Abstract Background Tumor-associated macrophages (TAMs), as key immune components of the TME, play a pivotal role in tumor progression by fostering an immunosuppressive environment. Programmed death 1 (PD-1), a critical immune checkpoint molecule predominantly expressed on T cells, mediates immune suppression by binding to programmed death-ligand 1 (PD-L1) on tumor cells within the tumor microenvironment (TME). Emerging evidence reveals that TAMs also express PD-1, however, the expression and functional regulatory mechanisms of PD-1 on TAM remain poorly understood. Methods In this study, we combined bulk RNA sequencing and single-cell RNA sequencing (scRNA-seq) data to investigate the association between PD-1 expression on macrophages and patient prognosis, while also uncovering the molecular mechanisms by which PD-1 regulates macrophage function. To further investigate the role of PD-1 in macrophage activity, we established a fluorescence-labeled tumor-bearing mouse model using CT26 cells, a murine colorectal cancer cell line, to evaluate the relationship between PD-1 expression on TAMs and their phagocytic activity as well as other functions. Additionally, to mimic the TME in vitro, we cultured bone marrow-derived macrophages (BMDMs) with CT26-conditioned medium (CT26-CM). Results Our results suggest that PD-1 expression on TAMs drives macrophage polarization toward an M2-like phenotype, suppresses their phagocytic activity, inhibits the synthesis of interferon-γ (IFN-γ) signaling molecules, and ultimately promotes tumor progression. Mechanistically, we demonstrated that PD-1 regulates the synthesis of IFN-γ signaling molecules and the polarization of M2-type macrophages in BMDMs through the JAK2-STAT3 signaling pathway. Overall, our study demonstrates that PD-1 expression on TAMs facilitates the formation of an immunosuppressive microenvironment, ultimately accelerating tumor progression. Clinical trial number Not applicable. Supplementary Information The online version contains supplementary material available at 10.1186/s12967-025-06469-4. Keywords: Programmed death-1, Tumor-associated macrophages, Anti-tumor, JAK2-STAT3 signaling pathway, Bone marrow-derived macrophages Introduction Colorectal cancer (CRC) is the third most common cancer worldwide [[42]1]. In recent years, immune checkpoint inhibitors have gained increasing attention as a promising therapeutic strategy for CRC patients [[43]2, [44]3]. In 2015, Dung T. Le et al. discovered that monoclonal antibodies targeting programmed cell death protein 1 (PD-1, encoded by PDCD1) exhibited significant efficacy in patients with high microsatellite instability/deficient DNA mismatch repair (MSI-H/dMMR) CRC, whereas resistance was observed in patients with microsatellite stable/proficient DNA mismatch repair (MSS/pMMR) CRC [[45]4]. PD-1, an apoptosis-related inhibitory receptor, is primarily expressed on activated T cells [[46]5]. By interacting with programmed death-ligand 1 (PD-L1) on tumor cells, PD-1 suppresses T cell-mediated anti-tumor immune responses, thereby promoting immune evasion [[47]6–[48]8]. The role of the PD-1/PD-L1 axis in adaptive immunity has been extensively studied [[49]9, [50]10]. Increasing evidence suggests that interactions between tumor cells and macrophages may contribute to resistance to anti-PD-1 therapy [[51]11]. Therefore, to overcome the variability in PD-1 immune therapy sensitivity and resistance across different CRC subtypes, there is an urgent need to gain a comprehensive understanding of the mechanisms of PD-1 action from a multi-cellular perspective. Tumor-associated macrophages (TAMs) are key components of the tumor microenvironment (TME) [[52]12], classified into pro-inflammatory M1 and anti-inflammatory M2 types [[53]13–[54]16]. TAMs promote tumor progression by establishing an immunosuppressive microenvironment that suppresses the host’s anti-tumor immune response [[55]17–[56]24]. Research by Strauss L et al. has shown that PD-1 expression on the surface of macrophages plays a crucial role in anti-tumor immune responses. Compared to T cell-specific PD-1 knockout, conditional deletion of PD-1 in myeloid cells significantly suppresses tumor growth [[57]25]. This finding underscores the need to shift our research focus toward macrophages to further investigate the specific mechanisms of PD-1. Existing evidence suggests that high macrophage infiltration is closely associated with resistance to PD-1/PD-L1 immune checkpoint inhibitors. Therefore, TAMs are considered potential targets for overcoming PD-1 therapy resistance [[58]26–[59]29]. Further investigation into the expression of PD-1 on macrophages and its regulatory mechanisms has become a key focus of current research. Sydney R. Gordon’s research on PD-1 expression in macrophages has laid the foundation for this field, initiating new explorations into the role of PD-1 in immune regulation. It has been confirmed that PD-1 is predominantly expressed on the surface of M2 macrophages. Moreover, Giemsa staining of TAMs and in vitro phagocytosis assays using Staphylococcus aureus bio-particles revealed that macrophages expressing PD-1 exhibit relatively lower phagocytic capacity [[60]30]. Recent studies on the mechanisms of intracellular PD-1 expression in macrophages have also been explored in chronic inflammation models [[61]31, [62]32]. The high expression of PD-1 in macrophages has been shown to depend on transforming growth factor-beta1, which sustains PD-1 expression through the SMAD3/STAT3 signaling pathways [[63]33]. However, comprehensive studies on the regulation of macrophage function by PD-1 are still lacking, and the specific intracellular regulatory mechanisms of PD-1 in macrophages remain underexplored. This study investigates the impact of PD-1 expression on the surface of macrophages within the CRC tumor microenvironment on their anti-tumor immune functions. By combining bulk RNA sequencing and single-cell RNA sequencing (scRNA-seq) data, we provide a comprehensive analysis of the regulatory effects and underlying mechanisms of PD-1 expression in macrophages. To validate our