3.1. Identification and analysis of DEGs in macrophages of different phenotypes
Our previous research showed that a high density M2 macrophage in the TME is closely associated with poor prognosis of ESCC patients and promotes the occurrence and progression of ESCC [6]. Therefore, in order to explore the mechanisms related to tumour occurrence and development, we sought to identify the DEGs in macrophages of different phenotypes. As shown in the Venn diagram, we found that 25 overlapping DEGs were identified in macrophages and M2 macrophages from three datasets (GSE57614, GSE36537, GSE5099) (Fig. 2a). Moreover, 91 overlapping DEGs were shared in M1 and M2 macrophages based on data from four datasets (GSE57614, GSE36537, GSE5099, and GSE95405) (Fig. 2b). Coincidentally, all 25 DEGs were highly expressed in samples of M2 macrophages. Quantification of the expression of the 25 DEGs in TCGA ESCA using cBioPortal revealed that some of these genes are highly expressed in ESCA tissue (Fig. 2c). A volcano plot revealed that TNFRSF11A expression is highest and CXCL10 is lowest in M2 macrophages (Fig. 2d).
3.2. FGL2 expression correlates with level of immune cell infiltration in esophageal carcinoma
To further investigate whether DEGs expression correlated with prognosis of esophageal cancer patients, we used the Kaplan-Meier Plotter online platform to draw survival curves of the 25 DEGs. This analysis revealed that FGL2, ERI1 and WNT5B are related to overall survival (OS) and relapse-free survival (RFS) in ESCC. Notably, FGL2 expression significantly impacts prognosis in ESCC, with high FGL2 expression marginally associated with poorer prognosis (OS HR = 2.57, 95% CI = 1.05 to 6.28, P = 0.033; RFS HR = 3.78, 95% CI = 1.43 to 9.98, P = 0.0039) (Fig. 3a-3b). However, low ERI1 expression was associated with poor prognosis (OS HR = 0.22, 95% CI = 0.08 to 0.59, P = 0.0011; RFS HR = 0.32, 95% CI = 0.12 to 0.84, P = 0.015) (Fig. 3c-3d). Likewise, low WNT5B expression was associated with poor prognosis (OS HR = 0.41, 95% CI = 0.19 to 0.93, P = 0.027; RFS HR = 4.32, 95% CI = 0.99 to 18.93, P = 0.034) (Fig. 3e-3f). For more information about the functional roles of FGL2, ERI1 and WNT5B, see Table 1.
Table 1
Functional roles of FGL2, ERI1 and WNT5B.
Gene symbol | Full name | Function |
FGL2 | Fibrinogen-like 2 | This protein was cloned from cytotoxic T lymphocytes and showed 36% homology to fibrinogen β and γ chains, a member of the fibrinogen super family. It is a pleiotropic cytokine that impacts diverse cellular functions. |
ERI1 | Exoribonuclease 1 | RNA exonuclease that binds to the 3'-end of histone mRNAs and degrades them, suggesting that it plays an essential role in histone mRNA decay after replication. Also able to degrade the 3'-overhangs of short interfering RNAs (siRNAs) in vitro, suggesting a possible role as regulator of RNA interference (RNAi). |
WNT5B | Wnt-family member 5B | This gene is a member of the WNT gene family. It encodes a protein which shows 94% and 80% amino acid identity to the mouse Wnt5B protein and the human WNT5A protein, respectively. These proteins have been implicated in oncogenesis and in several developmental processes. |
These results led us to examine why highly expressed genes in M2 macrophages are closely linked with poor prognosis in ESCA and the potential important role they play in regulating TIICs in the TME. Thus, we assessed whether correlations exist between FGL2, ERI1 and WNT5B expression and immune cell infiltration levels in ESCA using TIMER. Tumour purity is a significant factor that influences the genomic analysis of immune cell infiltration in clinical tumour samples [39]. The results show that FGL2 expression was significantly negatively correlated to ESCA tumour purity with significant positive correlations with infiltrating levels of B cells (r = 0.331, P = 5.85e-06), CD8 + T cells (r = 0.147, P = 4.93e-02), CD4 + T cells (r = 0.321, P = 1.07e-05), macrophages (r = 0.559, P = 3.37e-16), neutrophils (r = 0.337, P = 3.66e-06) and dendritic cells (r = 0.268, P = 2.73e-04) (Fig. 4a). However, ERI1 expression did not exhibit significant correlation with ESCA tumour purity, and only correlated weakly with B cells (r = 0.243, P = 10.4e-03), CD8 + T cells (r = 0.179, P = 1.59e-02) and dendritic cells (r = 0.185, P = 1.28e-02) (Fig. 4b). Similarly, WNT5B expression did not correlate significantly with ESCA tumour purity, showing only a weak correlation with macrophages (r = 0.239, P = 1.21e-03) (Fig. 4c). These findings strongly suggest that FGL2 plays a specific role in immune cell infiltration in ESCA, especially macrophages.
