bims-gerecp Biomed News
on Gene regulatory networks of epithelial cell plasticity
Issue of 2025–09–21
sixteen papers selected by
Xiao Qin, University of Oxford



  1. Nat Methods. 2025 Sep;22(9): 1753
      
    DOI:  https://doi.org/10.1038/s41592-025-02838-5
  2. Nat Methods. 2025 Sep;22(9): 1788-1799
      Microbes within tumors have been recognized and experimentally related to oncogenesis, tumor growth, metastasis and therapeutic responsiveness. Studying the tumor microbiome presents difficulties, as early indications suggest that microbe populations are low in abundance, sparse and highly heterogeneous. Disparate results from computational profiling of the tumor microbiome have cast doubt on the premise of microbes in tumors. Yet decades of experimental evidence support the presence of tumor microbes, at least in a limited number of tumor types. In this Perspective, we discuss the importance of iteratively improving microbe-targeted sequencing techniques, established analytical pipelines, robust computational tools and solid validations to address current challenges and fill existing knowledge gaps. The vast amount of human tumor sequencing data available could greatly enhance systematic investigations of microbiome-tumor interactions with methods to quantify the composition of the tumor microbiome accurately.
    DOI:  https://doi.org/10.1038/s41592-025-02807-y
  3. Cancer Cell. 2025 Sep 18. pii: S1535-6108(25)00366-6. [Epub ahead of print]
      Tumor heterogeneity fueled by plasticity of cancer cells is a key to therapy failure. Here, we define the role of proximal communications of malignant cells in glioblastoma plasticity. We find that tumor cell state coherence is maximal in cells organized in homotypic clusters with defined relationships with non-malignant cells, whereas randomly dispersed cells downregulate the original state, acquire alternative phenotypes and exhibit changes in the microenvironment. We demonstrate the intrinsic propensity of glioblastoma cells to develop into clustered and dispersed spatial patterns in orthotopic mouse models and experimentally validate the cell state-specific mechanisms of cell-cell adhesion that prevent phenotype deviation with pharmacologic perturbations in patients-derived glioblastoma models. We establish the generality of "homotypic clustered cell identity" in circulating clustered and single breast cancer cells and show that the glioblastoma glycolytic-plurimetabolic dispersed cellular state uniquely confers shorter survival, thus assigning clinical significance to the spatial patterning of cancer cells in human tumors.
    Keywords:  cancer cell plasticity; glioblastoma; intratumor heterogeneity; single-cell spatial proteomics; single-cell spatial transciptomic; tumor ecosystem
    DOI:  https://doi.org/10.1016/j.ccell.2025.08.009
  4. Cancer Res. 2025 Sep 18.
      The prolyl isomerase PIN1 is overexpressed in cancer and contributes to cancer cell-intrinsic phenotypes including proliferation and migration. However, PIN1 may also function in stromal cells within the tumor microenvironment (TME). Here, we showed that PIN1 is a critical regulator of pancreatic stellate cell (PSC) state at baseline and in response to the myofibroblast activating factor TGF-β. Loss or inhibition of PIN1 altered the epigenetic and transcriptional response of PSCs to TGF-β, preventing PSC differentiation to a myofibroblast state and altering expression of secreted matrix proteins and signaling molecules. Consistent with inhibition of the TGF-β response, low fibroblast PIN1 expression in mouse and human pancreatic ductal adenocarcinoma (PDAC) correlated with low expression of α-SMA, a marker of myofibroblast activation. Decreased PIN1 expression at baseline also altered paracrine HGF signaling from fibroblasts to tumor cells. PSCs with low PIN1 expression displayed reduced expression and secretion of HGF, resulting in an attenuation of c-MET receptor phosphorylation and signaling in nearby cancer cells. In allograft models, host PIN1 was critical for normal growth of a subset of pancreatic cancer cell lines that are responsive to HGF signaling. Through the identification of changes to fibroblast activation state and crosstalk following PIN1 loss or inhibition, these data suggest that systemic targeting of PIN1 will suppress the pro-tumorigenic PDAC microenvironment and may differentially affect heterogeneous patient populations.
