bims-gerecp Biomed News
on Gene regulatory networks of epithelial cell plasticity
Issue of 2025–03–16
seventeen papers selected by
Xiao Qin, University of Oxford
  1. Optimal transport for single-cell genomics.
  2. Feature selection methods affect the performance of scRNA-seq data integration and querying.
  3. Compromised epigenetic robustness in cancer: fueling evolution, exposing weakness.
  4. Simultaneous CRISPR screening and spatial transcriptomics reveal intracellular, intercellular, and functional transcriptional circuits.
  5. Modes of Notch signalling in development and disease.
  6. High-dimensional signalling analysis of organoids.
  7. CT Colonography to Screen for Colorectal Cancer: Learn It, Leverage It, Lower Cancer's Incidence!
  8. Adapting systems biology to address the complexity of human disease in the single-cell era.
  9. Colorectal cancer staging-time for a re-think on TNM?
  10. Human stem cells with in vivo high plasticity generated by cell-cell communication.
  11. Evolution of organoid genetics.
  12. A large-scale benchmark for network inference from single-cell perturbation data.
  13. Mucosal macrophages govern intestinal regeneration in response to injury.
  14. Evolving our understanding of cancer: an interview with Charles Swanton.
  15. Optimizing Xenium In Situ data utility by quality assessment and best-practice analysis workflows.
  16. CT Colonography for Colorectal Cancer Prevention and Detection: Integration Into Clinical Practice, From the AJR Special Series on Screening.
  17. A systematic benchmark of Nanopore long-read RNA sequencing for transcript-level analysis in human cell lines.
  1. Nat Methods. 2025 Mar;22(3): 452
    Optimal transport for single-cell genomics.
    Lin Tang.
      
    DOI:  https://doi.org/10.1038/s41592-025-02639-w
  2. Nat Methods. 2025 Mar 13.
    Feature selection methods affect the performance of scRNA-seq data integration and querying.
    Luke Zappia, Sabrina Richter, Ciro Ramírez-Suástegui, Raphael Kfuri-Rubens, Larsen Vornholz, Weixu Wang, Oliver Dietrich, Amit Frishberg, Malte D Luecken, Fabian J Theis.
      The availability of single-cell transcriptomics has allowed the construction of reference cell atlases, but their usefulness depends on the quality of dataset integration and the ability to map new samples. Previous benchmarks have compared integration methods and suggest that feature selection improves performance but have not explored how best to select features. Here, we benchmark feature selection methods for single-cell RNA sequencing integration using metrics beyond batch correction and preservation of biological variation to assess query mapping, label transfer and the detection of unseen populations. We reinforce common practice by showing that highly variable feature selection is effective for producing high-quality integrations and provide further guidance on the effect of the number of features selected, batch-aware feature selection, lineage-specific feature selection and integration and the interaction between feature selection and integration models. These results are informative for analysts working on large-scale tissue atlases, using atlases or integrating their own data to tackle specific biological questions.
    DOI:  https://doi.org/10.1038/s41592-025-02624-3
  3. Trends Cancer. 2025 Mar 06. pii: S2405-8033(25)00044-5. [Epub ahead of print]
    Compromised epigenetic robustness in cancer: fueling evolution, exposing weakness.
    Thomas Stuart Wilson, Paola Scaffidi.
      The complex network of proteins that regulate chromatin and DNA methylation landscapes is often disrupted in cancer. Clonal and subclonal mutations targeting a wide range of molecular functions are frequently observed across cancer types, and emerging evidence suggests that loss of robust epigenetic control promotes both cancer initiation and evolution, independently of context-specific effects. Here, we review how diverse genetic alterations that destabilize the epigenetic regulatory network (ERN) may converge into common phenotypes. We also discuss the implications of altered network topology and systemic epigenetic disorder for the evolution, vulnerability, and therapeutic resistance of cancers.
    Keywords:  cancer; epigenetics; evolution; systems level; vulnerability
    DOI:  https://doi.org/10.1016/j.trecan.2025.02.001
  4. Cell. 2025 Mar 10. pii: S0092-8674(25)00197-7. [Epub ahead of print]
    Simultaneous CRISPR screening and spatial transcriptomics reveal intracellular, intercellular, and functional transcriptional circuits.
    Loϊc Binan, Aiping Jiang, Serwah A Danquah, Vera Valakh, Brooke Simonton, Jon Bezney, Robert T Manguso, Kathleen B Yates, Ralda Nehme, Brian Cleary, Samouil L Farhi.
