Aug 2026· Frontiers in Immunology· Vol 17· 0 citations· 48 references
Medicine
TL;DR
An integrated single-cell atlas defines a critical POSTN+ CAF–APOE+ macrophage unit that is associated with a fibrotic and immunosuppressive TME in advanced prostate cancer, and suggested conserved enrichment and adverse prognostic impact of this stromal-immune axis across diverse tumor types, though tissue-specific context should be considered.
Abstract
Background The progression of prostate cancer to lethal castration-resistant (CRPC) and metastatic (mCRPC) stages is driven by a profoundly remodeled tumor microenvironment (TME). However, the identity of key stromal cell populations, their developmental dynamics, and their precise crosstalk with immune cells remain incompletely understood, limiting our ability to target the TME therapeutically. Methods We integrated single-cell RNA sequencing (scRNA-seq) data from 222,529 cells across 10 studies, encompassing normal prostate, primary tumors, CRPC, and mCRPC. Fibroblast heterogeneity was resolved using unsupervised clustering, trajectory inference (Monocle2), and regulon analysis (pySCENIC). Intercellular communication was deciphered using CellChat. Spatial transcriptomic data were integrated via CellTrek and SpaGene for validation. Clinical associations were evaluated in multiple bulk transcriptomic cohorts (e.g., TCGA-PRAD, IMvigor210) and extended to a pan-cancer atlas of 11 tumor types. Results We identified a distinct POSTN+ CAF subset that was progressively enriched in advanced disease. Trajectory analysis positioned POSTN+ CAFs as a progenitor-like state potentially transitioning toward inflammatory or contractile subtypes, with STAT1-centered regulon activity associated with this process. POSTN+ CAFs created an extracellular matrix (ECM)-remodeled, immune-excluded niche, correlated with elevated T-cell exclusion scores. We further uncovered a predicted communication axis where POSTN+ CAFs are computationally inferred to interact with M2-like, immunoregulatory APOE+ macrophages via the MDK-NCL ligand-receptor pair. The co-occurrence of POSTN+ cancer-associated fibroblasts and APOE+ macrophages correlated with worse patient outcomes. In the IMvigor210 urothelial carcinoma cohort (as indirect cross-cancer evidence), high co-infiltration was associated with diminished anti-PD-L1 response, although this finding requires validation in prostate cancer-specific cohorts. Exploratory pan-cancer analysis suggested conserved enrichment and adverse prognostic impact of this stromal-immune axis across diverse tumor types, though tissue-specific context should be considered. Conclusions Our integrated single-cell atlas defines a critical POSTN+ CAF–APOE+ macrophage unit that is associated with a fibrotic and immunosuppressive TME in advanced prostate cancer. If functionally validated, targeting this stromal-immune crosstalk axis could represent a promising therapeutic strategy to remodel the TME and overcome treatment resistance, although this remains speculative at present.
Cancer‐associated fibroblasts (CAFs) orchestrate immune‐excluded tumor microenvironment (TME), but the CAF heterogeneity remains incompletely understood in gastric cancer (GC). In this study, we integrated multicohort single‐cell RNA sequencing (scRNA‐seq), spatial transcriptomics, and bulk transcriptomic data to construct a comprehensive atlas of the GC TME. Unsupervised clustering identified eight transcriptionally distinct CAF subpopulations, among which CTHRC1+ CAFs were selectively enriched in tumors and showed the strongest association with T cell exclusion. Pseudotemporal trajectory analysis, gene regulatory network inference, and cell–cell communication analysis revealed that basic helix‐loop‐helix family member e41 (BHLHE41) serves as a key transcription factor driving CTHRC1+ CAF differentiation, whereas spatial analyses demonstrated these fibroblasts contribute to fibrotic niches at the tumor–stroma interface through macrophage migration inhibitory factor (MIF)–mediated signaling. Finally, we developed and validated a CTHRC1+ cancer‐associated fibroblast–related risk signature (CRS) that accurately predicts immunotherapy response across independent cohorts. These findings establish CTHRC1+ CAFs as a critical stromal determinant of immune exclusion in GC, suggesting that targeting the CTHRC1+ CAF‐MIF axis or applying CRS‐guided patient stratification may enhance immunotherapy efficacy.
