bims-gerecp Biomed News
on Gene regulatory networks of epithelial cell plasticity
Issue of 2026–01–18
24 papers selected by
Xiao Qin, University of Oxford



  1. Nat Rev Cancer. 2026 Jan 12.
      Since 2022, artificial intelligence (AI) methods have progressed far beyond their established capabilities of data classification and prediction. Large language models (LLMs) can perform logical reasoning, enabling them to plan and orchestrate complex workflows. By using this planning ability and equipped with the ability to act upon their environment, LLMs can function as agents. Agents are (semi-)autonomous systems capable of sensing, learning and acting upon their environments. As such, they can interact with external knowledge or external software and can execute sequences of tasks with minimal or no human input. In cancer research and oncology, evidence for the capability of AI agents is rapidly emerging. From autonomously optimizing drug design and development to proposing therapeutic strategies for clinical cases, AI agents can handle complex, multistep problems that were not addressable by previous generations of AI systems. Despite rapid developments, many translational and clinical cancer researchers still lack clarity regarding the precise capabilities, limitations, and ethical or regulatory frameworks associated with AI agents. Here we provide a primer on AI agents for cancer researchers and oncologists. We illustrate how this technology is set apart from and goes beyond traditional AI systems. We discuss existing and emerging applications in cancer research and address real-world challenges from the perspective of academic, clinical and industrial research.
    DOI:  https://doi.org/10.1038/s41568-025-00900-0
  2. Science. 2026 Jan 15. eadz9353
      Understanding how cells make decisions over time requires the ability to link past molecular states to future phenotypic outcomes. We present TimeVault, a genetically encoded system that records and stores transcriptomes within living mammalian cells for future readout. TimeVault leverages engineered vault particles that capture mRNA through poly(A) binding protein. We demonstrate that the transcriptome stored by TimeVaults is stable in living cells for over 7 days. TimeVault enables high-fidelity transcriptome-wide recording with minimal cellular perturbation, capturing transient stress responses and revealing gene expression changes underlying drug-naive persister states in lung cancer cells that evade EGFR inhibition. By linking past and present cellular states, TimeVault provides a powerful tool for decoding how cells respond to stress, make fate decisions, and resist therapy.
    DOI:  https://doi.org/10.1126/science.adz9353
  3. Nat Rev Cancer. 2026 Jan 16.
      A fibroinflammatory microenvironment coevolves with many tumour types and profoundly influences disease progression and response to therapy. Pancreatic cancer is the archetype of a fibroinflammatory tumour, with non-malignant stromal elements comprising the volumetric majority of the tumour tissue. A convergence of three factors - technological advances enabling deep understanding of heterocellular crosstalk in these complex tumours; therapeutic advances revealing meaningful vulnerabilities in this notoriously chemoresistant, immunosuppressive disease; and conceptual advances towards distilling the conserved features and key functions of stromal elements amid this complexity - has positioned the field in a promising era for discovery, wherein our ever-improving understanding of the pancreatic tumour microenvironment is poised for translational impact. Emerging pan-cancer analyses highlight features of tumour microenvironments conserved not only among pancreatic cancer specimens but also across anatomic sites, such that lessons learnt about the organization of tumour tissue architecture and the role of oncogenic KRAS signalling in this process in other tumours have shaped our understanding of heterocellular dependencies in pancreatic cancer and vice versa. Here, we review recent developments sculpting our current understanding of the diverse features of the pancreatic tumour microenvironment and emerging means to leverage these developments for the benefit of patients with pancreatic cancer.
    DOI:  https://doi.org/10.1038/s41568-025-00905-9
  4. Cancer Discov. 2026 Jan 12. 16(1): 16-34
      The risks and health consequences of cancers increase dramatically at older ages. To develop interventions to limit the impact of cancers, from preventative to therapeutic, we must seek both evolutionary and proximate explanations for this age-dependence. Here, we discuss how natural selection has erected barriers to delay malignancy and maximize reproductive fitness. Each barrier need not be perfect, as long as malignant progression is delayed till older ages. With aging, mechanisms ranging from epigenetic deregulation to inflammation to senescence to mutation-driven clonal expansions contribute to increased cancer pathogenesis through mutually enhancing mechanisms, creating tissue contexts more favorable for malignant evolution.
