A unified spatial-molecular atlas of DCIS-IBC progression is established, highlighting clonal expansion, transcriptional plasticity and TME remodeling as key drivers of invasion.
Abstract
The progression from ductal carcinoma in situ (DCIS) to invasive breast carcinoma (IBC) critically determines patient outcomes, yet its mechanisms remain incompletely understood. Integrating single-cell RNA sequencing, spatial transcriptomics, and genomics across 28 patients with synchronous DCIS and IBC, we delineate the spatial-molecular hierarchy of this transition. Invasion is primarily driven by clonal expansion of pre-existing DCIS subclones, emphasizing transcriptional reprogramming and tumor microenvironment (TME) remodeling over acquisition of additional driver alterations. IBC cells exhibit pronounced epithelial-mesenchymal transition and metabolic reprogramming. We uncover dynamic TME remodeling at the invasive front, identifying key ligand–receptor interactions (e.g., PPIA-BSG, MDK-LRP1, CXCL12-CXCR4) facilitating basement membrane disruption, angiogenesis and immunosuppression. Deconvolution of basement membrane breach reveals four molecularly defined stages (NMFT1–NMFT4) with progressively worsening patient survival. This study establishes a unified spatial-molecular atlas of DCIS-IBC progression, highlighting clonal expansion, transcriptional plasticity and TME remodeling as key drivers of invasion. The progression from ductal carcinoma in situ (DCIS) to invasive breast carcinoma (IBC) is not fully understood yet. Here, the authors integrate single-cell RNA-seq, spatial transcriptomics, and genomics data from patients with synchronous DCIS and IBC; they find clonal expansion, transcriptional plasticity, and tumour microenvironment remodelling as key drivers of DCIS-IBC progression.
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.
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
Background: Prostate cancer (PCa) exhibits strong multidimensional heterogeneity. The dynamic evolution of Luminal subsets and their crosstalk with the tumor microenvironment (TME) during malignant progression remain poorly understood. Conventional single-cell transcriptomics lacks spatial context, while low-resolution spatial technologies cannot resolve single-cell and subcellular interactions. This study aimed to map a high-resolution spatial transcriptomic atlas to characterize Luminal subset heterogeneity and stromal crosstalk across progressive PCa lesions. Methods: We used high-resolution CosMx spatial molecular imaging (SMI) to profile 6 treatment-naive PCa patients and constructed a single-cell spatial transcriptomic atlas covering 385 fields of view and 154,168 high-quality cells. Unsupervised clustering, functional enrichment, cell–cell communication analysis, and flow cytometry were performed. Results: We identified 28 cell clusters, including 8 Luminal subsets (0–7) and 9 Fibroblast subsets (0–8). Pathological microregion-specific spatial distribution was observed: Luminal 0–2 dominated in BPH/PIN, while Luminal 3–7 were enriched in poorly differentiated PCa and vacuolated adenocarcinoma. These subsets were functionally linked to androgen resistance, EMT, and immune regulation. COLLAGEN, FN1, and LAMININ were identified as key pathways mediating pathological-specific tumor–stromal crosstalk. Flow cytometry verified T-cell exhaustion and immunosuppression in the TME. Conclusions: This study delineated pathological microregion-specific Luminal subset plasticity and dynamic epithelial–stromal communication across the full spectrum of PCa lesions. The uncovered molecular signatures offered mechanistic clues linking EMT, hormone resistance, and local immune status during lesion evolution. Our spatial atlas provided preliminary molecular evidence to support pathological stratification and targeted precision therapeutic strategies for PCa.
Recent discoveries from single-cell and spatial analyses are summarized, their implications for biomarker development and treatment stratification are discussed, and ongoing technical challenges are outlined, including standardization, reproducibility, and clinical scalability.
R. Watanabe, T. Chu, N. Miura et al.· American journal of clinical...· 2 citations
Breast cancer is a heterogeneous disease in which a single oncogenic driver can give rise to divergent tumor phenotypes. How oncogenic mutations generate epithelial state plasticity and coordinately remodel the surrounding tissue remains incompletely understood. Here, we applied longitudinal single cell RNA-sequencing to trace the mammary landscape during Pik3caH1047R-driven tumor progression in the mouse. We identify an expansion of the epithelial transcriptional state space, in which luminal cells lose lineage fidelity and activate ciliated, basal, and squamous-like gene expression programs. While oncogene-expressing cells lose features of luminal identity, they retain expression of hormone-sensing genes such as Esr1, Pgr, and Foxa1. These transcriptional states are established early, and the transition to overt tumors is marked by the emergence of cancer-associated fibroblasts rather than new epithelial states. We identify a Postn+ fibroblast population enriched at the epithelial interface as a candidate progenitor of cancer-associated fibroblasts. Postn+ fibroblasts express an ECM-remodeling program and display altered epithelial crosstalk in oncogenic glands. Altogether, Pik3caH1047R activation initiates a tissue-level process beginning with epithelial lineage infidelity, followed by an altered stromal microenvironment, which together mark tumor initiation.
Jennifer T. Le, Eun K. Kim, Vasudha Srivastava et al.· bioRxiv· 0 citations