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

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.

Emerging roles of ATR beyond DNA damage repair: orchestrating transcriptional reprogramming during epithelial-to-mesenchymal transition

The ability of cancer cells to transition between epithelial and mesenchymal states, a process known as epithelial-to-mesenchymal transition (EMT), is a key driver of cancer metastasis and therapy resistance. While ataxia telangiectasia and Rad3-related (ATR) kinase was originally characterized as a responder to DNA damage and replication stress, recent discoveries implicate a critical role for ATR in EMT and metastasis. Two pivotal studies published in this issue of JCI provide key insights into how ATR intersects with EMT transcriptional reprogramming. Patel et al. demonstrated that ATR prevented R-loop accumulation at EMT-related gene loci, thereby facilitating the transcriptional reprogramming necessary for EMT as well as tumor growth and metastasis. Tu et al. further uncovered a role for ATR in ECM stiffness–induced EMT, which was associated with an immunosuppressive tumor microenvironment. Together, these studies highlight important therapeutic implications for ATR targeting in the context of metastasis and therapy resistance.

Unraveling the epigenetic code in cancer cell–tumor microenvironment crosstalk

Epigenetics plays a central role in cancer development and progression by governing the expression of genes involved in these processes. Accumulating evidence strongly indicates that these mechanisms not only alter cancer cell‐intrinsic properties but also mediate reciprocal interactions between cancer cells and the tumor microenvironment (TME). In the context of cancer cell‐intrinsic changes, epigenetic alterations contribute to cancer cell plasticity by regulating stemness, cell state transitions, and therapy resistance. In addition, epigenetic changes are a key driver of the establishment of a tumor‐supportive environment by modifying the states of TME components, including fibroblasts, macrophages, and myeloid‐derived suppressor cells. Epigenetic reprogramming in cancer cells and TME components is often induced by factors such as hypoxia and the secretion of exosomal long noncoding RNAs (lncRNAs), cytokines, and metabolites. In this review, we discuss various epigenetic mechanisms controlling cancer cell‐intrinsic states, cancer cell–TME crosstalk, current epigenetic therapies, and future research directions that may lead to the discovery of new biomarkers and the development of effective epigenetic anticancer therapeutics.

TNIK maintains a MYC-driven partial EMT state that supports proliferation and evasion of senescence in lung squamous cell carcinoma

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

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.

Single-Cell Transcriptome Analysis Reveals IRF1-Driven Epithelial States and Glycosaminoglycan–Glycolysis Coupling in Cisplatin-Resistant HGSOC

Objectives Cisplatin resistance is the principal cause of relapse in high-grade serous ovarian cancer (HGSOC), but bulk-expression signatures cannot localize resistant malignant states or the tumor–microenvironment (TME) interactions that sustain them. This study aimed to define cisplatin-resistant epithelial cell states and their regulatory and metabolic circuits by integrating multi-cohort single-cell transcriptomes with pharmacogenomic and clinical data. Methods We assembled 159,419 cells from 32 HGSOC tumors across six public single-cell RNA-sequencing cohorts and performed harmonized integration, clustering, and lineage annotation. Cisplatin response was mapped to single cells by coupling scRNA-seq data to Genomics of Drug Sensitivity in Cancer predicted cisplatin response score values using Scissor, with AUCell-based validation. We then applied receptor–ligand–based cell–cell communication analysis (CellChat), transcription-factor (TF) activity inference (SCENIC and NetAct with TRRUST), pseudotime trajectory reconstruction (Monocle3), and pathway-level metabolic scoring. Associations with drug sensitivity and patient outcome were evaluated in ovarian cancer cell lines and The Cancer Genome Atlas (TCGA) HGSOC cohort. Results Among 34 epithelial subclusters, 14 were significantly enriched for a cisplatin-resistant phenotype and collectively accounted for most predicted resistant cells. These states were transcriptionally characterized by stress, interferon, and apoptotic programs and formed dense communication hubs with endothelial cells, fibroblasts, myeloid cells, and T/NK cells via extracellular-matrix and adhesion pathways (for example, LAMA3–CD44, COL6A1/2–CD44, NECTIN3–NECTIN2, and CD99–CD99 interactions). TF-activity modeling converged on an IRF1-centered regulatory program that increased along an epithelial trajectory and coordinated inflammatory and apoptotic gene expression. Metabolically, resistance-enriched epithelial states showed selective up-regulation of glycosaminoglycan biosynthesis, particularly keratan sulfate, coupled to heightened glycolysis; glycolytic activity correlated with predicted cisplatin response score in cell lines and an IRF1/STAT1 readout (GBP3) stratified survival in TCGA HGSOC. Conclusion Cisplatin resistance in HGSOC is encoded in discrete IRF1-driven epithelial states that are supported by specific TME communication networks and a glycosaminoglycan–glycolysis metabolic axis. This integrative single-cell informatics framework yields testable biomarkers and therapeutic targets for overcoming platinum resistance in ovarian cancer.