    SIGNIFICANCE: Better understanding of the multiple barriers that we have evolved to limit cancer development and how they can fail at older ages could enable the development of preventative and therapeutic interventions that boost these tumor-suppressive mechanisms.
    DOI:  https://doi.org/10.1158/2159-8290.CD-25-0779
  5. bioRxiv. 2026 Jan 09. pii: 2026.01.08.698516. [Epub ahead of print]
      Immune dysfunction in cancer is enacted by multiple programs, including tumor cell-intrinsic responses to distinct immune subpopulations. A subset of these immune evasion programs can be systematically recapitulated through direct tumor-immune interactions in vitro . Here, we present an integrated, high-throughput single-cell CRISPR screening framework focused on the protein kinome for mapping the tumor-intrinsic regulation of T cell-driven immune pressure in glioblastoma (GBM). We combine pooled CRISPR interference and activation (CRISPRi/a) with immune-matched NY-ESO-1 antigen-specific allogeneic GBM-T cell co-culture and massively multiplexed single-cell transcriptomics to systematically quantify how genetic perturbation reshapes baseline tumor state and adaptive responses across graded effector-to-target ratios. We further leverage deep generative models for analyzing pooled CRISPR screens to decipher the effects of genetic perturbations on the mechanisms of tumor resistance. This framework resolves distinct modules of immune evasion and survival, including the regulation of the antigen-presentation machinery, interferon/NF-κB signaling, oxidative stress resilience, and checkpoint/cytokine programs, while identifying perturbations that reroute the continuous tumor transcriptional trajectory induced by T cell engagement. A secondary chemical screen in patient-derived GBM cultures identified putative kinase targets of immune evasion phenotypes (e.g., EPHA2 and PDGFRA), whose inhibition leads to the blockade of evasive programs and enhances T cell-mediated GBM killing. Together, this workflow provides a scalable blueprint for comprehensive charting of the genetic control of tumor-immune interactions.
    DOI:  https://doi.org/10.64898/2026.01.08.698516
  6. Nat Cancer. 2026 Jan 16.
      The concept of cellular neighborhoods, defined as recurring structures within the tissue with characteristic cell compositions and interactions, has transformed our understanding of the complexity and dynamics of tumor ecosystems. Recent advances in spatial omics and computational modeling have enabled high-resolution mapping of these neighborhoods, providing unprecedented insights into their roles in shaping tumor heterogeneity, evolution and therapeutic responses. Despite these advances, a unified framework for interpreting cellular neighborhoods remains lacking. This Perspective synthesizes emerging concepts and insights, focusing on the definition and classification of cellular neighborhoods in cancer, computational methods for identifying and comparing them, and their clinical relevance.
    DOI:  https://doi.org/10.1038/s43018-025-01107-w
  7. FEBS J. 2026 Jan 12.
      Organoid formation is driven by poorly understood intrinsic cellular properties and transcriptional programs that govern plasticity and differentiation. Deciphering these regulatory networks is essential for understanding normal tissue homeostasis and tumor initiation. Using a 3D organotypic model, which better recapitulates cell-matrix interactions and biochemical cues, we performed a miRNA-based screening strategy to identify key regulators of organoid initiation from human primary mammary epithelial cells. Our findings reveal that miR-106a-3p acts as a central modulator of mammary epithelial plasticity, enriching for stem/progenitor-like cells (CD44high/CD24low phenotype), driving organoid expansion, fostering K14+/K19+ lineage intermixing, and promoting branching morphogenesis characteristic of early ductal development. Further analysis revealed a core transcriptional network involving CBFB, NF-YA, GATA3, and REST, which supports organoid-forming potential. This regulatory program also induces a hybrid epithelial-mesenchymal transition (EMT) state, enhancing cellular plasticity while preserving organoid structural integrity. Extending these findings to cancer, we demonstrate that enforced expression of miR-106a-3p significantly increases tumoroid formation, suggesting that the tumor microenvironment, as modeled by 3D culture, promotes miR-106a-3p expression and functional relevance in tumorigenic processes. Collectively, these data indicate that miR-106a-3p drives a transient expansion of progenitor-like states and orchestrates transcriptional reprogramming during organoid initiation, with broader implications for breast tissue homeostasis and pathophysiological remodeling in cancer.