Yingxin Wu, Ling-han Tang, Ping Li et al.· Human Mutation· 0 citations
Background Colon cancer (CC) remains a leading cause of cancer‐related mortality worldwide, driven largely by the complex interactions within the tumor microenvironment (TME). Fibroblast activation protein (FAP) is highly expressed in cancer‐associated fibroblasts (CAFs) and is associated with poor prognosis, yet its role in coordinating immune evasion and cancer stemness remains to be fully elucidated. Methods We integrated multiomics data from TCGA and GEO databases, utilizing bulk RNA‐seq and single‐cell RNA‐seq (scRNA‐seq) analyses. Findings were validated via tissue microarray (TMA) immunohistochemistry (IHC). We further employed cell–cell communication analysis, pseudotime trajectory modeling, and the Connectivity Map (CMap) for drug sensitivity prediction and molecular docking. Results FAP was significantly upregulated in CC tissues and correlated with advanced clinical stages. scRNA‐seq confirmed that FAP is predominantly expressed in CAFs. Functional analysis revealed that FAP‐high tumors are enriched in extracellular matrix (ECM) remodeling and immunosuppressive pathways. Cell–cell communication analysis identified that FAP+ CAFs interact with T cells and cancer stem cells (CSCs) primarily through the COL1A1/2‐CD44 axis. Specifically, FAP+ CAFs promote the differentiation of naive T cells into regulatory T cells (Tregs) and are positively correlated with various stemness markers, including CD44, ABCG2, and BMI1. Based on these findings, we established a 14‐gene prognostic risk model with robust predictive accuracy (area under the curve [AUC] > 0.64) and identified AS604850 and LY364947 as potential therapeutic agents. Conclusion Our study demonstrates that FAP+ CAFs orchestrate a dual‐functional “immunosuppressive stem cell niche” via the COL1A1/2‐CD44 signaling axis. Targeting this FAP‐driven niche provides a promising strategy for overcoming immunotherapy resistance and improving clinical outcomes in CC.
BACKGROUND
Although PD-1/PD-L1 inhibitors are central to the management of advanced bladder cancer, most patients fail to achieve a meaningful response. While evidence ties MMT to fibrotic disease, its contribution to bladder cancer has yet to be examined.
METHODS
We assembled and analysed several complementary data modalities-bulk transcriptomes from TCGA-BLCA (n = 408 tumour, 19 normal) and incorporated single-cell RNA-seq, spatial transcriptomics (nine sections), and two independent immunotherapy cohorts (Kim 2019, n = 348; IMvigor210, n = 298)-to characterize MMT cells and construct an 18-gene MMT signature. Through spatial pseudotime analysis, in vitro overexpression, virtual knockout, FIMO motif scanning, and in vivo tumour models, we identified KLF6 as the key MMT driver. Virtual screening (L1000CDS2) and molecular docking (CB-Dock2) were performed to nominate drugs targeting the KLF6-MMT axis.
RESULTS
MMT cells were present in bladder cancer, and the MMT signature was strongly associated with immunotherapy resistance (P = 0.037 for overall survival) and poor prognosis. KLF6 emerged as the key transcriptional driver of MMT, directly binding the ACTA2 proximal promoter. KLF6 overexpression promoted MMT, tumour growth, and PD-L1 upregulation in vivo (P < 0.05 for tumour weight, P < 0.01 for tumour volume), whereas virtual knockout suppressed core MMT effector genes. Spatial analysis revealed enhanced CD274 (PD-L1) expression by MMT cells, which may contribute to immune evasion through engagement of PDCD1 (PD-1) on tumour-infiltrating T cells (P < 0.001). Among the candidates identified by virtual screening, the cardiac glycoside Periplocymarin ranked first (overlap score = 0.375). Docking placed it in the KLF6 C3 pocket-the DNA-binding cleft-with an affinity of -6.5 kcal/mol, a pose consistent with competitive inhibition.
CONCLUSIONS
This study provides the first multi-omics characterization of MMT in bladder cancer, identifies KLF6 as a previously unrecognized driver of this transition, and demonstrates that KLF6-driven MMT upregulates tumour PD-L1 through intercellular crosstalk. Furthermore, virtual screening and molecular docking identify Periplocymarin as a candidate compound targeting the KLF6-MMT axis. Our work thus connects KLF6-driven MMT to PD-L1-mediated immune evasion and suggests that disrupting this programme with Periplocymarin may provide a strategy to overcome immunotherapy resistance.
