Whole transcriptome analysis reveals differentially activated biological pathways and gene expression in DE-DLBCL compared with non-DE-DLBCL
RNA-seq analysis of 14 nodal DE-DLBCL and 14 nodal non-DE-DLBCL tissues revealed that DE-DLBCL upregulated the pathways associated with MYC target responses, unfolded protein responses, various mitochondria-related biological processes, and the cell cycle/apoptosis pathway (Fig. 1A; Supplementary Data 1). DEG analysis revealed 128 genes that met the stringent criteria (Padj, FDR < 0.05, fold change > 2), of which 18 were associated with immune responses (Fig. 1B; Supplementary Data 2). DE-DLBCL showed higher expression of anti-inflammatory and immunoglobulin genes than non-DE-DLBCL. In contrast, the expression levels of certain genes, such as ITGAM (CD11b) (primarily expressed in monocytes, macrophages, and granulocytes), ITGAX (CD11c) (predominantly expressed in dendritic cells, monocytes, macrophages, and granulocytes), and MHC II molecules (HLA-DRB5 and HLA-DRB1) (which are primarily found in antigen-presenting cells), were high in non-DE-DLBCL. DE-DLBCL cells displayed significantly higher expression of CCL2 and its receptor CCR2, which are key molecules involved in monocyte recruitment and M2 macrophage polarization. These observations suggest a distinct immune profile in DE-DLBCL.
The immune profile is distinctive between DE-DLBCL and non-DE-DLBCL, and M2 macrophages are elevated in DE-DLBCL
To investigate the immune cell composition, we conducted an immune cell deconvolution analysis of the whole transcriptome data using CIBERSORTx. There was a tendency toward a higher ratio of M2 macrophages/macrophages (M0 + M1 + M2 or M1 + M2) in DE-DLBCL than in non-DE-DLBCL (Supplementary Figure S1A). We extended the analysis to other large publicly available DLBCL datasets for validation (Schmitz et al. 2018, GSE181063, and GSE117556). Across all datasets, B cell populations were increased, whereas CD8+ T cells and various CD4+ T-cell subsets tended to be decreased in DE-DLBCL compared with non-DE-DLBCLs (Fig. 1C; Supplementary Figure S1B and C). Among the myeloid populations, the ratio of M2 macrophages/macrophages was consistently elevated in DE-DLBCL relative to non-DE-DLBCL (Fig. 1C; Supplementary Figure S1B and C).
The immune cell infiltration was validated in an extended IHC cohort. Given the variations in immune cell infiltration according to the tumor site (Supplementary Figure S2) in the IHC cohort and the tumor site (nodal) in our RNA-seq cohort, we restricted our comparison of immune cell infiltration to nodal cases. In nodal DLBCLs, a consistent immune cell infiltration pattern was observed between the transcriptome and IHC cohorts. Specifically, DE-DLBCL exhibited an increase in CD163+ M2 macrophages and a decrease in T-cell infiltration compared with non-DE-DLBCL (Fig. 1D). CD4+ T cells were significantly decreased, and CD8+ T cells and regulatory T cells (FOXP3+ cells, Tregs) tended to decrease in DE-DLBCL. The ratio of CD8+ T cells to Tregs was not significantly different between the DE-DLBCL and non-DE-DLBCL (Fig. 1D). MHC expression was significantly lower in extranodal tumors than in nodal tumors (Supplementary Figure S2S-U). In nodal cases, the expression of MHC class I molecules tended to be lower in DE-DLBCLs than in non-DE-DLBCLs, although the difference was not statistically significant (Supplementary Figure S3A-C). The Ki-67 index was higher in DE-DLBCLs (Supplementary Figure S3D and E), which was consistent with the increased cell cycle signature and elevated B cell population in DE-DLBCLs from our RNA-seq cohort and public datasets.
The comparison between non-GCB and GCB DLBCLs revealed decreased infiltration of CD8+ T cells and lower expression of MHC II molecules in non-GCB DLBCLs than in GCB DLBCLs (Supplementary Figure S4A–J). In nodal DLBCL cases, a significant reduction in the number of CD4+ T cells was observed in non-GCB DLBCL compared with GCB DLBCL (Supplementary Figure S4J–T).