    Keywords:  human primary mammary epithelial cells; miRNA; organoids; transcriptions factors
    DOI:  https://doi.org/10.1111/febs.70397
  8. Cell Syst. 2026 Jan 14. pii: S2405-4712(25)00290-X. [Epub ahead of print] 101457
      Direct reprogramming of immune cells holds promise for immunotherapy but is constrained by limited knowledge of transcription factor (TF) networks. Here, we developed REPROcode, a combinatorial single-cell screening platform to identify TF combinations for immune cell reprogramming. We first validated REPROcode by inducing type-1 conventional dendritic cells (cDC1s) with multiplexed sets of 9, 22, and 42 factors. With cDC1-enriched TFs, REPROcode enabled identification of optimal TF stoichiometry, fidelity enhancers, and regulators of cDC1 states. We then constructed an arrayed lentiviral library of 408 barcoded immune TFs to explore broader reprogramming capacity. Screening 48 TFs enriched in dendritic cell subsets yielded myeloid and lymphoid phenotypes and enabled the construction of a TF hierarchy map to guide immune reprogramming. Finally, we validated REPROcode's discovery power by inducing natural killer (NK)-like cells. This study deepens our understanding of immune transcriptional control and provides a versatile toolbox for engineering immune cells to advance immunotherapy.
    Keywords:  antigen-presenting cells; barcoding; cellular reprogramming; combinatorial screening; dendritic cells; innate lymphoid cells; machine learning; transcription factor; transcriptional hierarchy
    DOI:  https://doi.org/10.1016/j.cels.2025.101457
  9. Cancer Cell. 2026 Jan 12. pii: S1535-6108(25)00537-9. [Epub ahead of print]44(1): 146-165.e14
      The immune composition of the tumor microenvironment has a major impact on the therapy response in patients with colorectal cancer. Here, we built an atlas with 4.27 million single cells from 1,670 patient samples and complemented it with single-cell profiles from 266 patients, including cells with low mRNA content, spatial transcriptomics from 3.7 million cells, and protein profiles from 0.7 million cells. The analysis of the atlas allows tumor classification into immune desert, B cell enriched, T cell enriched, and myeloid cell enriched immune phenotypes. Within the myeloid compartment, we identify consensus myeloid gene expression programs with four immunomodulatory programs, and uncover a subpopulation of neutrophils with antigen-presenting properties. Moreover, functional experiments using patient-derived organoids show KRAS-dependent pro-tumorigenic polarization of neutrophils. Further, spatial multimodal single-cell profiling reveals niches with IL-1 signaling-based neutrophil-fibroblast interaction. Finally, using an orthotopic mouse model, we show that cancer-derived signals modify neutrophil production in the bone marrow.
    Keywords:  cellular niches; colorectal cancer; gut-bone marrow axis; single-cell atlas; single-cell sequencing; spatial single-cell profiling; spatial transcriptomics
    DOI:  https://doi.org/10.1016/j.ccell.2025.12.003
  10. Nature. 2026 Jan;649(8097): 529
      
    Keywords:  Machine learning; Scientific community; Technology
    DOI:  https://doi.org/10.1038/d41586-026-00049-2
  11. Commun Biol. 2026 Jan 13.
      Plasticity is a central mechanism underlying the robust regenerative capacity of the intestinal epithelium. Two major forms of plasticity have been described: spatial plasticity, in which differentiated cells revert to crypt base columnar cells (CBCs), and fetal reversion into revival stem cells (revSCs). However, the relationship among these two stem cell populations and differentiated cells remains to be clarified. Here, we demonstrated the bidirectional interconversion between CBCs and revSCs. Using lineage tracing, injury models and villus culture, we show that absorptive enterocytes can reprogram into revSCs and regenerate CBCs. These findings position fetal reversion as an entry point to spatial plasticity, establishing a regenerative hierarchy where CBCs, revSCs, and enterocytes collectively orchestrate intestinal repair. Furthermore, we identified revSCs as a highly stress-tolerant stem cell population, whose emergence would preserve the stem cell pool. Our results establish fetal reversion as a cellular escape mechanism safeguarding epithelial regeneration under inflammatory conditions.