    DOI:  https://doi.org/10.1158/0008-5472.CAN-24-3437
  5. bioRxiv. 2025 Sep 08. pii: 2025.09.05.674475. [Epub ahead of print]
      Interactions between genetic variants and environmental factors influence malignancy risk, including for colorectal cancer (CRC). Prevalent CRC susceptibility loci reside predominantly in noncoding regulatory DNA where they may interact with dietary influences to dysregulate expression of specific genes predisposing to neoplasia. The impacts of CRC protective and risk dietary metabolites, butyrate and deoxycholic acid, were thus studied on the transcription-directing activity of 3703 regulatory CRC-associated variants via massively parallel reporter assays (MPRA) in human colonic cells. 1595 variant-dietary metabolite interactions were identified, pointing to dysregulation of MED13L, NKD2, and several modulators of Wnt/β-catenin signaling in potential CRC gene-environment interactions (GxE). Opposing impacts of butyrate and deoxycholic acid were also uncovered, indicating dietary influences may converge on common CRC risk loci and nominating FOSL1 and SP1 as mediators of these opposing responses. Coupling MPRA to relevant environmental factors offers an approach to extend insight into GxE in common human cancers.
    DOI:  https://doi.org/10.1101/2025.09.05.674475
  6. Nat Metab. 2025 Sep 19.
      The consumption of sugar-sweetened beverages (SSBs), which contain high levels of fructose and glucose, has been causally and mechanistically linked to an increased risk of colorectal cancer (CRC). However, the effects of SSB consumption on advanced stages of disease progression, including metastasis, remain poorly understood. Here we show that exposure of CRC cells to a glucose and fructose formulation-reflecting the composition of both high-fructose corn syrup and sucrose found in SSBs-enhances cellular motility and metastatic potential compared to glucose alone. Given that CRC cells grow poorly in fructose alone, and cells in vivo are not physiologically exposed to fructose without glucose, we excluded the fructose-only condition from our studies unless needed as a control. Mechanistically, the combination of glucose and fructose elevates the NAD⁺/NADH ratio by activation of the reverse reaction of sorbitol dehydrogenase in the polyol pathway. This redox shift relieves NAD⁺ limitations and accelerates glycolytic activity, which in turn fuels activation of the mevalonate pathway, ultimately promoting CRC cell motility and metastasis. Our findings highlight the detrimental impact of SSBs on CRC progression and suggest potential dietary and therapeutic strategies to mitigate metastasis in patients with CRC.
    DOI:  https://doi.org/10.1038/s42255-025-01368-w
  7. J Cancer. 2025 ;16(12): 3654-3663
      Cancer prognosis relies not only on genetic and molecular biomarkers but also on the spatial organization of tumor and immune cells within the tumor microenvironment. Recent advances in spatial biology, particularly hyperplex immunofluorescence (IMF) imaging, have enabled high-dimensional, quantitative assessment of cell-cell interactions at the protein level. Nearest neighbor analysis (NNA) and proximity analysis have emerged as crucial computational methods for quantifying spatial distributions of tumor, stromal, and immune cells in hyperplex IMF datasets, providing insights into tumor heterogeneity, immune infiltration, and treatment response. This review explores the current state of nearest neighbor and proximity analysis in cancer research, focusing on their applications in prognosis using single-cell spatial proteomics data generated by hyperplex IMF imaging. We summarize key computational approaches, including nearest neighbor distance metrics, Ripley's K-function, Voronoi tessellation, and graph-based models, that characterize spatial architecture within the tumor microenvironment. We highlight recent applications of hyperplex IMF in cancers showcasing how spatial proteomic signatures improve prognostic models. Furthermore, we discuss the integration of machine learning and AI-driven methods to leverage these spatial features for predictive modeling. Despite significant progress, challenges remain, including standardization of methodologies, variability in imaging technologies, and the need for large-scale, high-quality datasets. Addressing these challenges could lead to more accurate risk stratification and personalized treatment strategies. By providing a comprehensive overview of nearest neighbor and proximity analysis in the context of hyperplex IMF-based spatial proteomics, this review aims to bridge the gap between computational methodologies and clinical applications, offering new perspectives on how spatial organization at the protein level influences cancer prognosis.
    Keywords:  cancer; cancer prognosis; hyperplex IMF-based spatial proteomics; precision oncology; proximity analysis; spatial biology
    DOI:  https://doi.org/10.7150/jca.115037
  8. Nat Commun. 2025 Sep 17. 16(1): 8301
      Deciphering the pre-malignant cell of origin (COO) of different cancers is critical for understanding tumor development and improving diagnostic and therapeutic strategies in oncology. Prior work demonstrates that somatic mutations preferentially accumulate in closed chromatin regions of a cancer's COO. Leveraging this information, we combine 3,669 whole genome sequencing patient samples, 559 single-cell chromatin accessibility cellular profiles, and machine learning to predict the COO of 37 cancer subtypes with high robustness and accuracy, confirming both the known anatomical and cellular origins of numerous cancers, often at cell subset resolution. Importantly, our data-driven approach predicts a basal COO for most small cell lung cancers and a neuroendocrine COO for rare atypical cases. Our study also highlights distinct cellular trajectories during cancer development of different histological subtypes and uncovers an intermediate metaplastic state during tumorigenesis for multiple gastrointestinal cancers, which have important implications for cancer prevention, early detection, and treatment stratification.