Taken together, transcriptome and IHC analyses showed a distinct immune cell composition associated with DE status, especially highlighting increased M2 macrophage infiltration, which is in line with the increased CCL2-CCR2 gene expression observed in our transcriptomic data
CCL2-CCR2 axis is related to the poor prognosis of DLBCLs
To assess the prognostic significance of the CCL2-CCR2 axis in DLBCLs, we conducted survival analyses based on CCL2 and CCR2 mRNA expression using publicly available datasets. In all datasets, DE-DLBCLs exhibited significantly worse progression-free survival (PFS) and overall survival (OS) than non-DE-DLBCLs (Schmitz dataset, PFS: P < 0.001, OS: P = 0.007; GSE117556, PFS: P < 0.001, OS: P < 0.001; GSE181063 OS: P = 0.008) (Supplementary Figure S5).
In the Schmitz cohort, increased CCL2 expression was significantly associated with poor PFS and OS (P = 0.014 and P = 0.009, respectively) (Fig. 2A and B). Increased CCR2 expression was also significantly associated with worse PFS and OS (P = 0.005 and P = 0.010, respectively) (Fig. 2C and D). The combined high expression of CCL2 and CCR2 showed a significant associated with decreased PFS and OS (P = 0.013 and P = 0.017, respectively) (Fig. 2E and F). In the GSE117556 and GSE181063 datasets, high expression of CCL2 and CCR2 was associated with poor prognosis (Supplementary Figure S6). The combined high expression of CCL2 and CCR2 was significantly associated with poor prognosis (Fig. 2G-I). These findings indicate that the CCL2/CCR2 axis may contribute to poor clinical outcomes in patients with DLBCL, particularly in those with DE-DLBCL.
CCL2 production is increased by MYC and BCL2 in DLBCL cells
In the IHC of DLBCL tissues, CCR2 expression was mainly observed in tumor-associated macrophages (TAMs) rather than in tumor cells. Only 2.4% (3 of 126) of cases exhibited high tumoral CCR2 expression (Supplementary Figure S7A and B). In flow cytometry, CCR2 expression was low, except in the case of OCI-LY3 cells (Supplementary Figure S7C). Given that tumor cells and TAMs are significant sources of CCL2 [20–22], we hypothesized that CCL2 is secreted from DE-DLBCL cells and affects CCR2-expressing macrophages. To verify this hypothesis, 11 DLBCL cell lines were screened for basal protein expression of MYC and BCL2. HT and SUDHL10 were selected as MYClow/BCL2low cell lines (non-DE-DLBCLs), and OCI-LY8 and DOHH2 were selected as MYChigh/BCL2high cell lines (DE-DLBCL cells) (Supplementary Figure S8).
The mRNA expression and production of CCL2 was significantly higher in MYChigh/BCL2high cells than in MYClow/BCL2low cells, both in the resting and interleukin (IL)-4/IL-13-activated states (Fig. 3A). At baseline, the CCL2 expression and its transcription factor, phosphorylated NF-κB p65, was also higher in MYChigh/BCL2high cells than in MYClow/BCL2low cells (Fig. 3B). When either MYC- or BCL2-expression vectors were transfected into MYClow/BCL2low HT and SUDHL10 cells, CCL2 expression increased at the mRNA and protein levels. Moreover, when both the MYC- and BCL2-expression vectors were co-transfected, CCL2 expression increased additively (Fig. 3C-E). The levels of phosphorylated NF-κB p65 were also increased in MYC/BCL2-overexpressing cells compared with control (Fig. 3D). MYC/BCL2 overexpression-induced NF-κB p65 phosphorylation and CCL2 expression and secretion were restored by NF-κB inhibitor, JSH-23 treatment (Fig. 3F and G).
When MYC and BCL2 were inhibited in MYChigh/BCL2high OCI-LY8 and DOHH2 cells using bioavailable inhibitors, that is JQ-1 and fimepinostat for MYC and venetoclax for BCL2, CCL2 expression decreased (Fig. 3H-K and Supplementary Figure S9). Consistently, transfection of siRNAs against MYC and BCL2 into MYChigh/BCL2high cells decreased CCL2 expression and secretion (Supplementary Figure S10A-C). These findings indicate that MYC and BCL2 upregulate CCL2 expression and secretion through NF-κB activation in DLBCL cells.