findings, we employed in vivo and in vitro models, including Enhanced Green Fluorescent Protein (EGFP)^+CT26 BALB/c (a murine colorectal cancer cell line) tumor-bearing mice, CT26 cell models and bone marrow-derived macrophage (BMDM) models. These experiments confirmed the broad impact of PD-1 expression in the TME on macrophage function and further elucidated the mechanisms by which PD-1 regulates macrophage activity. Overall, this study aims to advance our understanding of how PD-1 influences macrophage-mediated anti-tumor immunity in CRC and to uncover its potential regulatory mechanisms. Methods Cell culture and construction of EGFP^+ CT26 cell line CT26 and Raw264.7 cells were obtained from the National Collection of Authenticated Cell Cultures, China, and cultured at the Northern Translational Medicine Center, Harbin Medical University. CT26 cells were maintained in Roswell Park Memorial Institute 1640 medium (RPMI 1640, Thermo Fisher Scientific, USA) supplemented with 10% fetal bovine serum (FBS, Thermo Fisher Scientific, USA) and 1% penicillin-streptomycin. Raw264.7 cells were cultured in Dulbecco’s Modified Eagle’s Medium (DMEM, Thermo Fisher Scientific, USA) under the same supplementation conditions. HEK 293T cells were used as host cells for lentivirus production. The lentiviral plasmid PLV (VectorBuilder, China), carrying an EGFP fluorescent tag and a neomycin resistance gene, was utilized. Plasmids PxpaX2, PMD2g and PLV were mixed at a mass ratio of 3:2:1 and transfected into 293T cells using Lipofectamine 3000 (Thermo Fisher Scientific, USA) to form plasmid-reagent complexes, which were then internalized by the cells. Viral supernatants were collected 48–72 h post-transfection and subsequently used to infect CT26 cells in the presence of 8 µg/ml Polybrene (Univ, China) to enhance infection efficiency. Finally, stable cell lines were established by selecting resistant clones with 800 µg/ml G418 (Thermo Fisher Scientific, USA). Bone marrow-derived macrophages Cervical dislocation was performed to euthanize 6- to 8-week-old C57BL/6 mice. After femurs and tibias were harvested, bone marrow was collected and cultured in DMEM containing 10% FBS and 10 ng/ml recombinant mouse macrophage colony-stimulating factor (M-CSF). After 3 days, half of the medium was replaced and BMDMs were harvested on day 7. To detach the cells, BMDMs were incubated with Accutase (Sigma-Aldrich, USA) in a CO[2] incubator for 25 min, facilitating cell detachment from the culture dish. Mice and tumor establishment SPF-grade BALB/c mice (Vitalriver, China) were subcutaneously injected with 100 µl of CT26 cell suspension (5 × 10⁵ cells per mouse) into the left flank. A nodular elevation appeared immediately after injection, with palpable granules detectable on day 5. Tumor size was measured on day 7 using the formula: length × width^2/2. If multiple nodules were present, their measurements were summed. During the modeling period, temperature, humidity, airflow, and lighting were strictly controlled to simulate day/night cycles in the animal facilities. Mice were provided with adequate feed and sterilized water, with regular replacement of high-pressure processed bedding and cages. Continuous access to drinking water and food was ensured. All animal procedures were approved by the Ethics Committee of Harbin Medical University (Harbin, China). Flow cytometry For macrophage detection, the CD16/CD32 (Biolegend, USA) blocking antibody was used. Macrophage markers and polarization-related antibodies included PerCP-anti-F4/80, PE-anti-CD86, and FITC-anti-CD206 (BioLegend, USA). Additionally, anti-mouse PD-1 (BIO X Cell, USA), anti-mouse PD-L1, PerCP-anti-Interferon-γ (IFN-γ) (BioLegend, USA) and PE-anti-Rat IgG (Abcam, UK) were employed. For intracellular staining, the Fix/Permeabilization Kit (BD Biosciences, USA) was utilized. Macrophage phagocytosis Bone marrow-derived macrophages (BMDMs) were seeded at 200,000 cells per well in a 12-well plate. After the cells had fully adhered and spread, 1 μm latex beads (Sigma-Aldrich, USA) were added at a 1:250 dilution and incubated for 1 h. Non-phagocytosed fluorescent microspheres were then removed by washing with PBS. Subsequently, cells were stained with DiD membrane dye (Absin, China) at a 1:10 dilution, followed by DAPI (Beyotime, China) for nuclear staining. SiPD-1 To knock down PD-1 on the surface of BMDMs, siPD-1 (5’-3’: CACUUCUAGGGACUUGAGATT; 3’-5’: UCUCAAGUCCCUAGAAGUGTT) and simock (5’-3’: TTCTCCGAACGTGTCACGT; 3’-5’: ACGTGACACGTTCGGAGAA) were transfected using INTERFERin^® transfection reagent (Polyplus-transfection^®, France). For siRNA-mediated knockdown in a 24-well plate, 8.4 ng of siRNA was first diluted in 100 µl of serum-free medium, followed by the addition of 2 µl INTERFERin^®. The mixture was gently vortexed and incubated at room temperature for 10 min to allow the formation of transfection complexes. Subsequently, the transfection complex was added to each well containing cells at 50% confluency in 500 µl of fresh medium. After a 72-hour incubation, protein levels were assessed to confirm knockdown efficiency. Migration and invasion For the migration assay, the lower chamber of the 24-well transwell plate was filled with 600 µl RPMI 1640 containing 20% FBS and 1% penicillin-streptomycin. The upper chamber was seeded with 20,000 cells in RPMI 1640. After 24 h of incubation, cells were fixed with 4% formaldehyde and stained with 0.2% crystal violet to assess migration. For the invasion assay, the transwell chamber was coated with Matrigel (Corning, USA) to mimic the extracellular matrix. The lower chamber was filled with 600 µl RPMI 1640 containing 20% FBS and 1% penicillin-streptomycin, while the upper chamber contained 40,000 cells in RPMI 1640. After 24 h of incubation, cells were fixed with 4% formaldehyde and stained with 0.2% crystal violet to evaluate invasion. Western blot JAK2 Antibody (Abmart, China), Phospho-JAK2 (Tyr931) Antibody (Abmart, China), STAT3 Antibody (Abmart, China), and Phospho-STAT3 (Y705) Antibody (Abmart, China) were used for Western blot analysis to detect signaling proteins in