      Pooled optical screens have enabled the study of cellular interactions, morphology, or dynamics at massive scale, but they have not yet leveraged the power of highly plexed single-cell resolved transcriptomic readouts to inform molecular pathways. Here, we present a combination of imaging spatial transcriptomics with parallel optical detection of in situ amplified guide RNAs (Perturb-FISH). Perturb-FISH recovers intracellular effects that are consistent with single-cell RNA-sequencing-based readouts of perturbation effects (Perturb-seq) in a screen of lipopolysaccharide response in cultured monocytes, and it uncovers intercellular and density-dependent regulation of the innate immune response. Similarly, in three-dimensional xenograft models, Perturb-FISH identifies tumor-immune interactions altered by genetic knockout. When paired with a functional readout in a separate screen of autism spectrum disorder risk genes in human-induced pluripotent stem cell (hIPSC) astrocytes, Perturb-FISH shows common calcium activity phenotypes and their associated genetic interactions and dysregulated molecular pathways. Perturb-FISH is thus a general method for studying the genetic and molecular associations of spatial and functional biology at single-cell resolution.
    Keywords:  multimodal screening; pooled CRISPR screen; pooled optical profiling; single-cell perturbations; spatial transcriptomics
    DOI:  https://doi.org/10.1016/j.cell.2025.02.012
  5. Nat Rev Mol Cell Biol. 2025 Mar 10.
    Modes of Notch signalling in development and disease.
    Sarah J Bray, Anna Bigas.
      Many different animal developmental and homeostatic processes rely on signalling via the highly conserved Notch pathway. Often Notch signalling has iterative roles during cell specification and differentiation, controlling not only the state of progenitor cells but also the fate and function of their progeny. Its roles continue throughout the lifespan of the organism, regulating normal tissue maintenance, as well as operating in response to damage. Consistent with such fundamental roles, the pathway has been associated with numerous diseases, including cancers. Understanding how Notch signalling is orchestrated to bring about different outcomes is challenging, given that it has many diverse functions. Classic models proposed that stochastic differences in cell states were important to polarise signalling during cell fate decisions. Subsequently, the importance of oscillatory Notch signalling was uncovered, and it became clear that it operates in different modalities depending on the regulatory inputs. With the advent of ever-more-sensitive live-imaging and quantitative approaches, it is becoming evident that differences in the dynamics, levels and architectures of Notch signalling are critical in shaping and maintaining tissues. This Review focuses on the cellular and molecular mechanisms involved in conferring different modalities on Notch pathway operations and how these enable different types of functional outcomes from pathway activation. We also discuss their dysregulation in cancer.
    DOI:  https://doi.org/10.1038/s41580-025-00835-2
  6. Curr Opin Cell Biol. 2025 Mar 09. pii: S0955-0674(25)00026-2. [Epub ahead of print]94 102488
    High-dimensional signalling analysis of organoids.
    Aurélie Dobric, Christopher J Tape.
      Cellular phenotypes are regulated by dynamic signalling processes that involve proteins, post-translational modifications, epigenetic events, and transcriptional responses. Functional perturbation studies are required to understand cell signalling mechanisms and organoids have recently emerged as scalable biomimetic models amenable to large-scale perturbation. Here, we review the recent advances in high-dimensional analysis of cell signalling in organoids. Single-cell technologies provide cell-type specific analysis of multiple biochemical modalities, enabling a deeper understanding of the signalling mechanisms driving cell-fate dynamics. Emerging multimodal techniques are further revealing coordination between signalling layers and are poised to increase our mechanistic understanding of cell signalling.
    DOI:  https://doi.org/10.1016/j.ceb.2025.102488
  7. AJR Am J Roentgenol. 2025 Mar 12.
    CT Colonography to Screen for Colorectal Cancer: Learn It, Leverage It, Lower Cancer's Incidence!
    Marc J Gollub.
      
    DOI:  https://doi.org/10.2214/AJR.25.32920
  8. Nat Rev Genet. 2025 Mar 10.
    Adapting systems biology to address the complexity of human disease in the single-cell era.
    David S Fischer, Martin A Villanueva, Peter S Winter, Alex K Shalek.