    DOI:  https://doi.org/10.1038/s41467-025-63957-3
  9. Nature. 2025 Sep 17.
      Neuroendocrine and tuft cells are rare chemosensory epithelial lineages defined by the expression of ASCL1 and POU2F3 transcription factors, respectively. Neuroendocrine cancers, including small cell lung cancer (SCLC), frequently display tuft-like subsets, a feature linked to poor patient outcomes1-9. The mechanisms driving neuroendocrine-tuft tumour heterogeneity and the origins of tuft-like cancers are unknown. Using multiple genetically engineered animal models of SCLC, we demonstrate that a basal cell of origin (but not the accepted neuroendocrine origin) generates neuroendocrine-tuft-like tumours that highly recapitulate human SCLC. Single-cell clonal analyses of basal-derived SCLC further uncovered unexpected transcriptional states, including an Atoh1+ state, and lineage trajectories underlying neuroendocrine-tuft plasticity. Uniquely in basal cells, the introduction of genetic alterations enriched in human tuft-like SCLC, including high MYC, PTEN loss and ASCL1 suppression, cooperates to promote tuft-like tumours. Transcriptomics of 944 human SCLCs revealed a basal-like subset and a tuft-ionocyte-like state that altogether demonstrate notable conservation between cancer states and normal basal cell injury response mechanisms10-13. Together, these data indicate that the basal cell is a probable origin for SCLC and other neuroendocrine-tuft cancers that can explain neuroendocrine-tuft heterogeneity, offering new insights for targeting lineage plasticity.
    DOI:  https://doi.org/10.1038/s41586-025-09503-z
  10. Br J Cancer. 2025 Sep 15.
       BACKGROUND: Cancer metastasis, primarily driven by epithelial-to-mesenchymal transition (EMT), is responsible for most cancer-related mortalities. Traditional pre-clinical models fail to fully capture mesenchymal characteristics due to the loss of human stroma. The extracellular matrix (ECM) plays a crucial role in EMT, yet conventional in vitro models often rely on defined ECM components, which may not adequately replicate the human physiological ECM niche.
    METHODS: To mimic the in situ dissemination of cancer cells, we employed a patient-derived extracellular matrix (pdECM). We transitioned the culture matrix for patient-derived colorectal cancer organoids from a basement membrane extract (BME) to a patient-derived ECM (pdECM). We performed single-cell multiomic analyses, integrating transcriptomic and epigenomic data, to investigate changes in organoid phenotypes and reconstruct the EMT trajectory.
    RESULTS: Organoids cultured in the pdECM exhibited increased tumor cell dissemination and motility, resembling in situ lesions without exogenous ligand treatment. Single-cell multiomic analysis revealed TNF-α signaling as an early metastatic event in the EMT trajectory. Epigenomic changes led to increased accessibility of AP-1 complex target genes, particularly MMP7, which promoted an invasive phenotype. Our multimodal computational approach distinguished early and late EMT states, demonstrating that pdECM-induced EMT occurs independently of traditional EMT master regulators. Notably, pdECM organoids exhibited a partial EMT phenotype, characterized by hybrid epithelial-mesenchymal states.
    CONCLUSION: This study presents an advanced in vitro model that closely recapitulates in situ tumorigenesis and provides novel insights into the metastatic cascade. The pdECM system enables the reconstruction of EMT dynamics, highlighting the critical role of ECM composition in metastasis and offering a physiologically relevant platform for the development of targeted therapies.
    DOI:  https://doi.org/10.1038/s41416-025-03181-4
  11. Science. 2025 Sep 18. 389(6766): eads6552
      Genes are often activated by enhancers located at large genomic distances, and the importance of this positioning is poorly understood. By relocating promoter-reporter constructs into thousands of alternative positions within a single locus, we dissected the positional relationship between the mouse Sox2 gene and its distal enhancer. This revealed an intricate, sharply confined activation landscape in which the native Sox2 gene occupies an optimal position for its activation. Deletion of the gene relaxes this confinement and broadly increases reporter activity. The confining effect of the Sox2 gene is partially conferred by its ~1-kilobase coding region. Our local relocation approach provides high-resolution functional maps of a genomic locus and reveals that a gene can strongly constrain the realm of influence of its enhancer.