3.3. Correlation analysis between FGL2 expression and immune cell marker sets
To explore the relationship between FGL2 and the various immune infiltrating cells, we focused on examining the correlations between FGL2 expression and various immune cell markers, such as monocytes, TAMs, M1 and M2 macrophages, B cells, T cells (general), CD8 + T cells, neutrophils, NK cells and DCs, in ESCA using the TIMER and GEPIA databases. We also evaluated the different functional T cells, including Tregs, exhausted T cells, Th1, Th2, Tfh and Th17 cells in ESCA (Table 2). After adjusting for purity, we found that the FGL2 expression level was significantly correlated with most immune cells markers and different T cells in ESCA (Table 2).
Table 2
Correlation analysis between FGL2 and related immune cell genes and markers using TIMER.
Description | Gene markers | ESCA |
| | None | Purity |
| | Cor | P | Cor | P |
Monocyte | CD86 | 0.683 | *** | 0.637 | *** |
| CD115 (CSF1R) | 0.779 | *** | 0.752 | *** |
| CD14 | 0.553 | *** | 0.489 | *** |
TAM | CD68 | 0.328 | *** | 0.269 | ** |
| IL10 | 0.522 | *** | 0.479 | *** |
| CCL2 | 0.578 | *** | 0.532 | *** |
M1 Macrophage | IRF5 | 0.058 | 0.431 | 0.015 | 0.84 |
| INOS (NOS2) | -0.06 | 0.419 | -0.029 | 0.696 |
| COX2 (PTGS2) | 0.13 | 0.03 | 0.135 | 0.071 |
M2 Macrophage | CD163 | 0.66 | *** | 0.616 | *** |
| VSIG4 | 0.647 | *** | 0.604 | *** |
| MS4A6A | 0.727 | *** | 0.687 | *** |
Treg | FOXP3 | 0.663 | *** | 0.621 | *** |
| CCR8 | 0.662 | *** | 0.622 | *** |
| STAT5B | 0.395 | *** | 0.431 | *** |
| CD4 | 0.778 | *** | 0.744 | *** |
T cell exhaustion | PD-1 (PDCD1) | 0.647 | *** | 0.597 | *** |
| CTLA4 | 0.646 | *** | 0.588 | *** |
| LAG3 | 0.602 | *** | 0.554 | *** |
| TIM-3(HAVCR2) | 0.753 | *** | 0.718 | *** |
| GZMB | 0.531 | *** | 0.462 | *** |
CD8 + T cell | CD8A | 0.634 | *** | 0.585 | *** |
| CD8B | 0.583 | *** | 0.54 | *** |
T cell (general) | CD3D | 0.609 | *** | 0.54 | *** |
| CD3E | 0.642 | *** | 0.574 | *** |
| CD2 | 0.662 | *** | 0.606 | *** |
B cell | CD19 | 0.356 | *** | 0.248 | ** |
| CD79A | 0.427 | *** | 0.333 | *** |
Neutrophils | CD66b(CEACAM8) | 0.028 | 0.707 | -0.008 | 0.91 |
| CD11b (ITGAM) | 0.488 | *** | 0.421 | *** |
| CCR7 | 0.515 | *** | 0.435 | *** |
Natural killer cell | KIR2DL1 | 0.271 | ** | 0.192 | * |
| KIR2DL3 | 0.302 | *** | 0.278 | ** |
| KIR2DL4 | 0.394 | *** | 0.342 | *** |
| KIR3DL1 | 0.281 | ** | 0.224 | * |