      Systems biology aims to achieve holistic insights into the molecular workings of cellular systems through iterative loops of measurement, analysis and perturbation. This framework has had remarkable success in unicellular model organisms, and recent experimental and computational advances - from single-cell and spatial profiling to CRISPR genome editing and machine learning - have raised the exciting possibility of leveraging such strategies to prevent, diagnose and treat human diseases. However, adapting systems-inspired approaches to dissect human disease complexity is challenging, given that discrepancies between the biological features of human tissues and the experimental models typically used to probe function (which we term 'translational distance') can confound insight. Here we review how samples, measurements and analyses can be contextualized within overall multiscale human disease processes to mitigate data and representation gaps. We then examine ways to bridge the translational distance between systems-inspired human discovery loops and model system validation loops to empower precision interventions in the era of single-cell genomics.
    DOI:  https://doi.org/10.1038/s41576-025-00821-6
  9. Br J Surg. 2025 Mar 04. pii: znaf047. [Epub ahead of print]112(3):
    Colorectal cancer staging-time for a re-think on TNM?
    Jenny F Seligmann.
      
    DOI:  https://doi.org/10.1093/bjs/znaf047
  10. Proc Natl Acad Sci U S A. 2025 Mar 18. 122(11): e2413043122
    Human stem cells with in vivo high plasticity generated by cell-cell communication.
    Shaowei Li, Xi Chen, Jingxue Xin, Bowen Liu, Bo Liu, Min Hu, Wing Hung Wong.
      Stem cells possess inherent properties of self-renewal and differentiation, and thus hold significant promise for regenerating damaged tissues or replacing lost cells. Unless their therapeutic effects are solely mediated by paracrine, transplanted stem cells need to be highly plastic to adapt to the host tissue environment and differentiate into constituent tissue-specific cells for tissue repair. Stem cells used in current cell-based therapies either have limited differentiation potential or are pluripotent but must be strictly restricted to avoid tumorigenicity risk in vivo. Here, we describe the derivation of human adult high-plasticity stem cells, which we call guide-integrated adult stem cells (giaSCs), from the interaction of blood-derived guide cells and umbilical cord tissue-derived mesenchymal stromal cells (UC-MSCs). The guide cells are a cell population derived from the peripheral blood of human adults. Unidirectional transfer through nanotube-like structures of granular substances from the guide cells into the recipient UC-MSCs gave rise to giaSCs. Topical application of human giaSCs into full-layer excisional wounds of wild-type mice led to reconstitution of skin tissue. Systemically administered human giaSCs migrated to and reside in mouse small intestinal tissue damaged by lipopolysaccharides and then differentiated into small intestinal epithelial cells for tissue repair. These transplantation experiments demonstrated that giaSCs have in vivo high plasticity. Additional in vivo and in vitro data showed that giaSCs have low immunogenicity and are nontumorigenic. These data indicate that giaSCs offer a highly promising approach to stem cell therapy.
    Keywords:  intercellular communication; plasticity; stem cell; tissue repair; transcriptomic analysis
    DOI:  https://doi.org/10.1073/pnas.2413043122
  11. Eur J Cell Biol. 2025 Feb 28. pii: S0171-9335(25)00006-8. [Epub ahead of print]104(2): 151481
    Evolution of organoid genetics.
    Thomas M Klompstra, Ki-Jun Yoon, Bon-Kyoung Koo.
      Organoids have revolutionized in vitro research by offering three-dimensional, multicellular systems that recapitulate the structure, function, and genetics of human tissues. Initially developed from both pluripotent stem cells (PSCs) and adult stem cells (AdSCs), organoids have expanded to model nearly every major human organ, significantly advancing developmental biology, disease modeling, and therapeutic screening. This review highlights the progression of organoid technologies, emphasizing the integration of genetic tools, including CRISPR-Cas9, prime editing, and lineage tracing. These advancements have facilitated precise modeling of human-specific pathologies and drug responses, often surpassing traditional 2D cultures and animal models in accuracy. Emerging technologies, such as organoid fusion, xenografting, and optogenetics, are expected to further enhance our understanding of cellular interactions and microenvironmental dynamics. As organoid complexity and genetic engineering methods continue to evolve, they will become increasingly indispensable for personalized medicine and translational research, bridging gaps between in vitro and in vivo systems.
    Keywords:  CRISPR-Cas9; Genetic Engineering; IPSC; Organoid; Organoid Genetics; Review
    DOI:  https://doi.org/10.1016/j.ejcb.2025.151481
  12. Commun Biol. 2025 Mar 11. 8(1): 412
    A large-scale benchmark for network inference from single-cell perturbation data.
