Single-cell and spatial transcriptomics map lung-adaptive metastasis programs through Exoc4, Cd36-vasculogenic mimicry, and Cxcr2 signaling in triple-negative breast cancer.
These results highlight novel prognostic markers and therapeutic vulnerabilities with translational potential for treating TNBC lung metastasis and establish Exoc4, the Hif-2α-Cd36 vasculogenic mimicry axis, Cxcrl1/2-Cxcr2 signaling, and Sftpc as critical mediators of metastatic adaptation.
Abstract
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.
Triple-negative breast cancer (TNBC) is an aggressive subtype associated with poor prognosis and limited therapeutic options, largely due to its unique tumor microenvironment (TME). Cancer-associated fibroblasts (CAFs) critically influence tumor progression and metastasis, yet their functional heterogeneity in TNBC remain poorly understood. An integrated multi-omic analysis was conducted using single-cell RNA sequencing and single-cell ATAC sequencing from TNBC and hormone receptor-positive/HER2-negative (HR + HER2-) breast cancers. The signaling axis was validated critically regulates both TNBC progression and CAF subtype switching. We identified a distinct CAF subpopulation, termed my_iCAFs, characterized by co-expression of myofibroblastic (FAP, ACTA2) and inflammatory markers (CXCL12), significantly enriched within the TNBC TME. My_iCAFs possess elevated activity of pathways involved in epithelial-mesenchymal transition, PI3K/AKT signaling, and pro-inflammatory TNF/NF-κB signaling. Multi-omic integration pinpointed FOSB as a central transcription factor whose expression and chromatin accessibility were selectively enhanced in my_iCAFs, potentially regulated by tumor-derived CXCL8 signaling via syndecan receptors. Also, we found that the FOSB-HES1 axis can effectively activate the transition of CAFs into my_iCAFs. This study reveals a novel FOSB-driven myofibroinflammatory CAF subtype prominently enriched in TNBC, suggesting crucial roles in tumor aggressiveness and highlighting potential therapeutic targets within the stromal compartment of this challenging breast cancer subtype.
Min Li, Jun Lin, Changwei Yang et al.· Cell Death Discovery· 0 citations
Advanced renal cell carcinoma frequently acquires resistance to immune checkpoint blockade (ICB), underscoring the pivotal influence of the tumor immune microenvironment (TME) on therapeutic efficacy. While recent studies have implicated multicellular crosstalk within the TME as a central driver of ICB resistance, the precise multicellular programs (MCPs) that orchestrate this process remain poorly defined. Here, through integrative single-cell and spatial transcriptomic profiling of clear cell RCC (ccRCC) cohorts, we delineated a previously unrecognized MCP associated with ICB resistance, distinguished by heightened lysosomal activity, adipogenic signaling, and rewired fatty acid metabolism. Within this program, we uncover a coordinated interplay among TAM_APOE, ccRCC_CXCL14, and endothelial cells, whereby ccRCC_CXCL14 recruits TAM_APOE, which subsequently promotes tumor lipid metabolic reprogramming and angiogenesis, forming a pro-tumorigenic feedforward loop. Spatial mapping revealed a malignant gene topic colocalizing with this MCP in tumor cores, which robustly predicted both unfavorable survival and resistance in ICB-treated patients. Functional assays confirmed that the CXCL14-TAM axis promotes metabolic reprogramming, while dual CXCR4 and PD-1 blockade synergistically reverses the resistant phenotype by restoring CD8⁺ T-cell cytotoxicity. Multiplex immunofluorescence further validated the enrichment of this MCP specifically in non-responders. Collectively, our study defines a spatially organized, functionally coordinated multicellular niche that drives ICB resistance in ccRCC, establishing both a predictive biomarker for patient stratification and a mechanistic framework for therapeutic intervention.