macrophages. Colivelin (MCE, USA), a cell-permeable neuroprotective peptide, was utilized in this study as a potent activator of STAT3. The Western blotting procedure was performed according to standard protocols described in previous literature [[64]34]. Briefly, treated cells were collected and thoroughly lysed, followed by centrifugation to obtain the supernatant. Protein samples were prepared by boiling the collected supernatant. After protein quantification, samples were subjected to electrophoresis using 10% and 12.5% SDS-polyacrylamide gels, followed by wet transfer (300 mA, 90 min) onto PVDF membranes. The membranes were then blocked and sequentially incubated with primary and secondary antibodies. For signal detection, ECL substrate solution was freshly prepared by mixing solution A and B at recommended ratios. The PVDF membranes were evenly coated with the ECL mixture and immediately analyzed using a chemiluminescence imaging system. Transcriptomic data collection The bulk RNA-seq data of colorectal cancer (TCGA-COAD) used in this study were obtained from the UCSC Xena database ([65]http://xenabrowser.net/hub). The scRNA-seq data from CRC murine models were sourced from the Gene Expression Omnibus (GEO) database ([66]GSE150970; [67]http://www.ncbi.nlm.nih.gov/geo/). Bulk RNA-Seq data processing and normalization By integrating clinical information with gene expression profiles, a total of 379 samples were included for subsequent analysis. To normalize the gene expression data, we converted the raw count data to transcripts per million (TPM) and applied a log[2](TPM + 1) transformation to the TPM values. Quantification of PDCD1 High-Activity macrophage To quantify the PDCD1-related activity level of macrophages in the samples, we developed an activity score (PDCD1Score) based on the expression levels of the PDCD1 and CD64 genes. The calculation formula is as follows: graphic file with name d33e435.gif where exp represents the gene expression level. This score reflects the intensity of PDCD1-related activity in macrophages. Based on the third quartile (75th percentile) of the activity score, samples were categorized into two groups: the high-activity group (PD-1^high TAM) and the low-activity group (PD-1^low TAM). Prognostic analysis To evaluate the survival difference between PD-1^high TAM and PD-1^low TAM, we used Kaplan-Meier analysis to generate survival curves and used the log-rank test to assess statistical significance between the two groups. Additionally, we integrated multiple clinical indicators and assessed the independent prognostic value of the PDCD1Score through multivariate Cox regression analysis. Forest plots were constructed to visually present the results of the multivariate analysis. Single-cell RNA-seq data processing and analysis The Seurat package in R software was used for the basic analysis workflow. After preprocessing the data, a linear transformation was performed using ScaleData, followed by principal component analysis with RunPCA to identify the significant dimensions in the dataset. Clustering analysis was performed with FindClusters using the Louvain algorithm after constructing the shared nearest neighbor graph. Visualization was generated on a two-dimensional map using UMAP. Cell annotation files provided by the contributors and well-known marker genes of mouse cell lineage (Cd79a, Cd79b, Ms4a1, Fcmr, and Igkc for B cells; Col1a1, Dcn, Col1a2, and Tm4sf1 for CD45^− cells; Flt3, Cd80, and Cd209a for dendritic cells (DC); Cd14, Cd68, Adgre1, Apoe, and Lyz2 for macrophages; Gzma, Gzmb, Ncr1, Klrb1c, and Nkg7 for natural killer cells (NK); Cd2, Cd3e, Cd3d, and Cd3g for T cells) [[68]35] were used to identify cell types in CRC. Differentially expressed genes (DEGs) with high discriminatory power across distinct cell types were identified using FindAllMarkers and visualized with scRNAtoolVis. Functional and pathway enrichment analysis Functional enrichment analysis was performed to investigate the biological significance of the top 100 upregulated DEGs, which were selected based on their log fold change (logFC) values and filtered using an adjusted p-value threshold of < 0.05. The analysis was conducted with the clusterProfiler package in R. Gene Ontology (GO) enrichment analysis was carried out using the enrichGO function, covering three major categories: Biological Process (BP), Cellular Component (CC), and Molecular Function (MF). Additionally, pathway enrichment analysis was performed using the enrichKEGG function to identify significantly enriched pathways from the Kyoto Encyclopedia of Genes and Genomes (KEGG) database. For both GO and KEGG analyses, statistical significance was determined by a p-value threshold of < 0.01 and a q-value threshold of < 0.05. The significantly enriched GO terms and KEGG pathways were further refined and analyzed to elucidate the potential biological functions and regulatory pathways associated with the upregulated DEGs. Statistical analysis Experimental data are expressed as mean ± SD. Data from two experimental groups were analyzed using the t-test, while data from multiple groups were analyzed using one-way ANOVA. P-value of < 0.05 was considered statistically significant (*P < 0.05, **P < 0.01, ***P < 0.001). Statistical graphs were created using GraphPad Prism 10.1.2. Bioinformatics data were analyzed with RStudio 4.3.1, and data normality was assessed using SPSSAU. Results Single-cell and bulk transcriptomics reveals the anti-tumor effects of PD-1 expression on macrophages in colorectal cancer Given the potential impact of macrophage PD-1 expression on patient prognosis, we constructed a PDCD1Score based on the expression levels of PDCD1 and CD64, with Cd64 validated as a macrophage marker at the single-cell level (Fig. [69]1E). Patients were then stratified into PDCD1^high TAM and PDCD1^low TAM groups, and the results demonstrated that PDCD1Score effectively distinguished prognostic outcomes in COAD patients (Fig. [70]1A). Furthermore, multivariate Cox regression analysis, incorporating clinical variables such as sex, age, and pathological stage, identified