Data acquisition
The CGGA325 database including RNA sequencing and clinical characteristic information was downloaded from the Chinese Glioma Genome Atlas (http://www.cgga.org.cn/)(11). Similarly, TCGA RNA sequencing data and clinical information were downloaded from the TCGA database (https://portal.gdc.cancer.gov/) as a validation set. Single cell data was downloaded from GSE117891(12), with more than 6000 single-cell transcriptomes of 73 surgery points from 13 gliomas and one brain metastasis patient.
Prognostic analysis
We used CGGA325 as a test set and TCGA as a validation cohort for survival analysis. Glioma patients were divided into high and low groups according to the median value of FCGRT expression. Kaplan–Meier survival analysis was used to analyze the correlation of FCGRT expression on the prognosis of glioma patients by combining the survival time and survival status of patients. Subsequently, we performed a subgroup analysis of glioma patients by dividing the CGGA325 dataset into 12 subgroups based on age (Age < 42, Age ≥ 42), gender (Female, Male), grade (Grade 2, Grade 3, and Grade 4), IDH (Mutant, Wildtype), 1p19q (Codel, Non-codel) as well as MGMT status (Methylated, Un-methylated). Survival analysis was performed in each subgroup to analyze the effect of FCGRT on the prognosis of glioma patients. The TCGA database as a validation set was similarly analyzed.
Immunohistochemistry
The tissue microarray (TMA) for the glioma was obtained from the Shanghai Outdo Biotech Company (Shanghai, China). We used the ab64264 kit from Abcam for immunohistochemical staining, and the detailed staining procedure can be seen in the instructions. It should be noted that the antigen retrieval solution we used was Tris-EDTA, pH = 8.0. Immunohistochemical scoring criteria can be seen in previous publication from our team(13).
Single cell analysis
The single cell RNA-seq data was obtained from GSE117891, with more than 6000 single-cell transcriptomes of 73 surgery points from 13 gliomas and 1 brain metastasis patient. The single cell RNA-seq was analyzed using the R package Seurat(14). All cells with > 10% transcript alignment to mitochondrial genomes or with fewer than 400 RNA counts or more than 2500 counts were removed from downstream analysis. In addition, genes were filtered out when they expressed in less than 10 cells among all the samples. The Seurat package's FindMarkers function was used to identify the cell cluster.
Analysis of immune infiltration and tumor microenvironment
We analyzed the relationship between FCGRT and tumor microenvironment by four immune infiltration analysis methods, namely ssGSEA, ESTIMATE, EPIC, and xCell. SsGSEA was used to evaluate 24 types of immune cells that may infiltrate into the tumor immune microenvironment. ESTIMATE was to evaluate infiltration of immune cells and the presence of stromal cells in tumor samples, which generated three results, namely immune score (reflecting the level of immune cell infiltrations in tumor tissue), stromal score (reflecting the presence of stroma in tumor tissue), and estimate score (reflecting tumor purity). EPIC can analyze the infiltration proportion of eight types of immune cells according to the expression data, including B cells, tumor associated fibroblasts (CAFs), CD4 + T cells, CD8 + T cells, endothelial cells, macrophages and NK cells. xCell is a recently published method based on ssGSEA, which estimates the abundance scores of 64 immune cell types, including adaptive and innate immune cells, hematopoietic progenitors, epithelial cells, and extracellular matrix cells.
Non-negative matrix factorization (NMF) cluster analysis
In order to further explain the relationship between FCGRT and the immune microenvironment, we used the NMF cluster analysis method. Firstly, we downloaded monocyte-macrophage characteristic genes from previous reports(15). NMF is an effective dimensionality reduction method that is widely used for molecular pattern recognition of high-dimensional genomic data, and provides a powerful approach for class discovery. We extracted immune related gene expression quantities from the CGGA database and then performed NMF clustering analysis. The optimal number of clusters was calculated according to the values obtained from cophenetic calculations. We then performed survival analysis on different clusters. Finally, we measured the expression levels of FCGRT and immunoglobulin heavy chain gene 1 (IGHG1), and detected the differences in gene expression levels in different clusters by Wilcoxon rank sum test.
Gene set enrichment analysis (GSEA)
We obtained the GSEA software (version 3.0) from the following website: (http://software.broadinstitute.org/gsea/index.jsp). According to the expression levels of FCGRT, samples were divided into a high FCGRT expression group (≥ 50%) and a low FCGRT expression group (< 50%). Based on gene expression profile and phenotype grouping, the minimum gene set was 5, and the maximum gene set was 5000; 1000 resampling, NES > 1 and a FDR of < 0.05 were considered statistically significant.
Cell culture
The human glioma cell line U251 was obtained from the American Type Culture Collection (ATCC), and routinely cultured in RPMI 1640 medium containing 10% fetal bovine serum (FBS, Gibco) and 100 U/mL penicillin and 100 µg/mL streptomycin, in a humidified incubator at 37°C with 5% CO2. The medium was changed every 2 days, and cells were passaged when the growth density reached about 80%, about every 3 to 4 days.