    DOI:  https://doi.org/10.1126/science.ads6552
  12. Med Oncol. 2025 Sep 20. 42(11): 482
      The landscape of oncology is undergoing a paradigm shift, transitioning from conventional cytotoxic therapies to an integrative, intelligence-driven framework that combines precision genomics, immunoengineering, and modulation of the tumor microenvironment (TME). This review explores how cancer, as a complex adaptive system (CAS), evolves through genetic, epigenetic, and microenvironmental interactions, necessitating dynamic, multi-dimensional therapeutic strategies. Review highlights the limitations of mono-targeted therapies and the emergence of synergistic approaches, including AI-guided adaptive dosing, synthetic biology-enhanced CAR-T cells, and metabolic reprogramming of the tumor microenvironment (TME). Breakthroughs in molecular cartography, quantum biology, synthetic oncology, and dark genome mining are expanding therapeutic frontiers. Meanwhile, immuno-engineering innovations-such as next-generation checkpoint modulators, logic-gated CAR-T cells, and neoantigen vaccines-are redefining immune-oncology. Additionally, TME-targeted strategies, including stromal remodeling, hypoxia modulation, and microbiome engineering, are helping to overcome treatment resistance. The convergence of multi-omics profiling, combinatorial therapeutics, and computational oncology (e.g., digital twins) is enabling real-time, personalized interventions. Despite these advances, challenges persist-therapeutic resistance, toxicity, accessibility, and ethical concerns-demanding interdisciplinary collaboration and equitable innovation. The future lies in adaptive, autonomous oncology, integrating AI, closed-loop therapies, and modular mRNA platforms to deliver precision medicine at scale. This review underscores the imperative for a unified, systems-based approach to transform cancer into a manageable condition.
    Keywords:  Computational Oncology; Immuno-Engineering; Precision Genomics; Synthetic Oncology; Tumor Microenvironment (TME)
    DOI:  https://doi.org/10.1007/s12032-025-03042-3
  13. Nat Rev Clin Oncol. 2025 Sep 19.
      T cells can be reprogrammed with transgenic antigen recognition receptors, including chimeric antigen receptors and T cell receptors, to selectively recognize and kill cancer cells. Such adoptive T cell therapies are effective in patients with certain haematological cancers but challenges persist, including primary and secondary resistance, a lack of efficacy in patients with solid tumours, a narrow range of targetable antigens, and time-consuming and complex manufacturing processes. CRISPR-based genome editing is a potent strategy to enhance cellular immunotherapies. Conventional CRISPR-Cas9 systems are useful for gene editing, transgene knock-in or gene knockout but can result in undesired editing outcomes, including translocations and chromosomal truncations. Base editing and prime editing technologies constitute a new generation of CRISPR platforms and enable highly precise and programmable installation of defined nucleotide variants in primary T cells. Owing to their high precision and versatility, base editing and prime editing systems, hereafter collectively referred to as CRISPR 2.0, are advancing to become the new standard for precision-engineering of cellular immunotherapies. CRISPR 2.0 can be used to augment immune cell function, broaden the spectrum of targetable antigens and facilitate streamlined production of T cell therapies. Notably, CRISPR 2.0 is reaching clinical maturity, with multiple clinical trials of CRISPR 2.0-modified cellular therapies currently ongoing. In this Review, we discuss emerging CRISPR 2.0 technologies and their progress towards clinical translation, highlighting challenges and opportunities, and describe strategies for the use of CRISPR 2.0 to advance cellular immunotherapy for haematological malignancies and solid tumours in the future.
    DOI:  https://doi.org/10.1038/s41571-025-01072-4
  14. Nat Methods. 2025 Sep;22(9): 1900-1910
      The increased use of spatially resolved transcriptomics provides new biological insights into disease mechanisms. However, the high cost and complexity of these methods are barriers to broader application. Consequently, methods have been created to predict spot-based gene expression from routinely collected histology images. Recent benchmarking showed that current methodologies have limited accuracy and spatial resolution, constraining translational capacity. Here, we introduce GHIST, a deep learning-based framework that predicts spatial gene expression at single-cell resolution by leveraging subcellular spatial transcriptomics and synergistic relationships between multiple layers of biological information. We validated GHIST using public datasets and The Cancer Genome Atlas data, demonstrating its flexibility across different spatial resolutions and superior performance. Our results underscore the utility of in silico generation of single-cell spatial gene expression measurements and the capacity to enrich existing datasets with a spatially resolved omics modality, paving the way for scalable multi-omics analysis and biomarker identification.
    DOI:  https://doi.org/10.1038/s41592-025-02795-z