PDCD1^+ macrophage activity score as an independent prognostic factor for COAD patients, as demonstrated in the forest plot (Fig. [71]1B). Fig. 1. [72]Fig. 1 [73]Open in a new tab CRC single cell and bulk transcriptome data reveal the effect of PD-1 expression on macrophages in patient prognosis and function. (A) Kaplan-Meier survival curves for PDCD1^low TAM and PDCD1^high TAM patients. (B) Clinical characteristics of CRC patients and PDCD1score multivariate Cox regression analysis results. (C) UMAP visualization of all single cells, with colors representing different samples. (D) UMAP visualization of all single cells, with colors indicating annotated cell types. (E) UMAP visualization of Cd64 expression in macrophage subclusters. (F) Dot plot depicting marker gene expression across cell types, with point size indicating the proportion of cells expressing each gene and color gradient reflecting average expression levels. (G) Volcano plot illustrating significant DEGs across cell types, with upregulated genes in red and downregulated in blue; the top 5 for each category are labeled. (H) Stacked bar charts showing the proportion of cell components in all samples. (I) Enrichment bar plot of upregulated DEGs linked to biological functions in Pdcd1^+ macrophages, showcasing significant GO terms from BP, MF and CC, with validated pathways highlighted in red. CRC: Colorectal Cancer; DEGs: Differentially Expressed Genes; GO: Gene Ontology; BP: Biological Processes; MF: Molecular Functions; CC: Cellular Components To comprehensively investigate the expression of the immune checkpoint PD-1 on non-T lymphocytes and its impact on CRC progression, we performed an in-depth analysis of the publicly available single-cell sequencing dataset [74]GSE150970. After quality control and filtering steps, a total of 143,680 cells were retained for subsequent analysis. Due to the large sample size and potential batch effects, we examined the clustering pattern of the samples using a two-dimensional UMAP plot. The results showed minimal heterogeneity between the samples, with a good mixture of samples in the plot (Fig. [75]1C). We then annotated the cell types based on the expression of marker genes and the metadata provided by the dataset. The UMAP plot demonstrated the distribution of different cell types, including DC, B cells, macrophages, T cells, NK and CD45^− cells (Fig. [76]1D). A bubble plot showed the expression of typical marker genes for these cell types (Fig. [77]1F). Furthermore, we identified upregulated and downregulated DEGs in these six cell types (Fig. [78]1G), with most of the DEGs closely related to cell type-specific genes. We then used a stacked bar chart to display the cellular composition across different samples. The results showed significant differences in the proportions of cell types among the 30 CT26 tumor-bearing mouse model samples, reflecting the heterogeneity in cellular composition. Myeloid cells, particularly macrophages, exhibited a high infiltration proportion, with most samples showing more than 40% macrophage infiltration, while only five samples had less than 30% (Fig. [79]1H). This phenomenon suggests that excessive macrophage infiltration may have a potential impact on the TME and tumor progression. To delineate the impact of PD-1 expression on TAM functionality, we isolated 64,297 cells from macrophage subsets and stratified them into Pdcd1^+ (high Pdcd1 expression) and Pdcd1^− (low/undetectable Pdcd1 expression) groups based on Pdcd1 levels (PD-1 protein, encoded by the Pdcd1 gene). Differential expression analysis was then performed between the two groups, followed by functional enrichment analysis of the upregulated genes to explore their potential biological significance. The enrichment analysis results indicated that Pdcd1 levels in macrophages were associated with their anti-tumor functions, primarily involving phagocytosis, polarization, type II interferon production, and regulation of monocyte proliferation (Fig. [80]1I, Fig. [81]S1A and B). These findings suggest that PD-1 may play a key role in the anti-tumor functions of macrophages. The correlation between macrophage PD-1 expression and tumor progression as well as anti-tumor function in EGFP^+CT26 tumor-bearing mouse model Based on the functional enrichment analysis results from single-cell sequencing in Fig. [82]1, we further validated the impact of PD-1 expression levels in macrophages on their anti-tumor functionality through in vivo experiments. To facilitate subsequent detection, we developed an EGFP-overexpressing CT26 colorectal cancer cell line and implanted it subcutaneously into BALB/c mice (n = 19) to establish a tumor-bearing model (Fig. S2A). Punctate tumor nodules were first observed on day 7 post-transplantation, with continuous monitoring of tumor volume progression. On day 22 post-implantation, tumor tissues were harvested and photographed for documentation (Fig. [83]2A C). Macrophages were identified using F4/80 as a specific marker [[84]36]. Flow cytometric analysis was then conducted to assess the expression profiles and co-expression patterns of PD-1, CD86, and EGFP (Fig. S2B and S2C). Fig. 2. [85]Fig. 2 [86]Open in a new tab The expression of PD-1 on TAMs correlates positively with tumor growth and infiltration, but negatively with phagocytosis and M1 polarization in tumor-bearing mice. (A) Construction of CT26 subcutaneous tumor mouse model; tumor volume measured on days 7, 13, 16, 19, and 22 (n = 19). (B) SPSS test for normal distribution characteristics of F4/80^+, F4/80^+PD-1^+, F4/80^+CD86^+, and F4/80^+EGFP^+ flow results. (C) Changes of tumor volume in mice (n = 19). (D) Correlation analysis of TAM PD-1 expression and tumor volume, with sample order from low to high PD-1 expression (n = 19). (E) PD-1 expression in individual mice and its relation to tumor growth (n = 19). (F) Correlation analysis of TAM PD-1 expression (F4/80^+PD-1^+) and TAM infiltration (F4/80^+) (n = 19). (G) Correlation analysis of TAM PD-1 expression (F4/80^+PD-1^+) and TAM phagocytosis (F4/80^+EGFP^+) (n = 19). (H) Correlation analysis of TAM PD-1 expression (F4/80^+PD-1^+) and M1 macrophage polarization (F4/80^+CD86^+) (n = 19). PD-1: Programmed Death-1; TAMs: Tumor-Associated Macrophages Flow cytometry data from 19 samples were first tested for normality using the Shapiro-Wilk test to validate the assumptions for statistical analysis [[87]37]. Results indicated that all four datasets followed a normal distribution (Fig. [88]2B). Pearson correlation coefficients (r) were then calculated between PD-1 expression (F4/80^+PD-1^+) and tumor volume, TAM infiltration (F4/80^+), M1-like polarization (F4/80^+CD86^+), and phagocytic activity of TAM (F4/80^+EGFP^+). In the CT26-driven colorectal cancer model, PD-1 expression on macrophages was positively correlated with tumor volume and TAM infiltration, while negatively correlated with TAM phagocytic function and M1 polarization status (Fig. [89]2D-G). Mice were divided into PD-1^high and PD-1^low groups based on PD-1 expression levels on TAM. Compared to the PD-1^low group, the PD-1^high group exhibited higher tumor growth rates and TAM infiltration, along with relatively lower phagocytic activity and M1 polarization (Fig. [90]S3). These findings suggest that surface PD-1 expression on TAMs is closely associated with tumor progression and impaired anti-tumor macrophage function. The expression of PD-1 on the surface of BMDMs inhibits its phagocytic function To investigate the impact of the TME on PD-1 expression in macrophages, BMDMs isolated from the femur and tibia of C57BL/6 mice were utilized as an in vitro experimental model (Fig. [91]3A). BMDMs were stimulated with CT26-conditioned medium (CT26-CM), and PD-1 expression was analyzed by flow cytometry. The results demonstrated that CT26-CM significantly upregulated PD-1 expression on the surface of BMDMs in a time-dependent manner, with expression levels progressively increasing over time (Fig. [92]3B). Consistent findings were observed in Raw264.7 cells (Fig. [93]S4A). These data confirm that the TME induces PD-1 upregulation on macrophages. Fig. 3. [94]Fig. 3 [95]Open in a new tab The effect of PD-1 expression on morphological changes of macrophages and phagocytic functions were verified. (A) Examination of morphological changes in primary BMDMs cultures at day 3 and day 5. (B) Flow cytometry analysis of PD-1 expression on BMDMs induced by CT26-CM. (C) Microscopic assessment of morphological differences among BMDMs across various groups (100x). (D, E) Flow cytometry and immunofluorescence assess BMDMs phagocytosis of green fluorescent microspheres under varying treatments. PD-1: Programmed Death-1; BMDMs: Bone Marrow-Derived Macrophages; CT26-CM: CT26-Conditioned Medium. *P < 0.05 by unpaired t-test To further explore the functional role of PD-1 in macrophages, PD-1 expression was knocked down in BMDMs using siRNA (Fig. [96]S4B). Microscopic analysis revealed that PD-1-silenced BMDMs exhibited a significant increase in pseudopodia formation compared to the siRNA control (simock) group (Fig. [97]3C). To directly assess the impact of PD-1 knockdown on macrophage phagocytic function, BMDMs were transfected with PD-1-specific siRNA in the presence or absence of CT26-CM. Phagocytic activity was evaluated using green fluorescent microspheres, quantified by flow cytometry and visualization via immunofluorescence microscopy. Results demonstrated that PD-1 knockdown significantly enhanced the phagocytic capacity of BMDMs toward fluorescent microspheres in both untreated and CT26-CM-stimulated groups compared to their respective controls (Fig. [98]3D, E, and [99]S4C). These findings indicate that high PD-1 expression on BMDMs critically suppresses their phagocytic function. Knockdown of PD-1 in BMDMs promotes their polarization toward the M1 phenotype and suppresses tumor invasion and migration Macrophage polarization is often closely associated with tumor progression [[100]38, [101]39]. In this study, CD86 and CD206 were selected as surface markers for M1- and M2-polarized macrophages, respectively. The polarization state was evaluated by the CD86/CD206 ratio. Results showed that CT26-CM stimulation significantly reduced CD86 expression, increased CD206 expression, and markedly decreased the CD86/CD206 ratio (Fig. [102]4A), indicating that TME promotes macrophage polarization toward an M2 phenotype in vitro. Fig. 4. [103]Fig. 4 [104]Open in a new tab The expression of PD-1 on BMDMs promotes the polarization of macrophages M2 and ultimately promotes the invasion and migration of CT26 cells. (A) After CT26-CM stimulation, flow cytometry measures CD86 and CD206 expression in BMDMs, calculating the CD86/CD206 ratio to indicate macrophage polarization. (B) In NC and CM groups, PD-1 knockdown on BMDMs is followed by flow cytometry to measure CD86 and CD206 expression and calculate the CD86/CD206 ratio. (C) Collection of supernatants from NC simock, NC siPD-1, CM simock, and CM siPD-1 to stimulate CT26, followed by transwell assessment of CT26 invasion and migration in the four groups. PD-1: Programmed Death-1; CT26-CM: CT26-Conditioned Medium; BMDMs: Bone Marrow-Derived Macrophages. Data represent mean with SD. *P < 0.05, **P < 0.01, ***P < 0.001, ****P < 0.0001 by ordinary one-way ANOVA. *P < 0.05, **P < 0.01 by unpaired t-test Subsequently, PD-1 was knocked down in BMDMs. Flow cytometry analysis revealed that PD-1 silencing in macrophages promoted macrophage polarization toward the M1 phenotype in both untreated (NC) and CT26-CM-stimulated (CM) groups (Fig. [105]4B). In cancer research, reprogramming of M2-polarized macrophages toward the M1 phenotype holds significant antitumor potential [[106]40, [107]41]. These findings confirm that the TME upregulates PD-1 on macrophages, thereby driving M2 polarization, while PD-1 knockdown reverses this effect. To further validate the functional impact of PD-1 expression in BMDMs on tumor cells, supernatants from control (simock) and PD-1-silenced (siPD-1) BMDMs were collected and co-cultured with CT26 cells. Results demonstrated that supernatants from siPD-1 BMDMs significantly suppressed CT26 cells migration and invasion compared to control supernatants (Fig. [108]4C). Collectively, these findings suggest that PD-1 is a potential therapeutic target for reprogramming M2-polarized macrophages and inhibiting tumor progression. The expression of IFN-γ signaling protein in BMDMs is directly regulated by PD-1 Functional enrichment analysis of Result 1 suggested that Pdcd1 expression correlates with type II interferon production in macrophages. IFN-γ, a key member of the type II interferon family, is primarily produced by lymphocytes but can also be secreted by macrophages [[109]42, [110]43]. In this study, we investigated the changes in IFN-γ expression in BMDMs after CT26-CM treatment. Flow cytometry revealed that CT26-CM significantly reduced IFN-γ expression in BMDMs, with levels progressively decreasing over time (Fig. [111]5A). Strikingly, siRNA-mediated PD-1 silencing reversed this suppression of IFN-γ (Fig. [112]5B). Notably, PD-1 knockdown increased the frequency of CD86^+IFN-γ^+ and CD206^−IFN-γ^+ cell populations, highlighting stronger co-expression of IFN-γ with CD86 (Fig. [113]5C). These results demonstrate that PD-1 directly modulates IFN-γ signaling protein production in BMDMs, with IFN-γ exhibiting preferential synergy with CD86. Fig. 5. [114]Fig. 5 [115]Open in a new tab PD-1 expression of BMDMs affects IFN-γ signaling protein expression. (A) Flow cytometry analysis of IFN-γ protein expression in BMDMs stimulated by CT26-CM over time. (B) Knockdown of PD-1 in BMDMs within NC and CM groups, followed by flow cytometry measurement of IFN-γ protein expression. (C) Flow cytometry assessed the proportion of IFN-γ co-expressed with CD86 and CD206 in BMDMs before and after PD-1 knockdown. IFN-γ: Interferon-γ; PD-1: Programmed Death-1; BMDMs: Bone Marrow-Derived Macrophages; CT26-CM: CT26-Conditioned Medium; DEGs: Differentially Expressed Genes. Data represent mean with SD. *P < 0.05, **P < 0.01, ***P < 0.001 by ordinary one-way ANOVA. *P < 0.05, ***P < 0.001 by unpaired t-test PD-1 regulates macrophage polarization and anti-tumor function through JAK2-STAT3 signaling pathway To elucidate the molecular mechanisms underlying PD-1 expression-mediated regulation of macrophage function, we performed KEGG pathway enrichment analysis on the top 100 DEGs. The analysis revealed a significant association between PD-1 up-regulation in macrophages and the JAK-STAT3 signaling pathway (Fig. [116]6A). Previous studies have established the critical role of JAK2-STAT3 signaling in maintaining macrophage homeostasis and regulating polarization [[117]44, [118]45]. Phosphorylation is a key post-translational modification that regulates protein activity. In the JAK-STAT3 pathway, STAT3 phosphorylation is essential for its activation and nuclear translocation, driving downstream transcriptional programs. Thus, the phosphorylation levels of JAK2 and STAT3 (p-JAK2 and p-STAT3) are commonly used as direct indicators of JAK-STAT pathway activation [[119]46]. Western blot analysis demonstrated that PD-1 knockdown in BMDMs significantly decreased p-JAK2/JAK2 and p-STAT3/STAT3 ratios, suggesting inhibition of JAK2-STAT3 pathway activation (Fig. [120]6B and Fig. [121]S5A). Fig. 6. [122]Fig. 6 [123]Open in a new tab PD-1 of BMDMs affects macrophage polarization, IFN-γ signaling protein production and tumor promotion through JAK2-STAT3 pathway. (A) KEGG pathway enrichment bubble chart of DEGs in Pdcd1^+ macrophages. (B) Western blot detected the protein levels of STAT3, p-STAT3, JAK2, and p-JAK2 after PD-1 knockdown of BMDMs. (C) Flow cytometry was used to detect the expression of macrophage polarization-related proteins CD86 and CD206. (D) Flow cytometry was used to detect IFN-γ signaling protein production in macrophages in the three groups. (E) Collect supernatants from BMDMs treated with CM siPD-1, and CM siPD-1 + colivelin to stimulate CT26 and evaluate CT26 migration via transwell assays. (F) Collect supernatants from BMDMs treated with CM siPD-1, and CM siPD-1 + colivelin to stimulate CT26 and assess CT26 invasion through transwell assays. IFN-γ: Interferon-γ; PD-1: Programmed Death-1; Kyoto Encyclopedia of Genes and Genomes (KEGG); BMDMs: Bone Marrow-Derived Macrophages; DEGs: Differentially Expressed Genes. Data represent mean with SD. **P < 0.01 by unpaired t-test. *P < 0.05, **P < 0.01 by ordinary one-way ANOVA To investigate whether JAK2-STAT3 signaling mediates the regulatory effects of PD-1 on macrophage function, Colivelin, a potent STAT3 activator, was added to PD-1-silenced BMDMs treated with CT26-CM. Flow cytometry analysis revealed that colivelin treatment reversed the M1 polarization shift induced by PD-1 knockdown, redirecting macrophages toward M2 polarization (Fig. [124]6C). These findings demonstrate that PD-1 regulates macrophage polarization through the JAK2-STAT3 pathway. While PD-1 silencing enhanced macrophage phagocytic capacity, colivelin was unable to reverse this effect (Fig. [125]S5B), suggesting that alternative pathways may be involved in PD-1-mediated regulation of phagocytosis. However, the up-regulation of IFN-γ induced by PD-1 knockdown was fully suppressed by colivelin treatment (Fig. [126]6D and Fig. [127]S5C), supporting the STAT3-dependent regulation of IFN-γ production. We further evaluated the functional consequences by collecting BMDM-CM from differently treated macrophages (CT26-CM + siPD-1 vs. CT26-CM + siPD-1 + colivelin) to stimulate CT26 cell lines. Notably, colivelin reversed the suppression of tumor cell migration and invasion induced by PD-1-silenced macrophages (Fig. [128]6E and F). Collectively, these results demonstrate that PD-1 modulates macrophage polarization, IFN-γ secretion, and ultimately governs the invasive and migratory capacities of CT26 cells through the JAK2-STAT3 signaling pathway. Discussion Emerging evidence has expanded our understanding of PD-1, highlighting its role not only in T cells but also in macrophages [[129]25, [130]47, [131]48]. However, the role of PD-1^+ macrophages in regulating anti-tumor immunity remains underexplored. Given that current studies often focus on a single aspect of PD-1 function on macrophage surfaces [[132]49–[133]51], this