| KIR3DL2 | 0.22 | * | 0.153 | 0.039 |
| KIR3DL3 | -0.04 | 0.59 | -0.041 | 0.581 |
| KIR2DS4 | 0.2 | * | 0.183 | 0.014 |
Dendritic cell | HLA-DPB1 | 0.688 | *** | 0.635 | *** |
| HLA-DQB1 | 0.424 | *** | 0.35 | *** |
| HLA-DRA | 0.604 | *** | 0.548 | *** |
| HLA-DPA1 | 0.668 | *** | 0.623 | *** |
| BDCA-1(CD1C) | 0.576 | *** | 0.499 | *** |
| BDCA-4(NRP1) | 0.624 | *** | 0.595 | *** |
| CD11c (ITGAX) | 0.626 | *** | 0.55 | *** |
Th1 | T-bet (TBX21) | 0.638 | *** | 0.568 | *** |
| STAT4 | 0.672 | *** | 0.61 | *** |
| STAT1 | 0.437 | *** | 0.399 | *** |
| IFN-γ (IFNG) | 0.519 | *** | 0.462 | *** |
| TNF-α (TNF) | 0.165 | 0.025 | 0.106 | 0.155 |
Th2 | GATA3 | 0.372 | *** | 0.311 | *** |
| STAT6 | 0.081 | 0.273 | 0.113 | 0.131 |
| IL13 | 0.324 | *** | 0.245 | ** |
| STAT5A | 0.405 | *** | 0.37 | *** |
| IL2RA (CD25) | 0.649 | *** | 0.606 | *** |
| IL2RB (CD122) | 0.687 | *** | 0.648 | *** |
Tfh | BCL6 | 0.197 | * | 0.2 | * |
| IL21 | 0.252 | ** | 0.188 | 0.012 |
Th17 | STAT3 | 0.226 | * | 0.203 | * |
| IL17A | -0.009 | 0.907 | -0.008 | 0.919 |
| IL6 | 0.352 | *** | 0.307 | *** |
Th, T helper cell; Tfh, T follicular helper cell; Treg, T regulatory cell; Cor, R value of Spearman’s correlation; None, correlation without adjustment. Purity, correlation adjusted by purity. |
* P < 0.01; ** P < 0.001; *** P < 0.0001. |
Scatterplots of the correlations between FGL2 expression and markers of monocytes (e.g., CD86, CSF1R and CD14) and different macrophage phenotypes (e.g., CD68, CCL2, and IL10 of TAMs, IRF5, NOS2, and PTGS2 of M1 macrophages, CD163, VSIG4, and MS4A4A of M2 macrophages) are shown in Fig. 5. Interestingly, these results from the TIMER database demonstrate that the expression levels of all markers set of monocytes, TAMs and M2 macrophages correlate strongly with FGL2 expression (Fig. 5a, 5b and 5d). However, M1 macrophage markers did not correlate with FGL2 expression in ESCA (Fig. 5c). These data verify the overlapping results from the GEO database, indicating that the process of TAMs polarization into M2 macrophages may be accompanied by high FGL2 expression. Similar correlation results between FGL2 expression and markers of monocytes, TAMs and M2 macrophages were found using the GEPIA database (Table 3). These findings indicate that FGL2 may regulate TAMs polarization into M2 macrophages in ESCA.
Table 3
Correlation analysis between FGL2 and markers of monocyte and different phenotypes macrophages in GEPIA.
