Spatial transcriptomics in health and disease

Gall, J. G. The origin of in situ hybridization – a personal history. Methods 98, 4–9 (2016).

Article  CAS  PubMed  Google Scholar 

Tian, L., Chen, F. & Macosko, E. Z. The expanding vistas of spatial transcriptomics. Nat. Biotechnol. 41, 773–782 (2023).

Article  CAS  PubMed  Google Scholar 

Lopez, R. et al. DestVI identifies continuums of cell types in spatial transcriptomics data. Nat. Biotechnol. 40, 1360–1369 (2022).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Li, H. et al. A comprehensive benchmarking with practical guidelines for cellular deconvolution of spatial transcriptomics. Nat. Commun. 14, 1548 (2023).

Article  PubMed  PubMed Central  Google Scholar 

Longo, S. K., Guo, M. G., Ji, A. L. & Khavari, P. A. Integrating single-cell and spatial transcriptomics to elucidate intercellular tissue dynamics. Nat. Rev. Genet. 22, 627–644 (2021).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Dries, R. et al. Advances in spatial transcriptomic data analysis. Genome Res. 31, 1706–1718 (2021).

Article  PubMed  PubMed Central  Google Scholar 

Jain, S. et al. Advances and prospects for the Human BioMolecular Atlas Program (HuBMAP). Nat. Cell Biol. 25, 1089–1100 (2023).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Rozenblatt-Rosen, O., Stubbington, M. J. T., Regev, A. & Teichmann, S. A. The Human Cell Atlas: from vision to reality. Nature 550, 451–453 (2017).

Article  CAS  PubMed  Google Scholar 

Rozenblatt-Rosen, O. et al. The Human Tumor Atlas Network: charting tumor transitions across space and time at single-cell resolution. Cell 181, 236–249 (2020).

Article  CAS  PubMed  PubMed Central  Google Scholar 

de Boer, I. H. et al. Rationale and design of the Kidney Precision Medicine Project. Kidney Int. 99, 498–510 (2021).

Article  PubMed  PubMed Central  Google Scholar 

HuBMAP Consortium. The human body at cellular resolution: the NIH human biomolecular atlas program. Nature 574, 187–192 (2019).

Article  CAS  Google Scholar 

SenNet, C. NIH SenNet Consortium to map senescent cells throughout the human lifespan to understand physiological health. Nat. Aging 2, 1090–1100 (2022).

Article  Google Scholar 

Oxburgh, L. et al. (Re)Building a Kidney. J. Am. Soc. Nephrol. 28, 1370–1378 (2017).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Regev, A. et al. The Human Cell Atlas. Elife 6, e27041 (2017).

Article  PubMed  PubMed Central  Google Scholar 

Stahl, P. L. et al. Visualization and analysis of gene expression in tissue sections by spatial transcriptomics. Science 353, 78–82 (2016).

Article  CAS  PubMed  Google Scholar 

Rodriques, S. G. et al. Slide-seq: a scalable technology for measuring genome-wide expression at high spatial resolution. Science 363, 1463–1467 (2019).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Chen, A. et al. Spatiotemporal transcriptomic atlas of mouse organogenesis using DNA nanoball-patterned arrays. Cell 185, 1777–1792.e21 (2022).

Article  CAS  PubMed  Google Scholar 

Lake, B. B. et al. An atlas of healthy and injured cell states and niches in the human kidney. Nature 619, 585–594 (2023).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Fan, Y. et al. Expansion spatial transcriptomics. Nat. Methods 20, 1179–1182 (2023).

Article  CAS  PubMed  Google Scholar 

Wirth, J. et al. Spatial transcriptomics using multiplexed deterministic barcoding in tissue. Nat. Commun. 14, 1523 (2023).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Salem, F. et al. The spatially resolved transcriptional profile of acute T cell-mediated rejection in a kidney allograft. Kidney Int. 101, 131–136 (2022).

Article  CAS  PubMed  Google Scholar 

Srivatsan, S. R. et al. Embryo-scale, single-cell spatial transcriptomics. Science 373, 111–117 (2021).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Lee, Y. et al. XYZeq: spatially resolved single-cell RNA sequencing reveals expression heterogeneity in the tumor microenvironment. Sci. Adv. 7, eabg4755 (2021).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Nguyen, H. Q. et al. 3D mapping and accelerated super-resolution imaging of the human genome using in situ sequencing. Nat. Methods 17, 822–832 (2020).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Lee, J. H. et al. Fluorescent in situ sequencing (FISSEQ) of RNA for gene expression profiling in intact cells and tissues. Nat. Protoc. 10, 442–458 (2015).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Wang, X. et al. Three-dimensional intact-tissue sequencing of single-cell transcriptional states. Science 361, eaat5691 (2018).

Article  PubMed  PubMed Central  Google Scholar 

Biancalani, T. et al. Deep learning and alignment of spatially resolved single-cell transcriptomes with Tangram. Nat. Methods 18, 1352–1362 (2021).

Article  PubMed  PubMed Central  Google Scholar 

Chen, K. H., Boettiger, A. N., Moffitt, J. R., Wang, S. & Zhuang, X. RNA imaging. Spatially resolved, highly multiplexed RNA profiling in single cells. Science 348, aaa6090 (2015).

Article  PubMed  PubMed Central  Google Scholar 

He, S. et al. High-plex imaging of RNA and proteins at subcellular resolution in fixed tissue by spatial molecular imaging. Nat. Biotechnol. 40, 1794–1806 (2022).

Article  CAS  PubMed  Google Scholar 

Ke, R. et al. In situ sequencing for RNA analysis in preserved tissue and cells. Nat. Methods 10, 857–860 (2013).

Article  CAS  PubMed  Google Scholar 

Groiss, S. et al. Highly resolved spatial transcriptomics for detection of rare events in cells. Preprint at bioRxiv, https://doi.org/10.1101/2021.10.11.463936 (2021).

Eng, C. L. et al. Transcriptome-scale super-resolved imaging in tissues by RNA seqFISH. Nature 568, 235–239 (2019).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Andersson, A. et al. Single-cell and spatial transcriptomics enables probabilistic inference of cell type topography. Commun. Biol. 3, 565 (2020).

Article  PubMed  PubMed Central  Google Scholar 

Hao, Y. et al. Integrated analysis of multimodal single-cell data. Cell 184, 3573–3587.e29 (2021).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Melo Ferreira, R. et al. Integration of spatial and single cell transcriptomics localizes epithelial-immune cross-talk in kidney injury. JCI Insight 6, e147703 (2021).

Article  PubMed  Google Scholar 

Brbic, M. et al. Annotation of spatially resolved single-cell data with STELLAR. Nat. Methods 19, 1411–1418 (2022).

Article  CAS  PubMed  Google Scholar 

Wei, R. et al. Spatial charting of single-cell transcriptomes in tissues. Nat. Biotechnol. 40, 1190–1199 (2022).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Elosua-Bayes, M., Nieto, P., Mereu, E., Gut, I. & Heyn, H. SPOTlight: seeded NMF regression to deconvolute spatial transcriptomics spots with single-cell transcriptomes. Nucleic Acids Res. 49, e50 (2021).

Article  CAS  PubMed  PubMed Central 

留言 (0)

沒有登入
gif