study takes the lead in using a multi-omics strategy for a systematic analysis. Bulk transcriptomic analysis revealed significant correlations between PD-1 hyperexpression in macrophages and poor patient prognosis. Subsequent high-resolution single-cell transcriptomic analysis, complemented by in vitro and in vivo functional validation, demonstrated that PD-1 inhibits key antitumor immune functions of macrophages through the JAK2-STAT3 signaling pathway, ultimately promoting tumor progression. To comprehensively elucidate the role of PD-1 in macrophage-mediated anti-tumor immunity, we conducted further validation in tumor-bearing models. For subsequent evaluation of the relationship between macrophage phagocytic activity and PD-1 expression levels, we generated a stable EGFP^+CT26 cell line and established EGFP^+CT26-BALB/c murine tumor models. Analysis revealed that PD-1 expression on macrophages within the CT26 tumor microenvironment positively correlated with tumor progression and TAM infiltration, but negatively associated with both phagocytic capacity and M1-polarization status of TAMs. To further decipher the regulatory mechanism of PD-1 on macrophage functionality, we performed in vitro investigations using CT26-CM to simulate the TME. Clinical data have emphasized the significant correlation between a decreased M1/M2 TAM ratio and poor prognosis in certain cancers [[134]18, [135]52–[136]54]. Targeting the polarization signaling pathways to reprogram TAM from pro-tumorigenic M2 phenotype to anti-tumor M1 phenotype represents a promising therapeutic strategy in cancer treatment. This phenotypic switching has been demonstrated to effectively remodel the TME and augment anti-tumor immunity. Therefore, identification of key mediators governing macrophage polarization may provide novel insights for immunotherapy. In the current study, CT26-CM-stimulated BMDMs exhibited elongated morphological features. McWhorter et al. have established that macrophage polarization status correlates with morphological alterations, wherein M2-polarized cells display more elongated morphology compared to their M1 counterparts [[137]55]. We therefore systematically investigated CM-induced polarization dynamics and their functional implications within the TME. Flow cytometric analysis confirmed that such conditioning promoted M2 polarization concomitant with enhanced CT26 cell migration and invasion. Notably, genetic ablation of PD-1 in BMDMs effectively reversed M2 polarization and attenuated tumor cell motility. These findings collectively demonstrate that TME-driven PD-1 upregulation orchestrates macrophage M2 polarization, thereby facilitating tumor progression and metastasis. Intriguingly, parallel studies have revealed that adult worm excretory/secretory products-treated macrophages undergo M2 polarization with concomitant PD-1 elevation, a correlation consistent with our observations [[138]56]. Gordon’s team further corroborated that PD-1 expression on TAMs inversely correlates with phagocytic capacity, demonstrating that PD-1/PD-L1 blockade enhances macrophage-mediated tumor clearance and suppresses neoplastic growth [[139]30]. Mechanistically, PD-1 upregulation in BMDMs activates tumor immune evasion programs through JAK2-STAT3 signaling axis. Pharmacological inhibition of this pathway successfully reversed polarization commitment. Our study advances the understanding of macrophage-TME crosstalk, establishing PD-1 as a critical regulator of JAK2-STAT3-mediated polarization switch that ultimately governs tumor cell dissemination. Macrophages can directly eliminate tumor cells through phagocytosis or induce apoptosis, thereby suppressing tumor progression at early stages. Sydney R. Gordon observed through electron microscopy that PD-1^+ TAMs exhibited a “foamy” appearance, mainly composed of undigested phagosomes and lysosomes, which filled the cytosol with lipid-rich content. These findings suggest that PD-1 expression in macrophages inhibits phagocytosis [[140]30]. In this study, from single-cell transcriptomics to flow cytometry and immunofluorescence, we have qualitatively and quantitatively verified the effect of PD-1 on macrophage phagocytosis, providing a more comprehensive and intuitive comparison of how PD-1 expression affects macrophage phagocytic ability. Previous studies have shown that macrophages can use filopodia to pull particles toward the cell body for phagocytosis [[141]57]. Therefore, we hypothesized that the extension of pseudopodia in macrophages with downregulated PD-1 might be associated with changes in their phagocytic capacity. Our in vitro experiments demonstrated that PD-1, an inhibitory immune checkpoint protein expressed on macrophages, suppresses their phagocytic capacity. Interestingly, CT26-CM appears to activate the phagocytic function of BMDMs, suggesting that macrophage phagocytosis within the actual TME may undergo a transition from activation to exhaustion. In the complex TME, macrophages interact with diverse cytokines and factors, ultimately leading to inhibition of their phagocytic activity. Although two-dimensional in vitro models cannot fully replicate the intricate cellular interactions and signaling pathways of the TME, our study robustly highlights the impact of the single factor PD-1 on macrophage function. These individual factors collectively contribute to the complexity of the TME, and unraveling their interplay remains a primary objective of our research. In mechanistic investigations, we explored whether PD-1 influences macrophage phagocytosis via the JAK2-STAT3 signaling pathway; however, no statistically significant changes in phagocytosis were observed following modulation of this pathway. KEGG pathway enrichment analysis revealed that PD-1 upregulates the Fcγ receptor-mediated phagocytic pathway in macrophages. Thus, future studies will focus on elucidating the regulatory role of Fcγ receptors in PD-1-mediated modulation of macrophage phagocytosis. Integrative bioinformatics analysis further validated the involvement of the JAK2-STAT3 pathway in PD-1-regulated macrophage functions. We confirmed