    DOI:  https://doi.org/10.1038/s42003-026-09533-x
  12. Nat Rev Immunol. 2026 Jan 12.
      Alterations in key metabolic pathways are required for tumour development and the adaptation of tumour cells to intrinsic or extrinsic stresses, as well as for the regulation of immune cell fate and immune responses in the tumour microenvironment. In particular, the dysregulation or alteration of certain metabolites produced by tumour cells has been shown to be important in creating the immunosuppressive tumour microenvironment. Recent studies have broadened our understanding of the interactions between metabolites and antitumour immunity. Here we highlight how, beyond their metabolic role, metabolites can function as signalling molecules to modulate the behaviours of immune cells and tumour cells. We also discuss potential therapeutic strategies targeting specific metabolites and future research directions in metabolite sensing.
    DOI:  https://doi.org/10.1038/s41577-025-01258-y
  13. bioRxiv. 2026 Jan 05. pii: 2025.06.30.662330. [Epub ahead of print]
      Genetic interaction (GI) networks in model organisms have revealed how combinations of genome variants can impact phenotypes. To advance efforts toward a reference human GI network, we developed the q uantitative G enetic Interaction (qGI) score, a method for precise GI measurement from genome-wide CRISPR-Cas9 screens in different query mutants constructed in a single human cell line. We found surprising prevalent systematic variation unrelated to GIs in CRISPR screen data, including both genomically linked effects and functionally coherent covariation. Leveraging ∼40 control screens in wild-type cells and half a billion differential fitness effect measurements, we developed a pipeline for CRISPR screen data processing and normalization to correct these artifacts and measure accurate, quantitative GIs. We also comprehensively characterized GI reproducibility by characterizing 4 - 5 biological replicates for ∼125,000 unique gene pairs. The qGI framework enables systematic identification of human GIs and provides broadly applicable strategies for analyzing context-specific CRISPR screen data.
    DOI:  https://doi.org/10.1101/2025.06.30.662330
  14. Med. 2026 Jan 09. pii: S2666-6340(25)00398-8. [Epub ahead of print]7(1): 100971
      Translation of foundation models from benchmarks to clinical impact has been slow, revealing a fundamental limitation: correlation-based predictions from models trained on observational data miss causal pathways that determine disease course and treatment response. Hybrid models combining deep learning with representations of biological mechanisms will enable causal reasoning and provide mechanistic understanding required for disease intervention.
    DOI:  https://doi.org/10.1016/j.medj.2025.100971
  15. Cancer Cell. 2026 Jan 15. pii: S1535-6108(25)00552-5. [Epub ahead of print]
      Clinical trials targeting cancer-associated fibroblasts (CAFs)-crucial pro-tumoral factors in cancer-have almost all failed. This may be ascribed to their intrinsic functional plasticity and the opaque regulatory circuits underlying their heterogeneous phenotypes within tumors. We address these by developing a systematic screening approach for patient-derived fibroblasts using complementary CRISPR interference (CRISPRi) and activation (CRISPRa)-based Perturb-seq. An anti-tumoral interferon (IFN)-I response-associated program is identified as the primary antagonism axis counteracting TGF-β-driven pro-tumoral myofibroblast activation. ADAM12 emerges as a molecular checkpoint mediating this relationship. Its ablation elicits IFN-I-responsive programs, reconfigures myofibroblast population structures into progenitor-like states, revitalizes T cell-based immune responses, and induces tumor rejection across various murine models. Further combined with human genomics data analysis, our findings position ADAM12 as a potential target for fibroblasts, paving the way for actionable therapeutic interventions.