Background Small cell lung cancer (SCLC) is an aggressive neuroendocrine malignancy characterized by rapid proliferation, early dissemination, and limited durable benefit from current chemoimmunotherapy. Although immune checkpoint blockade has modestly improved clinical outcomes, the regulatory logic linking malignant cell states to the tumor immune microenvironment remains incompletely understood. Here, we applied an integrative single-nucleus transcriptomic framework to dissect tumor cell heterogeneity, regulatory programs, and immune-stromal communication networks in SCLC. Methods Publicly available Single-nucleus RNA sequencing data from primary and metastatic SCLC samples were analyzed using Seurat-based clustering, inferCNV-based malignant cell identification, differential expression analysis, pathway enrichment, metabolic and stemness scoring, pseudotime trajectory reconstruction, CellChat-mediated cell-cell communication inference, and transcription factor regulatory module analysis. A UBE2C-enriched proliferative tumor cell subpopulation was prioritized for functional validation. siRNA-mediated UBE2C knockdown was performed in DMS114 and NCI-H446 SCLC cell lines, followed by qRT-PCR, CCK-8, colony formation, transwell migration, and Annexin V/PI apoptosis assays. Results Using snRNA-seq, we identified multiple cell types and resolved a UBE2C+ subpopulation with marked proliferative features. UBE2C+ subpopulation displayed strong G2/M-phase enrichment, elevated mitotic and cell cycle programs. And pseudotime analysis positioned C3 UBE2C+ tumor cells at a proliferative state during tumor cell state evolution. Cell-cell communication analysis suggested that this subpopulation might interact with macrophages and fibroblasts through GRN-SORT1 and THBS1-CD47/CD36 signaling axes, indicating a potential link between proliferative tumor states and candidate communication axes. Transcription factor module analysis further revealed enrichment of cell cycle-associated regulators, including MYBL2, NFYB, E2F2, TGIF1, and RXRG, in the C3 subpopulation. Functionally, UBE2C knockdown significantly suppressed proliferation, clonogenic growth, and migration while increasing apoptosis in SCLC cells. Conclusions This study identified UBE2C+ proliferative tumor cells as a functionally relevant malignant subpopulation in SCLC and links this state to immune-stromal communication networks within the tumor microenvironment. By integrating single-nucleus transcriptomics, regulatory network inference, intercellular communication analysis, and in vitro validation, our findings nominate UBE2C as a potential candidate functional regulator and provide a systems-level framework for investigating the cancer-immunity regulome in SCLC.
Hongling Jia, Yongxuan An, Bing Chen et al.· Frontiers in Immunology· 0 citations
Triple-negative breast cancer (TNBC) is an aggressive, heterogeneous form of breast cancer with limited specific therapy options, prevalent metastasis and frequent relapse. Re-analysis of single-cell RNA-sequencing data characterizes the diverse cell subtypes within the tumor and microenvironment of TNBC, supporting a luminal progenitor origin for the cancer and providing clues as to the factors involved in progression of the disease. The relative burdens of these subtypes can be deconvolved from bulk RNA-sequencing data, readily identifying the stem-like, mesenchymal and stromal cell subtypes significantly associated with poor survival and enrichment in metastasis. Importantly, these can be simplified to ten-gene signatures with comparable predictive power, notably in response to different therapeutic strategies, which are linked to relative burdens of different subtypes of stromal fibroblasts. The expression level of these signatures could provide a cheap means for selecting therapy strategies in personalized medicine.
G. Davidson, V. Debien, Tom Sexton· bioRxiv· 0 citations
Colorectal cancer liver metastasis (CRLM) represents the leading cause of mortality in colorectal cancer (CRC). However, the molecular mechanisms enabling metastatic adaptation within the hepatic microenvironment remain unclear. We integrated single-cell RNA sequencing, spatial transcriptomics, and bulk transcriptomic data from CRC patients to characterize the immunometabolic landscape of CRLM. Machine learning models were used to identify key regulators, and functional assays were conducted to validate their biological roles. Nine major cell populations were delineated within CRLM, revealing enrichment of myeloid-derived suppressor cells and depletion of fibroblasts in metastatic lesions. Malignant cells displayed pronounced chromosomal instability and metabolic reprogramming. Among candidate regulators, PIGT emerged as a pivotal node linking metabolic adaptation and immune suppression. PIGT expression increased progressively from primary to metastatic states and was associated with immunosuppressive MIF, SPP1, and TGFβ signaling. Spatial transcriptomics demonstrated colocalization of PIGT-high tumor cells with ITGAM⁺ and CD163⁺ macrophages. Functionally, PIGT knockdown significantly suppressed cell invasion, migration, proliferation, and wound healing in vitro. Conversely, transcriptomic and qPCR analyses showed that PIGT-low tumors exhibited higher expression of inflammatory genes enriched in the IL-17 and TNF signaling pathways. Our integrative multi-omics and experimental analyses identify PIGT as a central regulator bridging tumor metabolism and immune modulation in CRLM. These findings highlight PIGT as a promising prognostic biomarker and potential therapeutic target for metastatic colorectal cancer.
Mengzhu Yan, Yixing Li, Yun Liu et al.· Functional & Integrative Gen...· 1 citation
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, Zhuo-Cheng Ji et al.· Research· 0 citations
