Integrated single-cell and spatial transcriptomic profiling decodes lineage plasticity and immune microenvironment remodeling in prostate cancer progression

Abstract

This study presents a comprehensive single-cell and spatial transcriptomic atlas of prostate cancer progression, integrating 127 single-cell RNA sequencing samples and 9 spatial transcriptomics profiles spanning the disease continuum from healthy prostate to neuroendocrine carcinoma. Our analysis defines four evolutionarily connected malignant epithelial subtypes: luminal-identity (sub1), stress-adaptive luminal (sub2), neuroendocrine (sub3), and a double-negative basal-like state (sub4). We identify FOSL1 as a key driver of lineage plasticity through direct transcriptional regulation of HMGA1, promoting treatment resistance via enhanced proliferation, EMT and stemness. The tumor microenvironment undergoes coordinated reprogramming during progression, with neoadjuvant hormone therapy inducing distinct cellular responses: FOLR2 + and CX3CR1 + TAMs upregulate TGF-β signaling to establish immunosuppressive niches, while CXCL12 + iCAFs and ACTA2 + myCAFs maintain spatial co-localization and facilitate immune cell recruitment. Spatial analyses reveal enhanced chemokine signaling post-therapy, particularly in specific TAM subsets, driving increased but functionally impaired lymphoid infiltration characterized by T-cell exhaustion and regulatory T-cell expansion. This integrated analysis establishes a unified paradigm connecting epithelial plasticity with microenvironmental reprogramming, revealing FOSL1-HMGA1 signaling and macrophage-driven immunosuppression as promising therapeutic targets for advanced prostate cancer.

Graphical Abstract:

Single-Cell Atlas of Lineage Plasticity and Immunosuppressive Niche Remodeling in Advanced Prostate Cancer. Based on our study which systematically reveals the mechanisms of lineage plasticity and immune microenvironment remodeling in prostate cancer, we have constructed an integrated progression model (Graphical Abstract). The model proposes that under therapeutic pressure (e.g., ADT/NHT), luminal adenocarcinoma (Subtype 1) can differentiate into either a neuroendocrine phenotype (NEPC, Subtype 3) or a double-negative prostate cancer (DNPC, Subtype 4) through distinct paths. During DNPC progression, the key transcription factor FOSL1 drives tumor cell stemness/EMT maintenance and enhanced proliferation and survival by directly activating HMGA1 transcription (A). Concurrently, the tumor microenvironment undergoes significant remodeling, marked by the enrichment of stromal and immune cell subsets such as CXCL12⁺ iCAFs, ACTA2⁺ myCAFs, and FOLR2⁺/CX3CR1⁺ TAMs, forming an active intercellular network (B). This remodeling ultimately fosters an immunosuppressive niche, where signals like TGF-β mediate the functional exhaustion of CD8⁺ T cells, thereby promoting tumor immune evasion and disease progression (C). Our study elucidates, at single-cell resolution, the cell-intrinsic drivers and microenvironmental synergies underlying prostate cancer malignant evolution, providing a novel theoretical foundation for combination therapeutic strategies targeting lineage plasticity and the immunosuppressive microenvironment

Supplementary Information: The online version contains supplementary material available at 10.1186/s12943-026-02617-6.

Keywords: Lineage plasticity; Prostate cancer; Single-cell RNA sequencing; Spatial transcriptomics; Treatment resistance; Tumor microenvironment.