Spatially Resolved Transcriptomics Technology Facilitates Cancer Research

Abstract

Single cell RNA sequencing (scRNA-seq) provides a great convenience for studying tumor occurrence and development for its ability to study gene expression at the individual cell level. However, patient-derived tumor tissues are composed of multiple types of cells including tumor cells and adjacent non-malignant cells such as stromal cells and immune cells. The spatial locations of various cells in situ tissues plays a pivotal role in the occurrence and development of tumors, which cannot be elucidated by scRNA-seq alone. Spatially resolved transcriptomics (SRT) technology emerges timely to explore the unrecognized relationship between the spatial background of a particular cell and its functions, and is increasingly used in cancer research. This review provides a systematic overview of the SRT technologies that are developed, in particular the more widely used cutting-edge SRT technologies based on next-generation sequencing (NGS). In addition, the main achievements by SRT technologies in precisely unveiling the underappreciated spatial locations on gene expression and cell function with unprecedented high-resolution in cancer research are emphasized, with the aim of developing more effective clinical therapeutics oriented to a deeper understanding of the interaction between tumor cells and surrounding non-malignant cells.

Keywords: cancer-associated fibroblast (CAF); spatially resolved transcriptomics (SRT); tertiary lymphoid structure (TLS); tumor heterogeneity; tumor immune microenvironment.

Figure 1

Commonly used spatially resolved transcriptomics technologies. a) 10x Visium. Tissue permeabilization releases mRNA to bind to the oligonucleotide array on slides. The cDNA obtained by reverse transcription is collected for library preparation and amplification. b) NanoString GeoMx. Special probes are bound to the target RNA, imaging and ROI selection are performed, and DNA indexed oligonucleotides are collected using UV photolysis. Finally, they are subjected to Illumina sequencing.

Figure 2

Spatial mapping of solid tumors using SRT technology. a) FAP⁺ fibroblasts are obviously enriched in CRC tissues. Cell trajectory analysis infers that they originate from FGFR2⁺ fibroblasts or ICAM1⁺ terminal cells, and this process is driven by the transcription factor TWIST1. The enrichment of FAP⁺ fibroblasts and SPP1⁺ macrophages form a physical barrier to restrict the infiltration of immune cells into the tumor, leading to an immune‐suppressive CRC microenvironment. b) Invasive epithelial subsets of TSK have complex interactions with CAFs and endothelial cells at the tumor‐stromal interface through multiple receptor complexes. c) CAFs are innovatively described as three superclusters: steady‐state‐like (SSL), mechanoresponsive (MR), and immunomodulatory (IM) CAFs. d) CRC cells at the invasion front express high levels of HLA‐G to induce an increase in of SPP1⁺ macrophages, which secrete IL‐1β to recruit additional SPP1⁺ macrophages, and they together deplete other immune cells and suppress tumor immunity. e) B cells expand and mature into plasma cells within the TLS and exhibit high secretion of IgG and IgA antibodies targeting tumor cells. Feature gene sets of TLS are highly expressed in this region.