Single-cell transcriptome analysis of tumor immune microenvironment characteristics in colorectal cancer liver metastasis

Yiting Geng; Jun Feng; Hao Huang; Ying Wang; Xing Yi; Shanshan Wei; Mingyue Zhang; Zhong Li; Wei Wang; Wenwei Hu

doi:10.21037/atm-22-5270

Single-cell transcriptome analysis of tumor immune microenvironment characteristics in colorectal cancer liver metastasis

Ann Transl Med. 2022 Nov;10(21):1170. doi: 10.21037/atm-22-5270.

Authors

Yiting Geng¹, Jun Feng¹, Hao Huang^{2

3}, Ying Wang¹, Xing Yi¹, Shanshan Wei¹, Mingyue Zhang¹, Zhong Li⁴, Wei Wang¹, Wenwei Hu^{1

3}

Affiliations

¹ Department of Oncology, The Third Affiliated Hospital of Soochow University, Changzhou, China.
² Department of Tumor Biological Treatment, The Third Affiliated Hospital of Soochow University, Changzhou, China.
³ Jiangsu Engineering Research Center for Tumor Immunotherapy, The Third Affiliated Hospital of Soochow University, Changzhou, China.
⁴ Department of Gastrointestinal Surgery, The Third Affiliated Hospital of Soochow University, Changzhou, China.

Abstract

Background: Liver metastasis is the leading cause of death in colorectal cancer (CRC) patients, and the precise mechanisms remain unclear. In this study, single-cell RNA sequencing (scRNA-seq) was used to analyze the cellular and molecular heterogeneity between CRC primary lesion and corresponding liver metastasis, and to clarify the characteristics of the tumor microenvironment (TME) in synchronous liver metastasis of CRC.

Methods: A case of microsatellite stable (MSS) sigmoid carcinoma with synchronous liver metastasis was selected, and tissues from the primary tumor and the liver metastasis were collected for scRNA-seq. The EdgeR package software was used to identify the differentially expressed genes between cells. Gene Set Enrichment Analysis (GSEA) was performed and the clusterProfiler R package was used for Gene Ontology (GO) enrichment analysis. The SCENIC and CellphoneDB packages were used to reconstruct the transcriptional regulatory networks and to analyze the intercellular interaction network, respectively.

Results: Compared to the primary tumor, the proportion of myeloid cells in the metastatic tumor was significantly increased, while B cells and plasma cells were decreased. In the metastatic tumor, the myeloid-derived suppressor cell (MDSC) characteristic gene, mannose receptor C-type 1 (MRC1) and tumor associated macrophage 2 (TAM2)-related gene, were highly expressed. Furthermore, angiogenesis, oxidative phosphorylation, and endothelial mesenchymal transition (EMT) of myeloid cells were also significantly enhanced. There were less myeloid cells in primary tumors, and these were mainly monocytes and TAM1; while the number of TAM2 was significantly upregulated in the metastatic samples. In liver metastasis, the T cell population was exhausted, and this was accompanied by a significant increase in the number of CD4⁺ T cells and a decrease in the number of CD8⁺ T cells. Furthermore, some immune checkpoint molecules were highly expressed. Interactions between myeloid cells and other cell populations appeared to be strong.

Conclusions: The TME of CRC liver metastasis is significantly immunosuppressed. Interactions between myeloid cells and other cell populations in the TME contribute to the establishment of a pro-metastatic niche that promotes colonization and growth of CRC cells in the liver. TAMs may be a potential immunotherapeutic target for MSS CRC.

Keywords: Colorectal cancer (CRC); liver metastasis; single-cell RNA sequencing; tumor immune microenvironment; tumor microenvironment.