that PD-1 modulates the production of IFN-γ signaling proteins through this pathway. IFN-γ signaling is essential for pro-inflammatory activation of macrophages [[142]58]. Our study also demonstrated stronger co-expression of IFN-γ with CD86, an M1 polarization marker. Additionally, evidence indicates that IFN-γ promotes tumor cell apoptosis and suppresses tumor growth [[143]59]. By modulating macrophage polarization states and enhancing IFN-γ signaling activity, we may develop more effective therapeutic strategies to counteract tumor immune evasion and improve patient outcomes. The clinical efficacy of PD-1/PD-L1 inhibitors as monotherapy in CRC remains to be improved, and enhancing patient response rates represents a persistent research priority. The immunosuppressive TME, particularly the potent immunosuppressive effects mediated by TAMs, has been critically linked to suboptimal responses to immunotherapy. Identifying key molecular targets and elucidating underlying mechanisms governing TAM-mediated immunosuppression may provide therapeutic opportunities to counteract their protumorigenic functions and improve the efficacy of PD-1/PD-L1 blockade. Current research has identified several potential regulatory targets across multiple domains, including metabolic reprogramming (e.g., glycolysis and lipid metabolism) [[144]60], signaling pathway modulation (e.g., CSF1R and STAT3 inhibition) [[145]61, [146]62], and phenotypic regulation (e.g., IRG1) [[147]63]. Notably, CSF1R-a critical regulator of TAM survival and differentiation-has been targeted in clinical trials using inhibitors such as PLX3397 and BLZ945, which exert antitumor effects by depleting TAM populations or suppressing their protumorigenic functions [[148]64]. In this study, we specifically investigate PD-1 expression on TAMs as a potential therapeutic target to overcome immunosuppression in CRC. Unlike previous studies that primarily focused on PD-1 in T cells, our research, for the first time, comprehensively elucidates the diverse functions of PD-1 in macrophages, particularly its effects on phagocytic capacity, polarization states, and IFN-γ signaling pathway activity, ultimately shaping the tumor immune microenvironment and promoting tumor progression. Given the pivotal role of PD-1 in macrophage regulation, targeting TAM (such as JAK2-STAT3 pathway inhibitors, TAM reprogramming agents, or IFN-γ pathway activators) in combination with immune checkpoint inhibitors holds promise for enhancing the anti-tumor effects of ICIs, improving response rates to immunotherapy, and overcoming resistance to PD-1/PD-L1 monotherapy in certain patients. Specifically, in refractory CRC patients, where blocking PD-1/PD-L1 in T cells alone has shown limited efficacy, interventions targeting PD-1 on macrophages may achieve more sustained immune reprogramming, thereby improving clinical outcomes. In conclusion, this study integrates single-cell and bulk transcriptomic data, in vivo mouse models, and in vitro primary cell stimulation experiments to systematically reveal the crucial role of PD-1 on TAM in driving CRC progression and its underlying molecular mechanisms (Fig. [149]7A). Fig. 7. [150]Fig. 7 [151]Open in a new tab Macrophages with high expression of PD-1 inhibit their anti-tumor immune function. (A) Tumor progression is closely related to the expression of PD-1 in macrophages, and macrophages with high PD-1 expression generally show M2 polarization, phagocytosis damage, and IFN-γ signaling protein synthesis block. Meanwhile, JAK2-STAT3 signaling pathway is considered to be a key signaling pathway for macrophage dysfunction. Macrophages can regulate macrophage polarization and signal protein synthesis through this pathway to promote tumor progression. The images are drawn by Adobe Illustrator software. IFN-γ: Interferon-γ; PD-1: Programmed Death-1 Electronic supplementary material Below is the link to the electronic supplementary material. [152]12967_2025_6469_MOESM1_ESM.jpg^ (478.2KB, jpg) Supplementary Material 1: Supplement Fig.1 Differential expression analysis and functional enrichment network analysis of Pdcd1^+ macrophages. (A) The volcano plot of DEGs between Pdcd1^+ macrophages and Pdcd1^- macrophages. (B) Gene-function network composed of 5 key GO terms. In the network, gray points represent genes, yellow points represent the enriched GO terms, and the size of GO nodes corresponds to the number of genes enriched in each term. DEGs: Differentially Expressed Genes; GO: Gene Ontology. [153]12967_2025_6469_MOESM2_ESM.jpg^ (285.4KB, jpg) Supplementary Material 2: Supplement Fig. 3 Grouping mice by median PD-1 expression from flow cytometry, comparing tumor growth curves for PD-1high and PD-1low groups, as well as macrophage PD-1 expression, phagocytosis, polarization, and infiltration within each group. PD-1: Programmed Death-1. Data represent mean with SD. *P<0.05, **P<0.01, ***P<0.001 by unpaired t-test. [154]12967_2025_6469_MOESM3_ESM.jpg^ (1.1MB, jpg) Supplementary Material 3: Supplement Fig.4 Validation of macrophage knockdown efficiency and phagocytic function. (A) Flow cytometry measurement of PD-1 levels in Raw264.7 cells stimulated with CT26-CM at 0h, 12h, and 24h. (B) Flow cytometry, Real-time PCR and Western Blotanalyses of PD-1 protein and RNA expression in BMDMs post-siPD-1 treatment. (C) Flow cytometry monitoring and statistical results of the phagocytic function of macrophages in four groups. PD-1: Programmed Death-1; CT26-CM: CT26-Conditioned Medium; BMDMs: Bone Marrow-Derived Macrophages. Data represent mean with SD. *P<0.05, **P<0.01, ***P<0.001 by unpaired t-test. [155]12967_2025_6469_MOESM4_ESM.jpg^ (919.2KB, jpg) Supplementary Material 4: Supplement Fig.5 Phagocytosis of BMDMs was detected after STAT3 activation. (A) Western Blot analysis of JAK2-STAT3 pathway related protein expression after siPD-1. (B) The effect of STAT3 agonist on phagocytosis of BMDMs was detected by flow cytometry. (C) Statistical results for IFN-γ. BMDMs: Bone Marrow-Derived Macrophages; IFN-γ: Interferon-γ. Data represent mean with SD. ***P<0.001 by unpaired t-test. Acknowledgements