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Cited by 40Cancer Genomics and DiagnosticsCancer Cells and MetastasisCRISPR and Genetic Engineering

In vivo single-cell CRISPR uncovers distinct TNF programmes in tumour evolution

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Renz, Peter F., Ghoshdastider, Umesh, Baghai Sain, Simona, Valdivia-Francia, Fabiola, Khandekar, Ameya, Ormiston, Mark, Bernasconi, Martino, Duré, Clara +9 more·2024·Nature
DOI 10.1038/s41586-024-07663-yPMC PMC11306103
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Abstract

The tumour evolution model posits that malignant transformation is preceded by randomly distributed driver mutations in cancer genes, which cause clonal expansions in phenotypically normal tissues. Although clonal expansions can remodel entire tissues 1–3 , the mechanisms that result in only a small number of clones transforming into malignant tumours remain unknown. Here we develop an in vivo single-cell CRISPR strategy to systematically investigate tissue-wide clonal dynamics of the 150 most frequently mutated squamous cell carcinoma genes. We couple ultrasound-guided in utero lentiviral microinjections, single-cell RNA sequencing and guide capture to longitudinally monitor clonal expansions and document their underlying gene programmes at single-cell transcriptomic resolution. We uncover a tumour necrosis factor (TNF) signalling module, which is dependent on TNF receptor 1 and involving macrophages, that acts as a generalizable driver of clonal expansions in epithelial tissues. Conversely, during tumorigenesis, the TNF signalling module is downregulated. Instead, we identify a subpopulation of invasive cancer cells that switch to an autocrine TNF gene programme associated with epithelial–mesenchymal transition. Finally, we provide in vivo evidence that the autocrine TNF gene programme is sufficient to mediate invasive properties and show that the TNF signature correlates with shorter overall survival of patients with squamous cell carcinoma. Collectively, our study demonstrates the power of applying in vivo single-cell CRISPR screening to mammalian tissues, unveils distinct TNF programmes in tumour evolution and highlights the importance of understanding the relationship between clonal expansions in epithelia and tumorigenesis.

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  • First-principles modeling has established a variety of PDE models that accurately represent the behavior of scratch assays with a high density of cells and under a variety of conditions.

    “First-principles modeling has established a variety of partial differential equation (PDE) models that accurately represent the behavior of scratch assays with a high density of cells and under a variety of conditions8,9.”

    From Inference of weak-form partial differential equations describing migration and proliferation mechanisms in wound healing experiments on cancer cells (2025) · cites this paper as [9]

    The Methods > Scratch assay passage describes an experimental cell-gap assay and image analysis, not a mathematical model. Searches for PDE models and first-principles modeling found no passage in our copy addressing whether such models accurately represent high-density scratch assays under varied conditions; page numbers were not provided. (LLM, conf=0.76)

    Experimental — accuracy not yet measured

  • Previous computational analyses of cell migration have identified diffusivity values from approximately 50 to 3000 μm2/hr.

    “Previous computational analyses of cell migration have identified a wide range of diffusivity values, from approximately 50 to 3000μm2/hr9,40,41.”

    From Inference of weak-form partial differential equations describing migration and proliferation mechanisms in wound healing experiments on cancer cells (2025) · cites this paper as [9]

    The Methods describe a scratch assay that images cells over 22 hours, but give no diffusivity estimates. Searches for the 50–3000 μm²/hr range and computational analyses of cell migration found no passage in our copy that addresses the claimed values. (LLM, conf=0.76)

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Cited by

Sorted by citations

Authors
Renz, P. F., Ghoshdastider, U., Baghai Sain, S., Valdivia-Francia, F., Khandekar, A., Ormiston, M., Bernasconi, M., Duré, C., Kretz, J. A., Lee, M., Hyams, K., Forny, M., Pohly, M., Ficht, X., Ellis, S. J., Moor, A. E., & Sendoel, A.
Affiliations
  • University of Zurich (CH)
  • University of Vienna (AT)
  • ETH Zurich (CH)
Corresponding author
  • Moor, Andreas E.
  • Sendoel, Ataman
ORCID
Venue
Nature
Publisher
Springer Science and Business Media LLC
Published
2024-07-17
Volume
632
Issue
8024
Pages
419-428
ISSN
  • 0028-0836 (ISSN-L)
  • 1476-4687
DOI
10.1038/s41586-024-07663-y
PMC
PMC11306103
OpenAlex
W4400729458
Cited by
40
References
14
Citations by year
2026: 16 · 2025: 20 · 2024: 4
FWCI
8.02
Type
journal article
Language
en
Open access
Licence
Locations
  • Nature (publishedVersion, cc-by)
  • PubMed Central (publishedVersion, cc-by)
  • PubMed (publishedVersion)
  • RePEc: Research Papers in Economics (submittedVersion)
  • Zurich Open Repository and Archive (University of Zurich) (submittedVersion, cc-by)
Funders
  • European Commission (HORIZON2020)
  • Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung (205601, 176825)
  • Swiss Cancer Research Foundation
  • Helmut Horten Stiftung
  • Functional Genomics Center Zurich
  • H2020 European Research Council (759006)
Topics
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Cancer Research › Cancer Genomics and Diagnostics
  • Health Sciences › Medicine › Oncology › Cancer Cells and Metastasis
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › CRISPR and Genetic Engineering
Keywords
tumor evolution, clonal expansion, squamous cell carcinoma, TNF receptor 1, macrophages, epithelial-mesenchymal transition, tumor invasion, clonal dynamics, carcinogenesis, epithelium, overall survival
MeSH terms
Animals, Carcinoma, Squamous Cell, Cell Transformation, Neoplastic, Clone Cells, Female, Humans, Macrophages, Male, Mutation, Neoplasm Invasiveness, Tumor Necrosis Factor-alpha, Signal Transduction, Gene Expression Regulation, Neoplastic, Survival Analysis, Autocrine Communication, Receptors, Tumor Necrosis Factor, Type I, Tumor Necrosis Factors, Mice, Epithelial-Mesenchymal Transition, Single-Cell Analysis, Transcriptome, Clonal Evolution, Carcinogenesis, Clustered Regularly Interspaced Short Palindromic Repeats, CRISPR-Cas Systems

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