High NLR after PD-1 antibody treatment indicated poor efficiency of AGC patients
The clinical information of 68 AGC patients (46 males and 22 females) was listed in Table 1. Nearly 78% patients treated with PD-1 antibody-based therapy as the second-line or more. Most patients received combination therapeutics. Median number of treatment cycles were 5 (2-26). Median NLR at BL, 2C and AE1 were 3.74, 2.91 and 3.28, respectively. No significant difference of NLR at three timepoints was found among patients with different metastatic organs, pervious lines of treatment and combination strategies.
NLR-AE1 was significantly different among patients with different objective response (PD vs. SD, 7.29±6.80 vs. 3.64±2.58, P=0.003; PD vs. PR, 7.29±6.80 vs. 2.92±1.24, P=0.013, Figure 1A). NLR-2C of PD patients was also higher than SD patients (4.76±2.83 vs. 3.26±2.71, P=0.037), while no significant different was identified comparing with PR patients (4.76±2.83 vs. 3.43±1.22, P=0.203, Fig. 1B). Correlation between NLR-BL and patients’ ORR was not identified (Fig. 1C).
Median PFS of all patients was 3.5 months (0.4 to 30.1 months). The 75th percentile of NLR was selected as the cut-off value to distinguish high and low NLR (NLR-2C=4.83; NLR-AE1=5.12). Kaplan-Meier analysis showed that patients with high NLR-2C had poorer PFS comparing with those with low NLR-2C (6.4m vs. 3.0m, P=0.025, Fig. 1D), as well as for patients with high NLR-AE1 (9.4m vs. 2.4mm, P=0.008, Fig. 1E). Multivariable analysis showed that high NLR-AE1 was the independent prognostic factor for those patients (HR=2.47, 95%CI 1.25-4.90, P=0.01).
Multiple samples analysis by scRNA-seq in patients treated by PD-1 antibody
Multiple samples from two treatment refractory AGC patients in this cohort were analyzed by scRNA-seq. PD-1 antibody plus anti-angiogenesis inhibitor was administrated for both patients. Patient 1 (P1) was a young female with hepatic and pleural metastases. Before treatment, samples from stomach primary lesion, peripheral blood, pleural and ascitic fluid were obtained. After 1 cycle of treatment, performance status of P1 deteriorated too rapidly to receive second cycle due to disease progression, then pleural fluid and peripheral blood samples were re-collected, and best support care was given afterward (Fig. 2A). Patient 2 (P2) was also a female with peritoneal metastasis. Samples from stomach primary lesion, peripheral blood and ascitic fluid were collected before and after treatment. The patient stopped treatment due to bowel obstruction caused by peritoneal metastasis, and no significant disease progression was observed at that time (Fig. 2B).
Total 80,680 cells from 12 samples were obtained, detail number of cells in each sample was showed in Table S1. UMAP algorithm was performed to visualize cell clusters (Fig. 2C). Major cell clusters including endothelial cells (ECs), epithelial cells, myeloid cells, myofibroblasts, pleural mesothelial cells (PMCs), pericytes, plasma cells, platelets, T cells, plasmacytoid dendritic cells (pDCs) and B cells were annotated by established marker genes (Fig. 2D, Fig S1).
Subcluster of neutrophil with activation phenotype accounted for major proportion in peripheral blood samples
Peripheral blood samples before and after treatment were analyzed first. Myeloid cells and T cells accounted for the major parts of all four samples. Proportion of myeloid cells increased while T cells decreased after treatment. The proportion of neutrophil which was a major part of myeloid cells significantly increased after treatment in both patients (Fig. 3A). Then, neutrophils in peripheral blood samples and ascites were divided into 7 cellular subclusters. The constitution of neutrophil subclusters between peripheral blood samples and ascites was different. Neutrophil cluster1 (NE-C1) dominated in peripheral blood samples (Fig. 3B).
GO enrichment analysis of biological function based on high-expression DEGs of NE-C1 showed that those DEGs were mainly enriched in neutrophil activation phenotype. The top 3 biological functions included neutrophil activation, neutrophil activation involved in immune response, and neutrophil degranulation (Fig. 3C). Furthermore, cancer-promoting genes including MMP9, S100A8, S100A9, PORK2, TGF-β1 were identified as high-expression DEGs in NE-C1 (Fig. 3D).