Description | Gene markers | ESCA |
| | Tumor | Normal |
| | R | P | R | P |
Monocyte | CD86 | 0.68 | *** | 0.65 | 0.017 |
| CD115 (CSF1R) | 0.77 | *** | 0.58 | 0.043 |
| CD14 | 0.54 | *** | 0.74 | * |
TAM | CD68 | 0.3 | *** | 0.42 | 0.15 |
| IL10 | 0.53 | *** | 0.82 | ** |
| CCL2 | 0.58 | *** | 0.82 | * |
M1 Macrophage | IRF5 | 0.029 | 0.7 | 0.33 | 0.27 |
| INOS (NOS2) | -0.066 | 0.38 | 0.42 | 0.16 |
| COX2 (PTGS2) | 0.16 | 0.028 | 0.75 | * |
M2 Macrophage | CD163 | 0.63 | *** | 0.87 | ** |
| VSIG4 | 0.64 | *** | 0.8 | * |
| MS4A6A | 0.72 | *** | 0.81 | * |
Tumour, correlation analysis in tumour tissue of TCG; Normal, correlation analysis in normal tissue of TCGA. |
* P < 0.01; ** P < 0.001; *** P < 0.0001. |
High FGL2 expression in M2 Macrophages is related to high levels of infiltration by various immune cells in ESCA, especially Tregs, exhausted T cells, DCs and CD8 + T cells. DCs can promote tumour metastasis by reducing CD8 + T cell cytotoxicity and increasing Treg numbers [40]. We also found significant correlations between FGL2 and markers of exhausted T cells and Tregs, such as PD-1, CTLA4, LAG3, TIM-3, FOXP3, CCR8 and STAT5B (Table 2). Therefore, these results further confirm that FGL2 is specifically correlated with immune infiltrating cells in ESCA, suggesting that M2 macrophages may regulate immune infiltrating cells by secreting the immunosuppressive factor FGL2 thereby producing a microenvironment that is conducive to tumour growth and which ultimately induces the occurrence and progression of ESCA.
3.4. FGL2 may promote the initiation and progression of esophageal carcinoma
We analysed mRNA sequencing data from 184 ESCA patients using the function module of LinkedOmics. The results demonstrate that 4,078 genes showed significant positive correlations with FGL2, whereas 1,177 genes showed significant negative correlations in the volcano plot (Fig. 6a, false discovery rate [FDR] < 0.01). The 50 most significant gene sets that correlated positively and negatively with FGL2 are shown in the heatmap (Fig. 5b-5c). These results indicate the widespread impact of FGL2 on the transcriptome.
FGL2 expression is reportedly upregulated in different cancers [41]. Surprisingly, there no statistically significant difference in FGL2 expression was observed between normal and tumour tissues of ESCA (Supplementary Fig. 1). Thus, to better understand whether FGL2 is a crucial factor that mediates the TME and tumour metastasis, we examined cytokines that exhibited significantly different expression levels in in vitro co-culture of macrophages and ESCC cells (Fig. 7a). We found that a 20% change in cytokine expression between groups was considered statistically significant. Compared with EC109/9706 culture alone or co-culture of macrophages and EC109/9706, we found that IL-10, MMP9, CCL5, TIM3, IL-13, VCAM1, M-CSF and FGF-7 expression levels were significantly up-regulated in the M2 macrophage and EC109/9706 co-culture samples (Fig. 7b-7e). Our previous research showed that MMP9 promotes the invasion and migration of ESCA [42]. TAMs polarised into M2 macrophages by cytokines such as macrophage colony-stimulating factor (CSF1, M-CSF), IL-10, IL-13 and IL-4 produce anti-inflammatory cytokines such as TGF-β and IL-10 [43]. CCL5 and vascular cell adhesion molecule 1 (VCAM1) promote tumour progression and metastasis in ESCC [44, 45]. Moreover, fibroblast growth factor-7 (FGF-7) regulates cell migration and invasion through activation of NF-KB transcription factors [46]. These results indicate that M2 macrophages are involved in the secretion of these cytokines in the TME, thereby mediating the occurrence and progression of esophageal carcinoma.
