Relationships of tumor differentiation and immune infiltration in gastric cancers revealed by single-cell RNA-seq analyses

Abstract

Gastric cancers are highly heterogeneous malignant tumors. To reveal the relationship between differentiation status of cancer cells and tumor immune microenvironments in gastric cancer, single-cell RNA-sequencing was performed on normal mucosa tissue, differentiated gastric cancer (DGC) tissue, poorly differentiated gastric cancer (PDGC) tissue and neuroendocrine carcinoma (NEC) tissue sampled from surgically resected gastric cancer specimens. We identified the signature genes for both DGC and PDGC, and found that signature genes of PDGC strongly enriched in the epithelial–mesenchymal transition (EMT) program. Furthermore, we found that DGC tends to be immune-rich type whereas PDGC tends to be immune-poor type defined according to the density of tumor-infiltrating CD8+ T cells. Additionally, interferon alpha and gamma responding genes were specifically expressed in the immune-rich malignant cells compared with immune-poor malignant cells. Through analyzing the mixed adenoneuroendocrine carcinoma, we identified intermediate state malignant cells during the trans-differentiation process from DGC to NEC, which showed double-negative expressions of both DGC marker genes and NEC marker genes. Interferon-related pathways were gradually downregulated along the DGC to NEC trans-differentiation path, which was accompanied by reduced CD8+ cytotoxic T-cell infiltration. In summary, molecular features of both malignant cells and immune microenvironment cells of DGC, PDGC and NEC were systematically revealed, which may partially explain the strong tumor heterogeneities of gastric cancer. Especially along the DGC to NEC trans-differentiation path, immune-evasion was gradually enhanced with the decreasing activities of interferon pathway responses in malignant cells.

Exploring the current landscape of single‐cell RNA sequencing applications in gastric cancer research

“…Furthermore, scRNA‐seq has enabled the identification of prognostically independent subtypes of gastric adenocarcinoma (GAC) based on intratumoral heterogeneity, leading to the development of a 12‐gene prognostic signature 6 . Additionally, scRNA‐seq analysis of various GC specimens, including differentiated GC (DGC), poorly differentiated GC (PDGC) and neuroendocrine carcinoma (NEC) has revealed the strong enrichment of PDGC in genes associated with the epithelial‐mesenchymal transition (EMT) program 24 . Moreover, immune‐rich DGC tends to express genes responsive to interferon alpha and gamma, while immune‐poor PDGC exhibits no such tendency 24 .…”

“…Additionally, scRNA‐seq analysis of various GC specimens, including differentiated GC (DGC), poorly differentiated GC (PDGC) and neuroendocrine carcinoma (NEC) has revealed the strong enrichment of PDGC in genes associated with the epithelial‐mesenchymal transition (EMT) program 24 . Moreover, immune‐rich DGC tends to express genes responsive to interferon alpha and gamma, while immune‐poor PDGC exhibits no such tendency 24 . During the transdifferentiation process from DGC to NEC, intermediate malignant cells display double‐negative expressions of DGC and NEC marker genes, accompanied by a gradual downregulation of interferon‐related pathways and decreased infiltration of CD8+ cytotoxic T cells 24 .…”

“…24 Moreover, immune-rich DGC tends to express genes responsive to interferon alpha and gamma, while immune-poor PDGC exhibits no such tendency. 24 During the transdifferentiation process from DGC to NEC, intermediate malignant cells display double-negative expressions of DGC and NEC marker genes, accompanied by a gradual downregulation of interferon-related pathways and decreased infiltration of CD8+ cytotoxic T cells. 24 Similarly, integrative analysis of scRNA-seq data from early gastric cardia adenocarcinoma (EGCA)…”

Correlation of Neuroendocrine Differentiation with a Distinctively Suppressive Immune Microenvironment in Gastric Cancer

“…It has been demonstrated that the TIMEs of NENs were significantly suppressive. Zhou et al [20] compared the TIMEs of differentiated, poorly differentiated GC and gastric neuroendocrine carcinoma (NEC), showing that gastric NECs or the NEC component in mixed adenoneuroendocrine carcinoma had a higher proportion of malignant cells, increased INHBA+ TAM, but reduced CD8+ T-cell infiltration, which was accompanied by the downregulated interferon-related pathways. In colorectal NECs, Chen et al [32] also reported lower scores of CD8+ T cells, B cells, myeloid dendritic cells, and macrophages/monocytes.…”

“…Since TIMEs are surrounded by tumor cells and tissue fluid, their composition and function are susceptible to tumor-specific factors that help different tumors shape their distinctive TIMEs. This phenomenon has been found in various types and grades of neuroendocrine neoplasms (NENs) [17][18][19][20]. However, regarding non-NENs but where ectopic NED occurred, such as GC-NED, their TIMEs have not been touched, and whether GC-NED harbored a different TIME from that of PGC was unknown.…”