Yuwen Chen, Zi-Huan Wang, Cheng-Wu He et al.· International Immunopharmaco...· 0 citations
Background: Human epidermal growth factor receptor 2 (HER2)-positive breast cancer exhibits high metastatic potential, linked not only to intrinsic cancer cell traits but also to critical crosstalk with the tumor microenvironment. However, the coevolutionary mechanisms between cancer cells and multiple stromal subpopulations in driving distant metastasis remain poorly understood. Therefore, this study aimed to explore the microenvironmental regulatory mechanisms of breast tumor-initiating cells and their roles in HER2-positive breast cancer metastasis. Methods: Integrated multi-omics analyses (spatial transcriptomics, metabolomics, spatial in situ analysis, and proteomics) were used to identify novel cell subpopulations and their interactions. High-throughput sequencing of exosomal microRNAs (miRNAs) and single-nucleus RNA from the same tissue was performed to explore the molecular mechanisms underlying cell crosstalk. In vitro experiments were conducted to verify the interaction between stromal cells and prominin 1 (PROM1)+ SMAD family member 5 (SMAD5)+ cells. In vivo murine breast cancer models were established to confirm the role of stromal subpopulations in pulmonary metastasis, and parabiosis assays were carried out to compare key cell subpopulations between tumor-bearing mice and normal mice. Clinical samples were analyzed to correlate key cell subpopulations with clinicopathological features and prognosis. Results: A breast tumor-initiating subpopulation, PROM1+ SMAD5+ cells, and its interactions with stromal cells, specifically adiponectin (ADIPOQ)+ notch receptor 4 (NOTCH4)+ adipocytes and decorin (DCN)+ transmembrane 4 L six family member 1 (TM4SF1)+ fibroblasts, were identified by integrated multi-omics analyses. Mechanistically, these 2 stromal subpopulations delivered functional miRNAs and mediated coatomer protein complex subunit alpha (COPA)-dependent epidermal growth factor receptor (EGFR) activation in PROM1+SMAD5+ cells, thereby triggering the EGFR–SMAD5–cytochrome P450 family 3 subfamily A member 4 (CYP3A4) axis to induce partial epithelial–mesenchymal transition (pEMT) and metastasis. Additionally, stroma-secreted exosomal miR-671-3p down-regulated Claudin1 in PROM1+SMAD5+ cells, promoting their evolution into PROM1+SMAD5+Claudin1− subpopulations with enhanced stemness and metastatic potential. In vivo experiments confirmed that the 2 stromal subpopulations markedly promoted pulmonary metastasis, and the 3 identified subpopulations preferentially accumulated in the primary tumors, lymph nodes, and pulmonary metastatic lesions of tumor-bearing mice. Clinically, these 3 subpopulations form a “trinity niche”, whose aggregation associated with HER2 positivity, high malignancy, and lymph node/pulmonary metastasis, and predicted poor prognosis. Conclusion: This study clarified the microenvironmental regulation of breast tumor-initiating cells and provided new insights into precision therapy.
Huijing Yin, Wei Wang, Jing Ge et al.· Cancer Communications· 0 citations
Colorectal cancer (CRC) exhibits marked cellular heterogeneity, and the cellular context of malignancy-associated epithelial programs remains incompletely defined. We integrated 2,993 CRC samples spanning bulk RNA-seq (n = 2,568; two OS/RFS cohorts), scRNA-seq (281,961 cells/152 specimens), spatial transcriptomics (n = 6), and proteomics (n = 267). Analyses included single-cell integration/annotation, GSVA/HALLMARK, interactome, pseudotime, and ligand–receptor mapping; functional CRISPR assays, EMT immunoblotting, and xenografts; TF profiling (SCENIC/JASPAR/ChIP-qPCR); and exploratory drug-response prediction (OncoPredict), cell-sensitivity assays, and docking/MD modeling. We constructed a stage-stratified single-cell atlas and resolved eleven malignant epithelial subsets, characterizing Epi_4 as late-stage–enriched with EMT, hypoxia, and inflammatory programs and adverse OS/RFS. GPRC5A marked this subset, which we define as GPRC5A+Epi; its expression rose from stage I→IV and was associated with poor outcomes across cohorts, with concordant spatial/proteomic observations. GPRC5A perturbation affected CRC proliferation, migration/invasion, EMT, and xenograft tumorigenicity, supporting a functionally important role in the tested models. SCENIC and ChIP-qPCR supported FOSL1 as an upstream regulator that occupies the GPRC5A promoter. Spatial and ligand–receptor analyses predicted close association and potentially reciprocal signaling between GPRC5A+Epi and POSTN+fibroblasts (COL1A1–SDC4, COL1A1/1A2–ITGA2/ITGB1, PPIA–BSG); concurrent high GPRC5A+Epi/POSTN+Fib signatures were associated with inferior OS/RFS. Drug-response analyses identified an association between GPRC5A status and trametinib sensitivity. Docking/MD produced a computational model of a possible trametinib–GPRC5A interaction, which remains experimentally unvalidated. GPRC5A⁺Epi is a malignancy-associated epithelial state in CRC, and GPRC5A is functionally important for malignant phenotypes in the tested models. Its inferred relationships with POSTN⁺ fibroblasts and the trametinib findings should be regarded as hypothesis-generating pending functional crosstalk, direct-binding, and therapeutic validation.
Wei-Chun Tang, Peng-Chen Xu, Sheng-Li Wang et al.· Journal of Translational Med...· 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.