Subclusters of malignant epithelial cells participated in regulating neutrophil activation
Malignant epithelial cells were identified by inferred CNV algorithm. Those cells could be found in primary lesion and pleural fluid of P1, and primary lesions of P2. Then, malignant epithelial cells were divided into 13 cellular subclusters (Fig. 4A). Distribution of subclusters in P1 and P2 was significantly different, while epithelial cell cluster 4 (EP-C4) could be found in both patients, especially as a new cluster for P2 after treatment (Fig. 4B).
GO enrichment analysis of biological function showed that high-expression DEGs in EP-C4 were mainly enriched in neutrophil activation, neutrophil mediated immunity, and neutrophil degranulation. Cell-cell junction organization and cell-matrix adhesion were also enriched (Fig. 4C). KEGG enrichment analysis showed that high-expression DEGs in EP-C4 were enriched in leukocyte trans-endothelial migration pathway, as well as in regulation of actin cytoskeleton and focal adhesion pathways (Fig. 4D).
Subcluster of M2 macrophage participated in regulating neutrophil activation
In all non-peripheral blood samples, myeloid cells had high proportion after malignant epithelial cells, and could be divided into macrophage, monocytes, dendritic cells, and neutrophils (Fig. S2). Macrophage polarization was reported participated in modulating tumor immune microenvironment. Therefore, macrophages were further classified as M1 and M2- macrophages, in which M2 macrophages accounted for a major part (Fig. 5A). Eight cellular subclusters of M2 macrophage were subdivided. M2 macrophage cluster1 (MF-C1) was only found in samples of P1, while MF-C2 was found in both patients and mainly in primary lesions (Fig. 5B).
GO enrichment analysis showed that high-expression DEGs of MF-C1 were mainly enriched in neutrophil activation, neutrophil degranulation, and neutrophil activation involved in immune response (Fig.5C). Meanwhile, high-expression DEGs of MF-C2 could also be enriched in regulation of leukocyte differentiation and positive regulation of leukocyte activation (Fig.5D).
Cellular interaction among neutrophil, M2 macrophage and tumor cell attributed to tumor progression during PD-1 antibody treatment
Cellular interaction among all cellular subclusters of neutrophil, M2 macrophage and malignant epithelial cell were illustrated by heatmap of paired ligands and receptors (pLRs) (Fig. 6A). For P1, EP-C3, EP-C4, EP-C6 and EP-C9 were found that had a high number of pLRs with both M2 macrophage and neutrophil. A high number of pLRs was also found among different cellular subclusters of M2 macrophage and neutrophils. For P2, EP-C4 and EP-C7 were found that had a high number of pLRs with M2 macrophage and neutrophil. MF-C2 had highest number of pLRs with all subclusters of neutrophil.
Interactions among NE-C1, EP-C4, MF-C1 and MF-C2 were further analyzed. Receptor-ligand interactions among those cellular subclusters showed that MF-C2 could provide ligands for both NE-C1 and EP-C4, while ligands of MF-C1 could only interact with receptors of NE-C1. Bi-directional interaction between NE-C1 and EP-C4 was identified (Fig. 6B).
Detail pLRs between different cellular subclusters were analyzed by communication score heatmap. Between NE-C1 and EP-C4, ligand-receptor interactions including OSM-OSMR, IL1B-IL1RAP, OSM-IL6ST and TGFB1-TGFBR2 were identified, and SERPINF1-LRP6, HGF-EPHA2, IGF1-INSR, HGF-ERBB2 and HGF-MET were found between MF-C2 and EP-C4. Chemokines and their receptors were identified as major interactions of MF-C1/NE-C1, MF-C2/NE-C1 and EP-C4/NE-C1. KEGG enrichment analysis showed that ligand-receptor interactions between NE-C1 and EP-C4 were enriched in MAPK signaling pathway and Jak-STAT signaling pathway. For MF-C2 and EP-C4, PI3K-Akt signaling pathway was identified. Chemokines signaling pathway was identified between MF-C1/NE-C1, MF-C2/NE-C1 and EP-C4/NE-C1 (Fig. 6C).