized tumor microenvironment (TME), and a lack of well-defined, tumor-restricted target antigens. To address these limitations, we performed an integrated analysis of EwS tumor samples using both single-nucleus and single-cell RNA sequencing datasets derived exclusively from patient samples, including matched primary tumors and orthotopic patient-derived xenograft (PDX) models. Our analyses reveal that primary EwS tumors are largely composed of highly heterogeneous malignant cell populations occupying multiple, multidirectional transcriptional states, including neuronal-like, proliferative, angiogenic, and fibroblast-like. We demonstrate that the EwS TME contains both classical cancer-associated fibroblasts (CAFs) and abundant EwS CAF-like tumor cells that transcriptionally resemble stromal cells while retaining tumor identity. Trajectory analyses define a progressive and coordinated tumor–CAF continuum, marked by gradual loss of neuronal programs and activation of mesenchymal and extracellular matrix remodeling programs, suggesting dynamic tumor cell reprogramming that may promote invasion, immune evasion, and therapeutic resistance. Notably, this structured transcriptional continuum was prominent in primary tumors but largely absent in matched PDX models, underscoring the importance of native tumor context for capturing clinically relevant tumor–TME interactions. We also developed a systematic surface-antigen discovery pipeline and identified ten novel putative tumor-associated surface target antigens (TAs), LRRC15, ATP2B3, CACNA1I, DCHS2, DSEL, LPAR4, PRRT4, TMEM229A, UNC5A, and UNC79, none of which have been previously described in EwS tumor biology. Characterization of these surface TAs revealed distinct expression patterns across EwS tumor cells, EwS CAF-like tumor cells, and classical CAFs. Moreover, some TAs expression differed between primary and metastatic tumors and between primary patient samples and matched PDX models, highlighting the critical importance of first validating therapeutic targets in primary tissues (PT). Together, these findings redefine the cellular architecture of EwS by revealing a dynamic tumor–CAF continuum that is uniquely preserved in primary tumors and establishes a framework for identifying clinically relevant tumor-associated surface TAs. These results provide a foundation for the rational development of next-generation immunotherapies and precision-targeted therapies for patients with EwS.
Mohamed A. Sharif, Abdul S. Khan, R. Brentjens et al.· bioRxiv· 0 citations