Spatial architecture of development and disease

Bressan, D., Battistoni, G. & Hannon, G. J. The dawn of spatial omics. Science 381, eabq4964 (2023).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Liu, L. et al. Spatiotemporal omics for biology and medicine. Cell 187, 4488–4519 (2024).

Article  CAS  PubMed  Google Scholar 

Jain, S. & Eadon, M. T. Spatial transcriptomics in health and disease. Nat. Rev. Nephrol. 20, 659–671 (2024).

Article  PubMed  PubMed Central  Google Scholar 

Moses, L. & Pachter, L. Museum of spatial transcriptomics. Nat. Methods 19, 534–546 (2022).

Article  CAS  PubMed  Google Scholar 

Moffitt, J. R., Lundberg, E. & Heyn, H. The emerging landscape of spatial profiling technologies. Nat. Rev. Genet. 23, 741–759 (2022).

Article  CAS  PubMed  Google Scholar 

Alexandrov, T., Saez-Rodriguez, J. & Saka, S. K. Enablers and challenges of spatial omics, a melting pot of technologies. Mol. Syst. Biol. 19, e10571 (2023).

Article  CAS  PubMed  PubMed Central  Google Scholar 

De Jonghe, J. et al. scTrends: a living review of commercial single-cell and spatial ’omic technologies. Cell Genom. 4, 100723 (2024).

Article  PubMed  PubMed Central  Google Scholar 

Gulati, G. S., D’Silva, J. P., Liu, Y., Wang, L. & Newman, A. M. Profiling cell identity and tissue architecture with single-cell and spatial transcriptomics. Nat. Rev. Mol. Cell Biol. 26, 11–31 (2025).

Article  CAS  PubMed  Google Scholar 

Palla, G., Fischer, D. S., Regev, A. & Theis, F. J. Spatial components of molecular tissue biology. Nat. Biotechnol. 40, 308–318 (2022).

Article  CAS  PubMed  Google Scholar 

Xiao, Z. et al. 3D reconstruction of a gastrulating human embryo. Cell 187, 2855–2874.e19 (2024).

Article  CAS  PubMed  Google Scholar 

Xu, Y. et al. A single-cell transcriptome atlas profiles early organogenesis in human embryos. Nat. Cell Biol. 25, 604–615 (2023).

Article  PubMed  Google Scholar 

Cui, L. et al. Spatial transcriptomic characterization of a Carnegie stage 7 human embryo. Nat. Cell Biol. 27, 360–369 (2025).

Article  CAS  PubMed  Google Scholar 

Pavon, N. et al. Patterning ganglionic eminences in developing human brain organoids using a morphogen-gradient-inducing device. Cell Rep. Methods 4, 100689 (2024).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Sanchís-Calleja, F. et al. Decoding morphogen patterning of human neural organoids with a multiplexed single-cell transcriptomic screen. Preprint at bioRxiv https://doi.org/10.1101/2024.02.08.579413 (2024).

Bertacchi, M., Maharaux, G., Loubat, A., Jung, M. & Studer, M. FGF8-mediated gene regulation affects regional identity in human cerebral organoids. eLife 13, e98096 (2024).

Article  PubMed  PubMed Central  Google Scholar 

Amin, N. D. et al. Generating human neural diversity with a multiplexed morphogen screen in organoids. Cell Stem Cell 31, 1831–1846.e9 (2024).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Chen, Z., Han, F., Du, Y., Shi, H. & Zhou, W. Hypoxic microenvironment in cancer: molecular mechanisms and therapeutic interventions. Signal Transduct. Target. Ther. 8, 70 (2023).

Article  PubMed  PubMed Central  Google Scholar 

Martínez-Reyes, I. & Chandel, N. S. Cancer metabolism: looking forward. Nat. Rev. Cancer 21, 669–680 (2021).

Article  PubMed  Google Scholar 

Carmona-Fontaine, C. et al. Metabolic origins of spatial organization in the tumor microenvironment. Proc. Natl Acad. Sci. USA 114, 2934–2939 (2017).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Haley, M. J. et al. Hypoxia coordinates the spatial landscape of myeloid cells within glioblastoma to affect survival. Sci. Adv. 10, eadj3301 (2024).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Wang, W. et al. Identification of hypoxic macrophages in glioblastoma with therapeutic potential for vasculature normalization. Cancer Cell 42, 815–832.e12 (2024).

Article  CAS  PubMed  Google Scholar 

Rashidi, A. et al. Myeloid cell-derived creatine in the hypoxic niche promotes glioblastoma growth. Cell Metab. 36, 62–77.e8 (2024).

Article  CAS  PubMed  Google Scholar 

Sun, H. et al. The relevance between hypoxia-dependent spatial transcriptomics and the prognosis and efficacy of immunotherapy in claudin-low breast cancer. Front. Immunol. 13, 1042835 (2022).

Article  CAS  PubMed  Google Scholar 

Malagoli Tagliazucchi, G., Wiecek, A. J., Withnell, E. & Secrier, M. Genomic and microenvironmental heterogeneity shaping epithelial-to-mesenchymal trajectories in cancer. Nat. Commun. 14, 789 (2023).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Kureshi, C. T. & Dougan, S. K. Cytokines in cancer. Cancer Cell 43, 15–35 (2025).

Article  CAS  PubMed  Google Scholar 

Nirmal, A. J. et al. The spatial landscape of progression and immunoediting in primary melanoma at single-cell resolution. Cancer Discov. 12, 1518–1541 (2022).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Zhao, L. et al. Tertiary lymphoid structures in diseases: immune mechanisms and therapeutic advances. Signal Transduct. Target. Ther. 9, 225 (2024).

Article  PubMed  PubMed Central  Google Scholar 

Wu, R. et al. Comprehensive analysis of spatial architecture in primary liver cancer. Sci. Adv. 7, eabg3750 (2021).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Jing, X. et al. Role of hypoxia in cancer therapy by regulating the tumor microenvironment. Mol. Cancer 18, 157 (2019).

Article  PubMed  PubMed Central  Google Scholar 

Campillo, N. et al. Differential oxygenation in tumor microenvironment modulates macrophage and cancer cell crosstalk: Novel experimental setting and proof of concept. Front. Oncol. 9, 43 (2019).

Article  PubMed  PubMed Central  Google Scholar 

Auxillos, J. et al. Spatially resolved analysis of microenvironmental gradient impact on cancer cell phenotypes. Sci. Adv. 10, eadn3448 (2024).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Keren, L. et al. A structured tumor-immune microenvironment in triple negative breast cancer revealed by multiplexed ion beam imaging. Cell 174, 1373–1387.e19 (2018).

Article  CAS  PubMed 

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