We hypothesized that the immunomodulatory activity of FGL2 plays an important role in the pathogenesis of ESCA. Thus, we investigated whether M2 macrophages regulate the TME by increasing FGL2 expression in ESCA. Next, we evaluated the correlation between FGL2 expression and cytokines, including IL-10, MMP9, CCL5, TIM3, IL-13, VCAM1, M-CSF and FGF-7, in ESCA through cBioPortal. Interestingly, scatterplots show that FGL2 expression correlates specifically with these cytokines and that its expression is strongly positively related to all of them (Fig. 8a-7 h). In addition, TIM-3 (HAVCR2) [47], as a crucial gene that regulates T cell exhaustion, showed a significant positive correlation with FGL2 expression, indicating that high FGL2 expression plays an important role in TIM-3-mediated T cell exhaustion. FOXP3 also plays an important role in Tregs, leading to the suppression of cytotoxic T cells attack of tumour cells [48]. A strong, positive correlation was found between PD-1 and CTLA-4 in T cell exhaustion (Supplementary Fig. 2), which is consistent with the results in Table 2. These results further confirm the findings that M2 macrophages regulate the TME via increased FGL2 expression in ESCA. In addition, FGL2 expression was specifically correlated with the presence of immune infiltrating cells in ESCA, suggesting that FGL2 plays a vital role in immune escape and immunosuppression in the esophageal cancer microenvironment.
3.5. Reversing TAM polarization may provide new targets for tumour immunotherapy
Our previous study showed that TAMs contribute directly to the survival, invasion and metastasis of esophageal cancer cells [49]. For the purpose of finding a potential effective immunotherapy target, we conducted an enrichment analysis of GO biological functions (Biological Process, Cellular Component and Molecular Function) and KEGG pathways of the 91 DEGs via DAVID. The results from this GO analysis indicate that the DEGs were primarily enriched for the following: Type I interferon signalling pathway, Response to interferon-beta, Pyroptosis, Protein polyubiquitination, Positive regulation of interleukin-1 beta secretion, NLRP3 inflammasome complex, Interferon-gamma-mediated signalling pathway, Innate immune response, Defence response to virus and AIM2 inflammasome complex (Fig. 9a). Furthermore, KEGG pathway enrichment analysis demonstrated that these DEGs were enriched for pathways involved in: the Toll-Like receptor signalling pathway, RIG-l-like receptor signalling pathway, NF-KB signalling pathway, Measles, Influenza A, Herpes simplex infection, Hepatitis C, Hepatitis B, Cytosolic DNA-sensing pathway and Cytokine-cytokine receptor interaction (Fig. 9b). These results suggest that activation of M1 macrophages up-regulate gene pathways and that blocking them may produce beneficial effects that improve anti-tumour immunity.
We also analysed the functional interaction between proteins to understand the underlying mechanisms leading to tumour occurrence and development. STRING database screening and the Cytoscape software were used to visualize closely connected regions in the PPI network. The MCODE plugin was used to identify the top hub genes, which constituted the most closely connected module. The PPI network includes 54 nodes and 422 edges (Fig. 9c). The top 30 genes out of the 54 hub genes are shown in Fig. 9d. These key genes provide new insight for developing novel molecular drugs that target TAMs in immunotherapies for treating esophageal carcinoma.
Research has shown that FGL2 is a potential molecular target for glioblastoma treatment [50]. Therefore, FGL2 gene set enrichment analysis (GSEA) was used to identify the functions or pathway activity variations involved in ESCA. This analysis revealed enrichment of the MAPK, JAK/STAT, Toll-Like Receptors (TLRs) and other immune-related pathways (Supplementary Fig. 3). A study showed that the presence of FGL2 in tumour cells inhibited granulocyte-macrophage colony-stimulating factor (GM-CSF)-induced CD103 + DC differentiation by suppressing STAT1/5 and p38 activation [51]. Liu, et al. also reported that MAPK-mediated up-regulation of FGL2 promotes proliferation, migration and invasion of colorectal cancer cells [52]. A schematic diagram depicting the potential role of FGL2 in esophageal carcinoma is shown in Fig. 10. Taken together, these results indicate that targeting FGL2 may potentially weaken the immunosuppressive activity of the tumour and thus inhibit its progression.