MYC and BCL2 expression in DLBCL cells promotes M2 polarization of macrophages
We hypothesized that MYC and BCL2 overexpression in DLBCL cells promotes the differentiation of macrophages into immunosuppressive M2 macrophages via CCL2, thereby contributing to poor clinical outcomes. DLBCL cells were co-cultured with THP-1 cell-derived macrophages. For comparison, THP-1-derived macrophages were differentiated into M1 or M2 macrophages using IFN-γ + LPS or IL4 + IL13 treatments, respectively. The expression of M2 markers (CD206, CD163, ARG1, and TGFB1), but not M1 markers (CD11c, CD80, CD86, and NOS2), was increased in macrophages co-cultured with OCI-LY8 and DOHH2 (MYChigh/BCL2high cells) compared with those co-cultured with HT and SU-DHL10 (MYClow/BCL2low cells) at the mRNA and surface protein expression levels (Fig. 4A and B).
MYClow/BCL2low cells were transfected with MYC- and/or BCL2-expression vectors and subsequently co-cultured with THP-1-derived macrophages, resulting in increased expression of M2 markers compared with those co-cultured with control cells (Fig. 4C and Supplementary Figure S11A-C).
Conversely, when MYChigh/BCL2high cells were transfected with siRNAs targeting MYC and BCL2, the expression of M2 markers decreased in macrophages compared with those co-cultured with control cells. However, the expression of M1 markers was slightly increased in macrophages co-cultured with MYC/BCL2-knockdown cells (Fig. 4D and Supplementary Figure S11D-F). Collectively, these findings suggest that MYC and BCL2 expression in DLBCL cells induces macrophage polarization, particularly toward the M2 phenotype.
CCL2 secreted from DE-DLBCL cells promotes macrophage migration and M2 polarization
CCL2 is a chemoattractant for various immune cells, especially monocytes/macrophages [20]. To investigate the significance of CCL2 in macrophage recruitment and M2 polarization within the DE-DLBCL microenvironment, MYChigh/BCL2high cells were co-cultured with THP-1-derived macrophages in the presence or absence of anti-CCL2 nAbs using a Transwell system. Macrophage migration toward MYChigh/BCL2high cells was significantly inhibited by anti-CCL2 nAb (Fig. 5A).
Anti-CCL2 nAb treatment led to a significant decrease in the expression of M2 markers but an increase in M1 markers in macrophages co-cultured with MYChigh/BCL2high cells (Fig. 5B–D). These findings indicate that CCL2 secreted from DE-DLBCL cells may play an important role in macrophage migration and M2 polarization.
CCL2 contributes to progression of DE-DLBCL and induces an immunosuppressive TME in vivo
To further determine whether CCL2 contributes to DE-DLBCL progression by increasing the number of M2 macrophages and inducing an immunosuppressive TME in vivo, MYC- and BCL2-overexpressing stable cell lines were established using A20 cells (Supplementary Figure S12A). These cells were subcutaneously injected into the flanks of mice. To evaluate whether macrophages are necessary for the aggressiveness of DE-DLBCLs, clodronate liposomes were injected intraperitoneally into mice (Fig. 6A). The growth of MYC/BCL2-overexpressing A20 cells was significantly higher than that of the control cells. However, macrophage depletion using clodronate liposomes significantly suppressed the growth of MYC/BCL2-overexpressing A20 cells (Fig. 6B), suggesting that macrophages play an important role in DE-DLBCL tumor progression.
To assess the role of CCL2 in vivo, an anti-CCL2 nAb was injected intraperitoneally into the mice (Fig. 6C). CCL2 depletion in tumor-bearing mice significantly suppressed the growth of MYC/BCL2-overexpressing A20 cells as well as control A20 cells (Fig. 6C). The TAM population (CD11b+F4/80+) was higher in MYC/BCL2-overexpressing tumors than in control tumors, which was restored by anti-CCL2 nAb. The surface expression of CD206 and CD163 on TAM from MYC/BCL2-overexpressing A20 tumors was significantly decreased, but the surface expression of CD11c and iNOS was slightly increased by anti-CCL2 nAbs (Fig. 6D and G). The population of monocytic myeloid-derived suppressor cells was also decreased by the anti-CCL2 nAb in MYC/BCL2-overexpressing A20 tumors (Supplementary Figure S12B and C). In contrast, tumor-infiltrating CD4+ and CD8+ T cells were increased, whereas FOXP3+ Tregs were decreased by anti-CCL2 nAbs (Fig. 6E and G). In particular, the population of IFN-γ-producing CD4+ and CD8+ T cells and cytotoxic CD8+ T cells (granzyme B+CD8+ T cells) increased after treatment with anti-CCL2 nAbs (Fig. 6F and G). These findings indicate that CCL2 secreted from DE-DLBCL cells promotes tumor progression by creating an immunosuppressive tumor immune microenvironment in vivo, and that CCL2 could be a therapeutic target in DE-DLBCL.