Profiling immune cell tissue niches in the spatial-omics era

被引:0
作者
Lee, Colin Y. C. [1 ,2 ]
Mccaffrey, James [1 ,2 ,3 ]
Mcgovern, Dominic [1 ,2 ,3 ]
Clatworthy, Menna R. [1 ,2 ,3 ]
机构
[1] Univ Cambridge, Cambridge Inst Therapeut Immunol & Infect Dis, Cambridge Biomed Campus,Puddicombe Way, Cambridge CB2 0AW, England
[2] Wellcome Sanger Inst, Cellular Genet, Wellcome Genome Campus, Cambridge, England
[3] Cambridge Univ Hosp NHS Fdn Trust, Cambridge, England
基金
英国惠康基金; 英国医学研究理事会;
关键词
Spatial profiling; spatial transcriptomics; spatial prote- omics; microscopy; immune niches; LASER CAPTURE MICRODISSECTION; GENOME-WIDE EXPRESSION; SINGLE-CELL; GENE-EXPRESSION; HIGH-THROUGHPUT; MULTI-OMICS; RNA; RESOLUTION; COMMUNICATION; MACROPHAGE;
D O I
10.1016/j.jaci.2024.11.001
中图分类号
R392 [医学免疫学];
学科分类号
100102 ;
摘要
Immune responses require complex, spatially coordinated interactions between immune cells and their tissue environment. For decades, we have imaged tissue sections to visualize a limited number of immune-related macromolecules in situ, functioning as surrogates for cell types or processes of interest. However, this inevitably provides a limited snapshot of the tissue's immune landscape. Recent developments in high- throughput spatial-omics technologies, particularly spatial transcriptomics, and its application to human samples has facilitated a more comprehensive understanding of tissue immunity by mapping fine-grained immune cell states to their precise tissue location while providing contextual information about their immediate cellular and tissue environment. These data provide opportunities to investigate mechanisms underlying the spatial distribution of immune cells and its functional implications, including the identification of immune niches, although the criteria used to define this term have been inconsistent. Here, we review recent technological and analytic advances in multiparameter spatial profiling, focusing on how these methods have generated new insights in translational immunology. We propose a 3-step framework for the definition and characterization of immune niches, which is powerfully facilitated by new spatial profiling methodologies. Finally, we summarize current approaches to analyze adaptive immune repertoires and lymphocyte clonal expansion in a spatially resolved manner. (J Allergy Clin Immunol 2025;155:663-77.)
引用
收藏
页码:663 / 677
页数:15
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