Single‐cell and spatial analyses reveal the association between gene expression of glutamine synthetase with the immunosuppressive phenotype of APOE+CTSZ+TAM in cancers

Abstract

An immunosuppressive state is regulated by various factors in the tumor microenvironment (TME), including, but not limited to, metabolic plasticity of immunosuppressive cells and cytokines secreted by these cells. We used single‐cell RNA‐sequencing (scRNA‐seq) data and applied single‐cell flux estimation analysis to characterize the link between metabolism and cellular function within the hypoxic TME of colorectal (CRC) and lung cancer. In terms of metabolic heterogeneity, we found myeloid cells potentially inclined to accumulate glutamine but tumor cells inclined to accumulate glutamate. In particular, we uncovered a tumor‐associated macrophage (TAM) subpopulation, APOE+CTSZ+TAM, that was present in high proportions in tumor samples and exhibited immunosuppressive characteristics through upregulating the expression of anti‐inflammatory genes. The proportion of APOE+CTSZ+TAM and regulatory T cells (Treg) were positively correlated across CRC scRNA‐seq samples. APOE+CTSZ+TAM potentially interacted with Treg via CXCL16–CCR6 signals, as seen by ligand–receptor interactions analysis. Notably, glutamate‐to‐glutamine metabolic flux score and glutamine synthetase ( GLUL ) expression were uniquely higher in APOE+CTSZ+TAM, compared with other cell types within the TME. GLUL expression in macrophages was positively correlated with anti‐inflammatory score and was higher in high‐grade and invasive tumor samples. Moreover, spatial transcriptome and multiplex immunofluorescence staining of samples showed that APOE+CTSZ+TAM and Treg potentially colocalized in the tissue sections from CRC clinical samples. These results highlight the specific role and metabolic characteristic of the APOE+CTSZ+TAM subpopulation and provide a new perspective for macrophage subcluster‐targeted therapeutic interventions or metabolic checkpoint‐based cancer therapies.

A method to identify high consensus predictions of single-cell metabolic flux

“…These results suggest that the systems should ideally be run in tandem when autoimmune conditions are considered, at least for murine t-cell data. Additionally, scFEA has been used solely to predict metabolic differences in fatty acid, TCA and glycolysis between non-tumorous osteoblast precursor cells and subsequent differentiated populations associated with kidney disease, as well as a wide range of flux imbalances in tumor associated lymphocytes [49, 50]. In these studies, however, metabolomics validation appeared to be absent.…”

Macrophage heterogeneity and its interactions with stromal cells in tumour microenvironment

“…In addition to glucose and lipid metabolism, TAMs also exhibit elevated consumption of glutamine and arginine. Single-cell analyses revealed that a TAM subpopulation, APOE + CTSZ + TAMs, was characterized by enhanced expression of glutamine synthetase, and the upregulation of glutamine metabolism was positively correlated with the anti-inflammatory and immunosuppressive properties of macrophages [ 65 ]. Accordingly, inhibiting glutamine metabolism showed an antitumour macrophage phenotype shift, including increased expression of TNF, TLR4, CD80 and CD86 but decreased expression of IL-10 [ 66 ].…”

Novel tumor-associated macrophage populations and subpopulations by single cell RNA sequencing

“…A subpopulation of TAMs expressing C1QA/B/C is present in multiple cancers, such as colorectal cancer ( 43 ), NSCLC ( 62 ), liver cancer ( 44 ), lung cancer ( 63 ), rental cancer ( 60 , 64 , 65 ), breast cancer ( 8 , 50 ), pancreatic cancer ( 58 ) and cervical cancer ( 57 ). Single-cell and spatial analyses revealed immunosuppressive phenotypes of C1Q + APOE + TAMs in CRCs ( 66 ). The patients with C1QC high TAMs had the best prognosis for cervical cancer, whereas the worst prognosis could appear in patients with C1QC low TAMs ( 57 ).…”