    Keywords:  CAFs; CRISPRa; CRISPRi; Perturb-seq; anti-tumoral fibroblasts; cancer-associated fibroblasts; immunotherapy; myofibroblast activation; patient-derived organoid-fibroblast co-culture; turning cold tumors hot
    DOI:  https://doi.org/10.1016/j.ccell.2025.12.018
  16. Nature. 2026 Jan 14.
      Therapies that harness the immune system to target and eliminate tumour cells have revolutionized cancer care. Immune checkpoint blockade (ICB), which boosts the anti-tumour immune response by inhibiting negative regulators of T cell activation1-3, is remarkably successful in a subset of cancer patients. Yet a significant proportion do not respond to treatment, emphasizing the need to understand factors influencing the therapeutic efficacy of ICB4-9. The gut microbiota, consisting of trillions of microorganisms residing in the gastrointestinal tract, has emerged as a critical determinant of immune function and response to cancer immunotherapy, with several studies demonstrating association of microbiota composition with clinical response10-16. However, a mechanistic understanding of how gut commensal bacteria influence the efficacy of ICB remains elusive. Here we use a gut commensal microorganism, segmented filamentous bacteria (SFB), which induces an antigen-specific T helper 17 (TH17) cell effector program in the small intestine lamina propria (SILP)17, to investigate how colonization with this microbe affects the efficacy of ICB in restraining distal growth of tumours sharing antigen with SFB. We find that anti-programmed cell death protein 1 (PD-1) treatment effectively inhibits the growth of implanted SFB antigen-expressing melanoma only if mice are colonized with SFB. Through T cell receptor (TCR) clonal lineage tracing, fate mapping and peptide-major histocompatability complex (MHC) tetramer staining, we identify tumour-associated SFB-specific T helper 1 (TH1)-like cells derived from the homeostatic TH17 cells induced by SFB colonization in the SILP. These gut-educated ex-TH17 cells produce high levels of the pro-inflammatory cytokines interferon (IFN)-γ and tumour necrosis factor (TNF) within the tumour microenvironment (TME), enhancing antigen presentation and promoting recruitment, expansion and effector functions of CD8+ tumour-infiltrating cytotoxic lymphocytes and thereby enabling anti-PD-1-mediated tumour control. Conditional ablation of SFB-induced IL-17A+CD4+ T cells, precursors of tumour-associated TH1-like cells, abolishes anti-PD-1-mediated tumour control and markedly impairs tumour-specific CD8+ T cell recruitment and effector function within the TME. Our data, as a proof of principle, define a cellular pathway by which a single, defined intestinal commensal imprints T cell plasticity that potentiates PD-1 blockade, and indicate targeted modulation of the microbiota as a strategy to broaden ICB efficacy.
    DOI:  https://doi.org/10.1038/s41586-025-09913-z
  17. Nat Protoc. 2026 Jan 12.
      Multimodal profiling of different molecular layers from the same single cell enables more comprehensive characterization of cellular heterogeneity compared with conventional single-modality approaches. A key example is co-detection of chromatin accessibility and gene expression that offers the opportunity to investigate cell type-resolved gene regulatory mechanisms. Here we describe a sensitive and robust protocol for in situ sequencing hetero RNA-DNA-hybrid after assay for transposase-accessible chromatin using sequencing (ISSAAC-seq) for the concurrent measurement of chromatin accessibility and gene expression from the same single nucleus. The method begins with dual Tn5 tagging of open chromatin regions and the RNA-cDNA hybrid produced by reverse transcription that take place in bulk nuclei. Then, various single-nucleus isolation strategies, including plate and droplet barcoding-based approaches, can be used based on the experimental purpose of the user. The protocol is highly modular with a flexible throughput ranging from several hundreds to tens of thousands of nuclei. The generated data are of high quality in both modalities. The entire workflow can be finished within 1 or 2 days, and the procedures work on multiple different single-nucleus isolation and barcoding platforms.
