Spatial Omics Solutions for Tumor Progression

The cellular machinery that constitutes malignancy is diverse, plastic, and adaptive. Many malignancies exhibit distinct compartments and heterogeneous phenotypes that support cancer progression. Tumor progression exhibits adaptive and evolutionary features in all aspects. This diversity is a key feature of many cancers and has a strong impact on tumor progression and treatment outcomes.

Figure 1. Spatially resolved imaging- and sequence-based technologies provide insight into mechanisms that contribute to cancer biology at multiple levels of scale. (Smith, E., A., et al., 2019)

How we use spatial omics in tumor progression

The development of spatial omics analysis technologies has significantly improved researchers' understanding of oncogenic effects. CD Genomics uses high-resolution approaches based on spatial omics and imaging to characterize epigenomic and phenotypic states at the single-cell level. This provides the opportunity to reveal complex tumor progression studies that contain a mix of cell types and states. Allows our customers to perform high-resolution dissection of the cancer process at the single-cell level to reveal previously unknown interactions in multicellular tissues that contribute to the study of tumor progression and therapeutic response.

General experimental procedure

Sample types: fresh pathological tissue samples, tissue sections

Technical methods and advantages

• We use the CyTOF tool to examine the heterogeneous cellular state within the tumor. Capable of highly multiparametric studies of protein abundance, providing single-cell analysis of up to 50 parameters per cell.
• By combining CyTOF with PLAYR, we can perform high-dimensional single-cell analysis of mRNA and protein simultaneously at a rate of thousands of cells per second, providing insight into the relationship between gene expression and protein abundance.
• We use LCM to be able to study tumor progression while preserving spatial information about the tumor tissue. Cells of interest are identified by microscopy on tissue sections before laser-assisted isolation. Cells are then separated using a high-intensity UV laser and collected by laser pressure ejection. This allows our customers to select and isolate cells of interest from different tumor regions with high precision and without contact.
• We use Slide-seq to provide spatial indexing for placing frozen sections of tissue. After reverse transcription, tissue digestion, and library amplification, spatial expression profiles are computationally reconstructed. has been used to spatially map individual cell types in tumor cryosections, as well as the different cell states induced by tumor progression.
• We also used the NICHE-seq technique to preserve cell states affected by surrounding cells or microenvironment so that the effect of these on tumor progression could be characterized.
• A spatial resolution of 1 μm was achieved in tissue sections, allowing the discovery of new subpopulations.

We do it better

The single-cell and spatially resolved analysis of tumor progression provided by CD Genomics can reveal environmentally relevant mechanisms and other spatially constrained cues controlling tumorigenesis, metastasis, and therapeutic response. Thus, able to characterize heterogeneous cellular states and processes in malignancies, we offer solutions that have become important tools for identifying previously hidden features of cancer.

Reference

1. Smith, E., A., et al., (2019). "The Spatial and Genomic Hierarchy of Tumor Ecosystems Revealed by Single-Cell Technologies." Trends in cancer, 5(7), 411-425.