Unveiling Tumor Diversity in Metastatic Gastric Cancer via Single-Cell Analysis
Although intratumoral heterogeneity (ITH) is a fundamental characteristic of cancer, it is still unclear where it came from. We profiled the transcriptome states of tumor cell populations and a map of 45,048 PC cells, performed single-cell transcriptome profiling of peritoneal carcinomatosis (PC) from 15 patients with gastric adenocarcinoma (GAC), incisively explored ITH of malignant PC cells, and discovered significant correlates with patient survival. Transcriptomic, genotypic, molecular, and phenotypic levels of analysis were used to illustrate the relationships between tumor cell lineage/state compositions and ITH. We identified the variety of tumor cell lineage/state compositions in PC specimens as a significant factor causing ITH. A 12-gene prognostic signature was developed and validated in numerous large-scale GAC cohorts. Single-cell analysis of ITH classified PC specimens into two subtypes that were prognostically independent of clinical variables. The prognostic signature appears crucial to the development and spread of GAC carcinomas and may be useful for patient stratification.
Research Criteria
They performed scRNA-seq of PC cells from ten long-term and ten short-term PC survivors and inferred tumor cell lineages and transcriptomic states at single-cell resolution by mapping the data to the Human Cell Landscape (HCL) database. Then, they constructed a single-cell map of malignant PC cells, comprehensively characterized the ITH of PC tumor cells via integrative approaches, and found significant correlates with patient survival. This study showed that tumor cell lineage/state diversity causes ITH. A 12-gene fundamental signature, derived from PC cells, was prognostic in independent, localized, and advanced large-scale GAC cohorts.
Fig.1 Experimental design. (Wang, 2021)
Sample Type
Cells from a human solid stomach tumor, PC (Peritoneal Carcinomatosis), were spun down and pelleted cells were isolated, cryopreserved at -80°C, and used for scRNA-seq.
Result—A Single-Cell Transcriptome Map of PC
scRNA-seq was conducted on cryopreserved PC cells from 20 patients with advanced-stage GAC (Gastric Adenocarcinoma), including ten long-term and ten short-term survivors. To profile the transcriptome landscape of PC tumor cells, unsupervised cell-clustering analysis was performed, and the results were illustrated using both t-distributed stochastic neighbor embedding (t-SNE) and UMAP, which identified 14 distinct cell clusters, with differentially expressed genes (DEGs) uniquely identifying each cell cluster.
Fig.2 The t-SNE and UMAP plots of the 31,131 PC tumor cells. (Wang, 2021)
Result—The Inferred Tumor Cell Lineages
They used HCL, a useful and well-annotated scRNA-seq resource for human biology, as a reference to map each individual tumor cell, determine its transcriptome state, and identify potential cells of the origin of PC. It's interesting to note that despite the clinical diagnosis of PC from GAC in each case in this study, the transcriptome-based analysis found significant cellular heterogeneity in inferred tumor cell lineages. Lineage-specific gene expression characteristics were discovered by DEG analysis in a number of major cell lineages, including colorectal-like, duodenal-like, and gastric cells, as well as between colorectal enterocytes and goblet cells.
Fig.3 The inferred tumor cell lineages. (Wang, 2021)
Result—Single-Cell Analysis of Tumor Cell Lineage Compositions Classified PC Cases into Two Subtypes with Significant Survival Difference
Based on tumor cell lineage compositions, they classified PC samples into two main subtypes: gastric-dominant (mainly gastric cell lineages) and GI-mixed (mixed gastric and colorectal-like cells). These subtypes had similar histopathological features. The cell-of-origin-based classification of PCR showed a strong correlation with patient survival: all six cases with a GI-mixed phenotype were long-term survivors, while six of eight cases with a gastric-dominant phenotype were short-term survivors. These findings suggest that PC tumor transcriptomics may predict patient survival.
Fig.4 Survival analysis of the discovery GAC-PC and primary GAC cohorts. (Wang, 2021)
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Reference
- Wang, R.; et al. Single-cell dissection of intratumoral heterogeneity and lineage diversity in metastatic gastric adenocarcinoma. Nature Medicine. 2021, 27: 141-151.