    DOI:  https://doi.org/10.1038/s41596-025-01304-y
  18. Nat Rev Genet. 2026 Jan 13.
    SCGE Dissemination and Coordinating Center Toolkit Team
      CRISPR-based genome editing therapeutics are entering the clinic, offering transformative potential but also presenting potential risks. Preclinical-to-clinical toolkits are needed to assess the safety and efficacy of these new therapies and accelerate progress. Emerging technologies to monitor the biological effects of genome editors cover a range of biological scales, from the direct measurement of editing outcomes in DNA, to human microphysiological systems, and non-invasive in vivo imaging. Measurements of on-target and off-target editing outcomes, including sequences unique to humans, provide essential benchmarks to understand functional responses. Microphysiological systems, including organoids and organs-on-chips, enable phenotypic evaluations of editing strategies in varied organ lineages and disease states. Non-invasive imaging modalities can track the biodistribution and activities of genome editors and edited cells in vivo. Collectively, these technologies provide complementary insights across different scales, from the single nucleotide to the whole organism, bridging preclinical therapeutics development with clinical trials.
    DOI:  https://doi.org/10.1038/s41576-025-00916-0
  19. Elife. 2026 Jan 14. pii: RP100555. [Epub ahead of print]13
      Genomic loci associated with common traits and diseases are typically non-coding and likely impact gene expression, sometimes coinciding with rare loss-of-function variants in the target gene. However, our understanding of how gradual changes in gene dosage affect molecular, cellular, and organismal traits is currently limited. To address this gap, we induced gradual changes in gene expression of four genes using CRISPR activation and inactivation in human-derived K562 cells. Downstream transcriptional consequences of dosage modulation of three master trans-regulators associated with blood cell traits (GFI1B, NFE2, and MYB) were examined using targeted single-cell multimodal sequencing. We showed that guide tiling around the TSS is the most effective way to modulate cis gene expression across a wide range of fold changes, with further effects from chromatin accessibility and histone marks that differ between the inhibition and activation systems. Our single-cell data allowed us to precisely detect subtle to large gene expression changes in dozens of trans genes, revealing that many responses to dosage changes of these three TFs are nonlinear, including non-monotonic behaviours, even when constraining the fold changes of the master regulators to a copy number gain or loss. We found that the dosage properties are linked to gene constraint and that some of these nonlinear responses are enriched for disease and GWAS genes. Overall, our study provides a straightforward and scalable method to precisely modulate gene expression and gain insights into its downstream consequences at high resolution.
    Keywords:  computational biology; gene expression; gene regulation; human; systems biology; transcription factors
    DOI:  https://doi.org/10.7554/eLife.100555
  20. Nature. 2026 Jan 15.
      
    Keywords:  Biochemistry; Cell biology; Transcriptomics
    DOI:  https://doi.org/10.1038/d41586-026-00116-8
  21. Mol Cancer. 2026 Jan 12.
      
    Keywords:  Gut microbiota; Immune microenvironment; Immunotherapy resistance; Metabolic reprogramming; Therapy resistance; Tumor microenvironment
    DOI:  https://doi.org/10.1186/s12943-025-02564-8
  22. Nat Commun. 2026 Jan 15.
      Susceptibility transcription factors (TF) whose DNA bindings are altered by genetic variants regulating colorectal cancer (CRC) risk genes remain poorly defined. Using generalized linear mixed models, we analyze 218 TF ChIP-Seq datasets alongside GWAS data from 100,204 CRC cases and 154,587 controls of East Asian and European ancestries. We identify 51 TFs and TF-cofactor interactions, including VDR-cofactors, as key regulators of CRC risk. Integrating these TF insights with transcriptome-wide association studies (TWAS), we further evaluate associations between genetically predicted gene expression, alternative splicing, and alternative polyadenylation with CRC risk, using RNA-seq data from 364 Asian-ancestry and 707 European-ancestry individuals. Multi-ancestry TWAS identify 222 risk genes, including 95 novel genes and 48 potentially druggable targets. Single-cell analysis provides additional functional evidence supporting ~45% of these genes, and experimental validation confirms oncogenic roles for RHPN2, IRS2, and TXN. Our findings elucidate key TF-gene regulatory networks and uncover novel CRC risk genes.
    DOI:  https://doi.org/10.1038/s41467-025-68127-z