    Mathieu Chevalley, Yusuf H Roohani, Arash Mehrjou, Jure Leskovec, Patrick Schwab.
      Mapping biological mechanisms in cellular systems is a fundamental step in early-stage drug discovery that serves to generate hypotheses on what disease-relevant molecular targets may effectively be modulated by pharmacological interventions. With the advent of high-throughput methods for measuring single-cell gene expression under genetic perturbations, we now have effective means for generating evidence for causal gene-gene interactions at scale. However, evaluating the performance of network inference methods in real-world environments is challenging due to the lack of ground-truth knowledge. Moreover, traditional evaluations conducted on synthetic datasets do not reflect the performance in real-world systems. We thus introduce CausalBench, a benchmark suite revolutionizing network inference evaluation with real-world, large-scale single-cell perturbation data. CausalBench, distinct from existing benchmarks, offers biologically-motivated metrics and distribution-based interventional measures, providing a more realistic evaluation of network inference methods. An initial systematic evaluation of state-of-the-art causal inference methods using our CausalBench suite highlights how poor scalability of existing methods limits performance. Moreover, methods that use interventional information do not outperform those that only use observational data, contrary to what is observed on synthetic benchmarks. CausalBench subsequently enables the development of numerous promising methods through a community challenge, thus demonstrating its potential as a transformative tool in the field of computational biology, bridging the gap between theoretical innovation and practical application in drug discovery and disease understanding. Thus, CausalBench opens new avenues for method developers in causal network inference research, and provides to practitioners a principled and reliable way to track progress in network methods for real-world interventional data.
    DOI:  https://doi.org/10.1038/s42003-025-07764-y
  13. Gastroenterology. 2025 Mar 03. pii: S0016-5085(25)00465-2. [Epub ahead of print]
    Mucosal macrophages govern intestinal regeneration in response to injury.
    Ilias Moraitis, Jasin Taelman, Borja Arozamena, Loris Mularoni, Olga Wienskowska, Xavier Sanjuan Garriga, Laura Arregui, Milica Stefanovic, Ignasi Modolell Farré, Ferran Guedea, Mònica Diaz, Jordi Guiu.
       BACKGROUND & AIMS: Cancer patients treated with radiotherapy in the abdominal and pelvic cavity develop radiation-induced enteritis, a condition that impairs their quality of life. Radiation injury depletes proliferative intestinal stem cells (ISCs); in response to this, the epithelium activates a regenerative program that facilitates the healing of the intestine. However, the mechanisms that induce the activation of the intestinal regenerative program are poorly characterized.
    METHODS: In this study, we induced radiation-induced enteritis in mice through abdominal irradiation, mimicking clinical scenarios. Through imaging and flow cytometric analysis, we investigated the recruitment of macrophages to the small intestine during injury and healing. Additionally, we developed a co-culture system for mouse and human intestinal organoids and macrophages to explore the crosstalk between these cells. Then combining in vivo ablation of macrophages, fluorescent lineage tracing, imaging, bulk RNA-sequencing (RNA-seq), single-cell RNA sequencing (scRNA-seq), human intestinal organoids and cell trajectory analysis, we study at cellular and molecular level the macrophage induction of intestinal regeneration.
    RESULTS: Our findings revealed that macrophages are recruited around the intestinal stem cell compartment upon radiation injury, promoting a fetal-like reprogramming and proliferation of epithelial cells that drives the regeneration process. In contrast macrophage ablation led to compromised regeneration. Moreover, our scRNA-seq analysis identified key secreted molecules, nrg1 and spp1, as pivotal players in regulating this process. Additionally, characterization of human macrophage/organoid co-cultures and cell trajectory inference confirmed the conservation of macrophages' role in triggering the regenerative program in primary human cells.
    CONCLUSIONS: This study identifies macrophages as essential contributors to intestinal regeneration beyond their innate immune response. Targeting macrophages therapeutically may hold promise in enhancing regeneration and improving the quality of life for cancer survivors.
    Keywords:  Inflammation; Macrophages; Nrg1; Radiation-induced enteritis; Spp1; intestinal organoids; intestinal regeneration
    DOI:  https://doi.org/10.1053/j.gastro.2025.01.252
  14. Dis Model Mech. 2025 Mar 01. pii: DMM052318. [Epub ahead of print]18(3):
    Evolving our understanding of cancer: an interview with Charles Swanton.
