Introduction
Materials and methods
Data download, process, and analysis
Sangerbox tools
Gene expression profiling interactive analysis (GEPIA)
Tumor immune estimation resource (TIMER)
Tissue sampling from glioma patients
Cell culture, real-time PCR, and immunohistochemistry
lentivirus infection assay
Cell counting Kit-8 assay
Colony formation assay
Cell invasion assays
5-Ethynyl-2’-deoxyuridine (EdU) incorporation assay
Genomic heterogeneity and cancer stemness
DNA methylation and alternative splicing
Survival analysis
Analysis of PROS1-interacting genes and proteins
Single-cell analysis
GO, KEGG pathways, and GSEA of PROS1
Tumor immune dysfunction and exclusion (TIDE)
Statistical analysis
Results
Analysis of PROS1 expression in patients with LGG
Identification of DEGs in LGG
PROS1 expression in LGG is associated with DNA methyltransferase expression, RNA modification genes, DNA mismatch repair system genes, copy number variations, and the frequency of single nucleotide variations
Correlation of PROS1 expression with DNA methylation and alternative splicing
PROS1 expression is associated with genomic heterogeneity and cancer stemness
Correlation between PROS1 expression and clinical parameters of patients with LGG
Correlation between PROS1 expression and the prognosis of patients with LGG
Identification of PROS1-interacting genes and proteins
Analysis of long noncoding RNA (lncRNA)- transcription factor (TF)-PROS1 triplets
Gene ontology (GO), kyoto encyclopedia of genes and genomes (KEGG) pathways, and gene set enrichment analysis (GSEA) of PROS1 in patients with LGG
Single-cell analysis of PROS1 functions in patients and experimental verification in GBM cell lines
PROS1 is correlated with immune cell infiltration and tumour microenvironment in LGG
Correlation of PROS1 expression with the expression of immune cell markers, immune checkpoint inhibitors, and immunomodulators
Immune cell | Biomarker | TIMER | GEPIA | ||
---|---|---|---|---|---|
R value | p value | R value | p value | ||
B cell | CD19 | 0.20*** | 7.11E − 06 | 0.24*** | 4.2E − 08 |
CD79A | 0.11* | 1.46E − 02 | 0.16*** | 2.3E − 04 | |
T cell | CD3D | 0.38*** | 1.01E − 18 | 0.34*** | 1E − 15 |
CD3E | 0.39*** | 2.59E − 20 | 0.41*** | 6.4E − 22 | |
CD2 | 0.44*** | 1.93E − 26 | 0.47*** | 2.6E − 30 | |
CD8 + T cell | CD8A | 0.19*** | 9.38E − 06 | 0.22*** | 2.9E − 07 |
CD8B | 0.18*** | 2.95E − 05 | 0.21*** | 1.9E − 06 | |
CD4 + T cell | CD4 | 0.41*** | 6.8E − 12 | 0.41*** | 6.8E − 22 |
Monocyte | CD86 | 0.33*** | 8.38E − 15 | 0.36*** | 3.1E − 17 |
CSF1R | 0.21*** | 1.55E − 06 | 0.23*** | 1.2E − 07 | |
TAM (general) | CCL2 | 0.35*** | 6.00E − 16 | 0.35*** | 4.5E − 16 |
CD68 | 0.42*** | 3.5E − 25 | 0.43*** | 3.5E − 25 | |
IL10 | 0.34*** | 4.17E − 15 | 0.37*** | 1.1E − 18 | |
M1 | IRF5 | 0.30*** | 5.12E − 12 | 0.31*** | 3.7E − 13 |
PTGS2 | 0.04* | 3.87E − 02 | 0.091** | 3.9E − 02 | |
NOS2 | − 0.13** | 2.3E − 03 | − 0.11** | 1.4E − 02 | |
M2 | CD163 | 0.45*** | 4.3E − 24 | 0.42*** | 4.3E − 24 |
VSIG4 | 0.30*** | 8.18E − 12 | 0.31*** | 2.5E − 13 | |
MS4A4A | 0.44*** | 2.8E − 29 | 0.47*** | 2.8E − 29 | |
Neutrophils | CEACAM8 | − 0.01 | 8.2E − 01 | 0.0019 | 9.7E − 01 |
ITGAM | 0.28*** | 8.97E − 11 | 0.29*** | 8.6E − 12 | |
CCR7 | 0.33*** | 3.68E − 14 | 0.34*** | 6.8E − 16 | |
Natural killer cell | KIR2DL1 | 0.12** | 5.1E − 03 | 0.16*** | 2.7E − 04 |
KIR2DL3 | 0.22*** | 3.79E − 07 | 0.25*** | 1.2E − 08 | |
KIR2DL4 | 0.23*** | 8.55E − 08 | 0.28*** | 1.8E − 10 | |
KIR3DL1 | 0.11* | 1.3E − 02 | 0.16*** | 3E − 04 | |
KIR3DL2 | 0.10* | 1.9E − 02 | 0.17*** | 1.3E − 04 | |
KIR3DL3 | 0.01 | 9.7E − 01 | 0.019 | 6.6E − 01 | |
KIR2DS4 | 0.18*** | 3.52E − 05 | 0.19*** | 1.1E − 05 | |
Dendritic cell | HLA-DPB1 | 0.49*** | 1.6E − 33 | 0.5*** | 1.6E − 33 |
HLA-DQB1 | 0.42*** | 6.5E − 15 | 0.33*** | 6.5E − 15 | |
HLA-DRA | 0.52*** | 4.6E − 38 | 0.53*** | 4.6E − 38 | |
HLA-DPA1 | 0.52*** | 7.7E − 38 | 0.52*** | 7.7E − 38 | |
CD1C | 0.36*** | 8.18E − 17 | 0.34*** | 8.2E − 16 | |
NRP1 | 0.49*** | 3.43E − 33 | 0.5*** | 1.5E − 34 | |
ITGAX | 0.23*** | 1.51E − 07 | 0.23*** | 1.2E − 07 | |
Microglia | CX3CR1 | 0.216*** | 7.78E − 07 | 0.23*** | 1.6E − 07 |
P2RY12 | 0.075 | 8,75E − 02 | 0.1 | 0.02 | |
ITGAX | 0.229*** | 1.51E − 07 | 0.23*** | 1.2E − 07 | |
FCGR1A | 0.29*** | 2.34E − 11 | 0.26*** | 3.9E − 09 | |
TMEM119 | 0.205*** | 2.6E − 06 | 0.23*** | 6.3E − 08 | |
CD33 | 0.331*** | 1.25E − 14 | 0.32*** | 1E − 13 | |
Monocyte-derived Macrophages | MRC1 | − 0.099 | 2.4E − 02 | − 0.061 | 0.16 |
CD163 | 0.45*** | P < 0.001 | 0.42*** | 4.3E − 24 | |
CD14 | 0.362*** | 1.23E − 17 | 0.38*** | 7.2E − 19 | |
TEK | − 0.033 | 4.49E − 01 | 0.0087 | 0.84 | |
THBD | 0.249*** | 1.14E − 08 | 0.29*** | 3.7E − 11 | |
ICAM1 | 0.429*** | 1.69E − 24 | 0.44*** | 2.2E − 26 | |
ITGA4 | 0.47*** | P < 0.001 | 0.49*** | 1.4E − 32 |