Cell proliferation assay
1×104 cells/well were seeded in 96-well plates in RPMI 1640 medium, and the proliferation rate of the U251 cells was measured by the MTT assay. After appropriate treatment, cells were washed with PBS and were replaced with 100 µl serum-free RPMI 1640 containing 10 µl of MTT reagent, and then incubated at 37°C for 4 h. An equal volume of supernatant from each well was transferred to a new 96-well plate. The absorbance at 490 nm was measured using a Multiskan spectrum and the absorbance of MTT reagent at 490 nm was used as a control to corrected absorbance.
Isolation of RNA and real-time PCR
Total RNA was extracted from U251 cells with TRIzol reagent (Qiagen, 10296-028) according to the manufacturer’s instructions. The quality of the RNA was measured using the NanoDrop 2000 Spectrophotometer (Thermo Scientific). Reverse transcription and qRT-PCR were carried out on ABI 7500 FAST system (Life Technologies) according to the manufacturer's protocol. β-actin was used as an internal control. All PCR experiments were performed in triplicate. The relative amount of transcripts was calculated using the 2−ΔΔCt formula. Primer sequences were as follows: FCGRT: 5'-GGGGAAAAGGTCCCTACACTC-3' and 5'-CCTGCTTGAGGTCGAAATTCAT-3'; β-actin: 5'- GGCTGTATTCCCCTCCATCG-3' and 5'-CCAGTTGGTAACAATGCCATGT-3'.
Western blot analysis
Proteins were isolated from cultured U251 cells with lysis buffer and were electrophoresed on 10% SDS-PAGE to separate. SDS-PAGE gels were transferred onto PVDF membranes and were blocked with 5% milk in TTBS for 2 h at 37ºC. membranes were incubated with primary antibodies overnight at 4°C. Antibodies used were: anti-FCGRT (rabbit polyclonal, 1:500, 16190-1-AP, Proteintech), anti-β-actin (mouse monoclonal, 1:1000, sc-47778, Santa Cruz). Membranes were then washed and incubated with the corresponding secondary antibodies conjugated with HRP (Cell Signaling Technology). Protein bands were detected by ECL (enhanced chemiluminescence) Fuazon Fx (Vilber Lourmat).
Cell transfection
U251 cells were transfected with small interfering RNAs (siRNAs) using Lipofectamine 3000 (Invitrogen). The sequences of human FCGRT (ID: 2217) specific siRNAs and non-specific siRNA (si-Ctl) were designed. These siRNA sequences used in the studies were synthesized by GenePharma. After 24 h of transfection, U251 cells were harvested and lysed for qRT-PCR or western blot analysis. FCGRT siRNA1: 5′- GCTCTTTCTGGAAGCTTTCAA − 3′; 5′- CGGCGAGGAGTTCATGAATTT − 3′; siRNA2: 5′- GGAUCUCUCCUACAGGUAAC − 3′; 5′- UUACCUGUAGGAGAGAUCCGA − 3′; si-Ctl: 5′-UUC UCC GAA CGU GUC ACG UTT-3′; 5′-ACG UGA CAC GUU CGG AGA ATT-3′.
Cell viability and colony formation assay
U251 proliferation was assessed by the CellTiter-Glo assay according to the manufacturer’s protocol. U251 cells, parental or with FCGRT knockdown were plated into 96-well plates with a seeding density of 2000 cells/well. Proliferation was assessed using CellTiter-Glo reagent (Promega). U251 cells were plated in six-well plates with a seeding density of 100 cells/well for the colony formation assay; after 12–16 days, plates were washed with PBS and stained with Geimsa. Geimsa-stained plates were washed after 30 minutes, and colonies were counted and analyzed.
Cell migration assays
U251 cells transfected with si-Ctl or si-FCGRT were grown to a confluence of 90%, and the cell monolayer was then scratched using a sterile micropipette tip. After replacing the medium, images at 0 h of the wounded area were captured. Cell migration into the wounded area was recorded again after 12 h. The migration abilities of U251 cells were quantified by measuring the change of scratch regions.
Cell invasion assays
Transwell Matrigel invasion assays were used to assess the invasive abilities of U251 cells, as previously described(16). Experiments were conducted in triplicate, and migration was expressed as the mean ± SEM per field of total cells counted.
Time-lapse experiments
Time-lapse images of U251 cells transfected with si-Ctl or si-FCGRT were acquired by Live Cell Imaging System. U251 cells maintained at 5% CO2 and 37°C on the inverted microscope at all times. Images were recorded every 30 minutes via a 40× objective. After 120 minutes, the migration distance of cells was observed and quantified by NIH Image J software.