A 3D morphogenetic blueprint for metastatic outgrowth in breast cancer

  • Cell. 2026 Jun 11;189(12):3701-3718.e30. doi: 10.1016/j.cell.2026.03.009.
Robin Caire  1 ,  Roberta Bordo  2 ,  Francesca Zanconato  1 ,  Tito Panciera  1 ,  Estelle Audoux  1 ,  Paolo Contessotto  1 ,  Michaela Fakiola  2 ,  Ramona Bason  2 ,  Oriana Romano  1 ,  Ambela Suli  1 ,  Giusy Battilana  1 ,  Matteo Marchionni  1 ,  Mattia Forcato  1 ,  Sara Donzelli  3 ,  Maria Vittoria Dieci  4 ,  Gaia Griguolo  4 ,  Mariantonia Carosi  3 ,  Matteo Fassan  5 ,  Vincenza Guzzardo  5 ,  Angelo Paolo Dei Tos  5 ,  Silvia Marsoni  6 ,  Pei-Hsun Wu  7 ,  Denis Wirtz  7 ,  Shanshan He  8 ,  Cecilia Casali  9 ,  Francesco Volpin  10 ,  Giovanni Blandino  3 ,  Claudio Tripodo  11 ,  Silvio Bicciato  1 ,  Valentina Guarneri  4 ,  Massimiliano Pagani  12 ,  Michelangelo Cordenonsi  13 ,  Stefano Piccolo  14
Affiliations
  • 1. Department of Molecular Medicine DMM, University of Padua, Padua, Italy.
  • 2. University of Milan, Milan, Italy; IFOM ETS - the AIRC Institute of Molecular Oncology, Milan, Italy.
  • 3. IRCCS Regina Elena National Cancer Institute, Rome, Italy.
  • 4. Istituto Oncologico Veneto IOV IRCCS Padua - Department of Surgery, Oncology and Gastroenterology DISCOG, University of Padua, Padua, Italy.
  • 5. Department of Medicine DIMED, University of Padua, Padua, Italy.
  • 6. University of Milan, Milan, Italy.
  • 7. Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, MD, USA.
  • 8. Bruker Spatial Biology, Inc., Seattle, WA, USA.
  • 9. Fondazione IRCCS Istituto Neurologico "Carlo Besta," Neurosurgery Department, Milan, Italy.
  • 10. Neurosurgery Unit, Azienda Ospedale, Università di Padova, 35128 Padua, Italy.
  • 11. IFOM ETS - the AIRC Institute of Molecular Oncology, Milan, Italy.
  • 12. University of Milan, Milan, Italy; IFOM ETS - the AIRC Institute of Molecular Oncology, Milan, Italy. Electronic address: [email protected].
  • 13. Department of Molecular Medicine DMM, University of Padua, Padua, Italy. Electronic address: [email protected].
  • 14. Department of Molecular Medicine DMM, University of Padua, Padua, Italy; IFOM ETS - the AIRC Institute of Molecular Oncology, Milan, Italy. Electronic address: [email protected].
PMID: 41923644 DOI: 10.1016/j.cell.2026.03.009
Abstract

The tissue-level processes underpinning metastatic outgrowth remain unclear. We combined single-cell RNA Sequencing, spatial transcriptomics, and AI-supported 3D imaging in human breast Cancer with functional investigations in mice to uncover a 3D morphogenetic process essential for macrometastatic expansion. Macrometastases pervasively activate a metastatic trabecular morphogenesis (MTM) gene-expression program that redeploys developmental branching morphogenesis to build macrometastases as a 3D trabecular lattice of epithelial cords. MTMHIGH cells pre-exist in primary tumors destined to metastasize, whereas MTMLOW primaries are non-metastatic and display a compact, expansile growth architecture. Chromatin immunoprecipitation Sequencing (ChIP-seq) on metastatic organoids identifies ETV1/4/5 as master regulators of MTM and branching Cancer morphogenesis, required for metastatic outgrowth but dispensable for primary tumor take, bulk growth, and initial metastatic dissemination. Spatial and functional analyses reveal stromal Fibroblast Growth Factor (FGF)→fibroblast growth factor receptor (FGFR) signaling as an actionable MTM dependency. Thus, we link metastatic outgrowth to a 3D developmental morphogenetic process, exposing therapeutic vulnerabilities specific to the lethal macrometastatic stage.

Keywords
3D branching morphogenesis; AI; ETV1/4/5; FGF signaling; breast cancer; cancer architecture; cancer epigenetics; cancer morphogenesis; digital pathology; machine learning; master gene of mestastasis; metastasis; metastatic cell state; metastatic vulnerabilities; prognostic predictors; single-cell transcriptomics; spatial transcriptomics; topological descriptors; trabecular shape; tubular morphogenesis.
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