    Charles Swanton.
      
    DOI:  https://doi.org/10.1242/dmm.052318
  15. Nat Methods. 2025 Mar 13.
    Optimizing Xenium In Situ data utility by quality assessment and best-practice analysis workflows.
    Sergio Marco Salas, Louis B Kuemmerle, Christoffer Mattsson-Langseth, Sebastian Tismeyer, Christophe Avenel, Taobo Hu, Habib Rehman, Marco Grillo, Paulo Czarnewski, Saga Helgadottir, Katarina Tiklova, Axel Andersson, Nima Rafati, Maria Chatzinikolaou, Fabian J Theis, Malte D Luecken, Carolina Wählby, Naveed Ishaque, Mats Nilsson.
      The Xenium In Situ platform is a new spatial transcriptomics product commercialized by 10x Genomics, capable of mapping hundreds of genes in situ at subcellular resolution. Given the multitude of commercially available spatial transcriptomics technologies, recommendations in choice of platform and analysis guidelines are increasingly important. Herein, we explore 25 Xenium datasets generated from multiple tissues and species, comparing scalability, resolution, data quality, capacities and limitations with eight other spatially resolved transcriptomics technologies and commercial platforms. In addition, we benchmark the performance of multiple open-source computational tools, when applied to Xenium datasets, in tasks including preprocessing, cell segmentation, selection of spatially variable features and domain identification. This study serves as an independent analysis of the performance of Xenium, and provides best practices and recommendations for analysis of such datasets.
    DOI:  https://doi.org/10.1038/s41592-025-02617-2
  16. AJR Am J Roentgenol. 2025 Mar 12.
    CT Colonography for Colorectal Cancer Prevention and Detection: Integration Into Clinical Practice, From the AJR Special Series on Screening.
    David H Kim, Anu E Obaro, Stuart A Taylor, Perry J Pickhardt.
      CT colonography (CTC) is a CT examination, performed with low dose and typically without IV contrast media, optimized to detect colorectal polyps and cancer. Despite extensive supporting data, CTC has had variable acceptance and use over the past two decades, particularly for a main indication of colorectal cancer screening. CTC is now at an inflection point after the approval in 2025 by CMS for reimbursement of CTC performed for colorectal cancer screening. Widespread use of CTC for CRC screening could help increase screening adherence rates and prevent cancer incidence. Nonetheless, radiologists must incorporate emerging knowledge regarding polyps' natural history and recognition of sessile serrated lesions, to leverage the screening efficiencies of CTC-based screening. The purposes of this article are to describe the current status of CRC in the United States and United Kingdom with consideration of historical reasons that have limited the test's use along with recent events that may portend a marked change in the test's acceptance; to highlight the challenges and potential solutions toward successful widespread CTC implementation; and to present new concepts in CTC and CRC screening relevant to radiologists.
    DOI:  https://doi.org/10.2214/AJR.25.32633
  17. Nat Methods. 2025 Mar 13.
    A systematic benchmark of Nanopore long-read RNA sequencing for transcript-level analysis in human cell lines.
    SG-NEx consortium
      The human genome contains instructions to transcribe more than 200,000 RNAs. However, many RNA transcripts are generated from the same gene, resulting in alternative isoforms that are highly similar and that remain difficult to quantify. To evaluate the ability to study RNA transcript expression, we profiled seven human cell lines with five different RNA-sequencing protocols, including short-read cDNA, Nanopore long-read direct RNA, amplification-free direct cDNA and PCR-amplified cDNA sequencing, and PacBio IsoSeq, with multiple spike-in controls, and additional transcriptome-wide N6-methyladenosine profiling data. We describe differences in read length, coverage, throughput and transcript expression, reporting that long-read RNA sequencing more robustly identifies major isoforms. We illustrate the value of the SG-NEx data to identify alternative isoforms, novel transcripts, fusion transcripts and N6-methyladenosine RNA modifications. Together, the SG-NEx data provide a comprehensive resource enabling the development and benchmarking of computational methods for profiling complex transcriptional events at isoform-level resolution.
    DOI:  https://doi.org/10.1038/s41592-025-02623-4
This page is being maintained by Thomas Krichel. It was last updated on 2025‒03‒31 at 19:19.