Three-dimensional imaging mass cytometry for highly multiplexed molecular and cellular mapping of tissues and the tumor microenvironment

Abstract

A holistic understanding of tissue and organ structure and function requires the detection of molecular constituents in their original three-dimensional (3D) context. Imaging mass cytometry (IMC) enables simultaneous detection of up to 40 antigens and transcripts using metal-tagged antibodies but has so far been restricted to two-dimensional imaging. Here we report the development of 3D IMC for multiplexed 3D tissue analysis at single-cell resolution and demonstrate the utility of the technology by analysis of human breast cancer samples. The resulting 3D models reveal cellular and microenvironmental heterogeneity and cell-level tissue organization not detectable in two dimensions. 3D IMC will prove powerful in the study of phenomena occurring in 3D space such as tumor cell invasion and is expected to provide invaluable insights into cellular microenvironments and tissue architecture.

Unsupervised discovery of tissue architecture in multiplexed imaging

“…Likewise, systematic application of UTAG in image data from various organs will undoubtedly accelerate projects such as spatial cell atlases 38–40 , by providing microanatomical context to the cells, and enabling ground-up discovery of tissue architecture beyond cell type composition of tissues. Another exciting future application is the discovery of microanatomy in volumetric images of tissue 13,41–43 , since there is no conceptual limitation to use UTAG in 3 dimensions. This would enable robust morphometry of tissue structures since a current challenge in two-dimensional analysis of tissue is the detection of structure independent of the cutting angle.…”

“…Another exciting future application is the discovery of microanatomy in volumetric images of tissue 13,[41][42][43] , since there is no conceptual limitation to use UTAG in 3 dimensions. This would enable robust morphometry of tissue structures since a current challenge in two-dimensional analysis of tissue is the detection of structure independent of the cutting angle.…”

Application of High-Throughput Imaging Mass Cytometry Hyperion in Cancer Research

“…In the article by Ali et al., they have pointed some new features of TME including cellular neighborhoods that could be of potential prognostic interest in this field. Of note, in their work, IMC was often combined with genomics methods to better decipher the complexity of breast cancer at different level and to correlate this complexity with prognostic features ( 9 , 14 , 15 , 19 , 47 ). Still in breast cancer patients, Carvajal-Hausdorf et al.…”

“…This method enables the analysis of cellular content and interactions in the volume and depth of the tissue and its feasibility has been demonstrated on a breast cancer sample by the team of Bodenmiller et al. ( 47 ). Nevertheless, this increasing level of analysis also greatly increases the time of acquisition and the related-cost of the analysis that constitutes a limitation in its wider application to date.…”

Spatial-CITE-seq: spatially resolved high-plex protein and whole transcriptome co-mapping

“…Latest advances in imaging-based protein mapping such as imaging mass cytometry (IMC) 16 or multiplex immunofluorescence (i.e., CODEX 17 , CyCIF 18, 19 , and seqIF 20 ) has realized 25-60-plex protein mapping and transformed spatial protein biomarker research. Our work utilized spatial barcoding and high-throughput sequencing for the mapping of ∼200-300 proteins, representing the highest multiplexing to date for spatial protein profiling despite the lack of subcellular resolution.…”