Longitudinal single cell RNA-sequencing of Pik3caH1047R-driven mammary tumorigenesis reveals coordinated transformation of epithelial and fibroblast transcriptional states

Single-cell transcriptomic analysis of cutaneous squamous cell carcinoma identifies an NR1H3-associated angiogenic macrophage state

Introduction Cutaneous squamous cell carcinoma (cSCC) is a common keratinocyte-derived malignancy whose progression is strongly influenced by the tumor microenvironment. Although recent studies have begun to describe cellular diversity in squamous cell carcinomas, the regulatory architecture coordinating epithelial, immune, and stromal interactions in cSCC remains incompletely understood. Methods We performed single-cell RNA sequencing on matched tumor tissues, adjacent normal skin, and peripheral blood from patients with cSCC to construct an integrated cellular landscape of the tumor ecosystem. Lineage trajectory analysis, transcription factor activity inference, and ligand–receptor modeling were used to characterize cellular differentiation, regulatory programs, and intercellular communication within the cSCC microenvironment. Results Analysis of 80,736 single cells revealed extensive heterogeneity across epithelial, immune, and stromal compartments. Trajectory analysis of the myeloid lineage suggested a tumor-associated differentiation continuum extending from circulating monocytes toward a specialized angiogenic macrophage state characterized by transcriptional programs associated with extracellular matrix remodeling and immunoregulatory signaling. Concurrently, malignant keratinocyte populations displayed inferred copy-number alterations and activation of invasive transcriptional programs, accompanied by the emergence of distinct cancer-associated fibroblast subsets associated with stromal remodeling. Ligand–receptor modeling further identified extensive predicted communication networks linking macrophages, fibroblasts, and malignant epithelial cells within the tumor niche. Furthermore, transcription factor activity inference highlighted the nuclear receptor NR1H3 as a candidate regulator associated with the angiogenic macrophage program, and the NR1H3-associated transcriptional signature correlated with poor survival across multiple squamous cell carcinoma cohorts. Discussion These findings define the cellular organization and molecular programs that shape the cSCC microenvironment and provide insights into the coordinated immune, stromal, and epithelial interactions involved in cSCC progression.

Single-cell profiling identifies STAT3/NF-κB regulatory hubs and cytokine crosstalk in the tumor microenvironment

Integrative single-cell RNA sequencing analysis of publicly available datasets from non-small cell lung cancer and breast cancer is performed to systematically map transcriptional heterogeneity and regulatory networks within the TME, providing a systems-level framework of TME organization.

Evolutionarily conserved epigenetic regulation of transcriptional cell states during vertebrate pancreatic tumorigenesis.

These findings suggest a highly conserved role for HDAC9 and class IIA HDACs in vertebrate pancreatic tumorigenesis and may lead to new strategies for reactivating (normal acinar/epithelial) differentiation programs to intercept and treat PDAC.

Pan-cancer single-cell analysis identifies a FOXF1/FOXF2-associated transitional CAF-like fibroblast state

Fibroblast heterogeneity shapes tumor progression, yet the transitional states linking normal-associated fibroblasts to cancer-associated fibroblasts (CAFs) remain poorly defined. Here, we integrated single-cell transcriptomic profiles of more than 90,000 stromal cells from 281 samples across nine cancer types to construct a pan-cancer atlas of fibroblast diversity. We identified a distinct CAF-like population positioned between normal-activated fibroblasts and established CAF subsets along the inferred fibroblast activation trajectory. Integration with single-nucleus chromatin accessibility data nominated FOXF1 and FOXF2 as candidate regulators of this CAF-like state. Functionally, CAF-like fibroblasts were characterized by non-canonical WNT activity, WNT5A-associated stromal communication, and a candidate GZMA–F2R/PAR immune–stromal signaling axis supported by spatial transcriptomics. Clinically, the CAF-like signature showed context-dependent prognostic relevance, with high expression associated with poorer survival in the tumor compartment of TCGA stomach adenocarcinoma. Together, this study defines a FOXF1/FOXF2-associated CAF-like transitional fibroblast state and links it to stromal signaling, immune–stromal communication, and cancer-type-specific clinical relevance.

Germline BRCA1 Mutation Deregulates Irradiation–Induced Cell Cycle Checkpoints in Human Mammary Luminal Progenitors

Single cell multiomics unravel the transcription networks controlling the different EMT tumor states

Epithelial-to-mesenchymal transition (EMT) is a dynamic process during which cells lose their epithelial characteristics and acquire mesenchymal traits. In cancer, EMT is closely associated with tumor initiation, progression, invasion, metastasis, and therapy resistance. Rather than being a binary state switch, EMT encompasses a spectrum of tumor states with distinct functional properties. However, the transcription factors (TFs) that govern transitions between these EMT states remain poorly defined. Here, using multi-omic approaches combining single-cell RNA-seq and single-cell ATAC-seq, we delineate the transcriptomic and chromatin landscapes of distinct EMT states in a mouse model of skin squamous cell carcinoma (SCC). Through CRISPR/Cas9-mediated loss-of-function studies coupled with in vitro and in vivo functional assays, we identify TFs regulating specific EMT states. Klf5 and Pitx1 control the early stages of EMT and are essential for metastasis formation. In contrast, Nfatc1 and Creb3l1 act at later stages of EMT. Similar EMT states and regulatory patterns are found in mouse pancreatic adenocarcinoma and human cancers. Altogether, our study defines the transcriptional and chromatin landscape controlling EMT progression in mouse skin SCC, identifies EMT state-specific TFs and highlights their essential roles in regulating metastasis. Epithelial-to-mesenchymal transition (EMT) involves cancer cells shifting between different states linked to tumor progression. Here, the authors use single-cell multiomics and CRISPR/Cas9-mediated loss-of-function studies to identify key transcription factors controlling EMT states and metastasis.