Data collection
Clinical information and bulk RNA-sequencing data of osteosarcoma were downloaded from The Cancer Genome Atlas (TCGA) and set as the training cohort (n = 84). GSE39055 and GSE21257 were downloaded from the Gene Expression Omnibus (GEO). After the adjustment for batches, the two datasets were then merged as validation cohort (n = 89)[17].
Construction and validation of the necroptosis-related prognostic gene signature
NRGs were retrieved from GeneCards. Prognostic genes were firstly identified by univariate Cox regression. The hub genes were further screened and confirmed by the least absolute shrinkage and selection operator (LASSO). The NS was calculated as followed: NS = \({\sum }_{\text{i}}^{\text{n}}\text{Exp}\text{i}\text{Coe}\text{i}\) (Exp = expression level; Coe = regression coefficient).
Principal component analysis (PCA), Cox regression and time-dependent receiver operating characteristic (ROC) curves were applied to evaluate the performance of the signature. According to the median NS in the training cohort, patients were divided into high- and low-score groups. Kaplan-Meier (KM) survival analysis was performed to compare survival rates between two groups.
Finally, gender, age and NS were combined to create a nomogram to assess prognosis (overall survival rate) of osteosarcoma patients. Calibration curves and decision curve analysis were applied to evaluate the nomogram.
Functional analysis in TCGA cohort
Compared to the low-score group, the differentially expressed genes (DEGs) in high-score group were identified using the ‘limma’ R package[18]. When the DEGs were obtained, false discovery rate (FDR) < 0.05 and |log2FC| > 1 was considered statistically significant. Enrichment analysis in Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) was performed with ‘ClusterProfiler’ R package[19]. Gene set enrichment analysis (GSEA) and gene set variation analysis (GSVA) were used to explore the alterations in biological function between two groups[20, 21]. The preset gene set was GOBP necroptotic signaling pathway and h.all.v7.5.1.symbols. | normalized enrichment score (NES)| > 1, nominal P < 0.05 and FDR q < 0.25 were considered statistically significant. The activity of apoptosis and necroptosis signal pathways in high-score group was visualized using the ‘pathview’ R package[22].
Immune infiltration levels were calculated by single sample gene set enrichment analysis (ssGSEA)[23]. Microenvironment scores and tumor purity of osteosarcoma were calculated by ‘ESTIMATE’ R package[24]. Stemness indices were calculated by one-class logistic regression (OCLR)[25]. Pearson correlation coefficient was used to assess the correlations between these parameters and NS.
Osteosarcoma samples were divided into two groups based on the median expression of gene. Then the effect of single gene was evaluated by KM survival analysis. Subgroup analysis was performed to assess whether the expression of TNFRSF21 and necroptosis mediators were associated with clinical characteristics. Finally, we calculated the Pearson correlation coefficient of TNFRSF21 and necroptosis mediators.
Single-cell data analysis
Osteosarcoma single-cell data (GSE162454) was collected from GEO and then imported into ‘Seurat’ R package with default parameters[26]. For count matrix in the dataset, a standard pipeline in ‘MAESTRO’ in TISCH website was used to perform quality control, clustering and cell-type annotation[27, 28].
According to the formula, we calculated the NS of each cell and average NS of each cell population. Malignant cells with the top 5% and bottom 5% NS were assigned to the high-NS and low-NS groups, respectively. The count matrix was imported in to ‘CellChat’ R package to investigate cell–cell interactions between two groups[29].
Cell culture and lentivirus infection
Human osteoblast cell line hFOB1.19 (RRID: CVCL_3708) and three human osteosarcoma cell lines HOS (RRID: CVCL_0312), MG63 (RRID: CVCL_0426) and U2OS (RRID: CVCL_0042) were used in this study. Osteosarcoma cell lines were purchased from Zhong Qiao Xin Zhou Biotechnology Co., Ltd. (Shanghai, China), hFOB1.19 was purchased from Procell Biotechnology Co., Ltd. (Wuhan, China). Before experiments, DNA types of cell lines were identified by short tandem repeat (STR) profiling and compared with DSMZ data. All experiments were performed with mycoplasma-free cells which were cultured according to the instructions.
Lentivirus containing pLVX-TNFRSF21-Puro and pLVX-Puro (vector) were purchased from Genechem (Shanghai, China) and used to infect HOS and MG63 according to the manufacturer's protocol. Stably transfected cells were selected with puromycin and validated by polymerase chain reaction (PCR) and western blot.
Western blot and PCR
Cells were lysed using RIPA buffer (Cell Signaling Technology, Danvers, MA, United States). Western blot was performed according to previous study[30]. B-actin (1:1000) was set as control. Other antibodies used were: TNFRSF21 (1:1000), RIPK1 (1:1000), p-RIPK1 (S166) (1:1000), RIPK3 (1:1000), p-RIPK3 (S227) (1:1000), MLKL (1:1000) and p-MLKL(S358) (1:1000). All antibodies were purchased from Cell Signaling Technology (Cell Signaling Technology, Danvers, MA, United States).
Cells were lysed using TRIzol reagent (Life Technologies, CA, USA). PCR was performed to determine mRNA expression levels according to previous study[31]. B-actin was set as control and relative mRNA expression levels were calculated by the 2–ΔΔCt method. The sequences of primers were included in Supplemental Table 1.
Detection of cell proliferation and motility
For CCK-8 assays, cells were seeded at a density of 1 × 103 cells/well in 96-well plate. Ten µl of CCK-8 reagent was added at specific timepoints. Optical density (OD) was measured at 450 nm after incubation at 37°C for one hour.
For colony formation assays, cells were seeded at a density of 1 × 103 cells/well in 6-well plate. Medium was changed every two days. After one week, cell colonies were fixed with paraformaldehyde (4%) for 30 minutes and stained with crystal violet.
The fraction of DNA-replicating cells, which represented cell proliferation status, was assessed using EdU Detection Kit (RiboBio, Guangzhou, China).
Four-week-old male BALB/c nude mice were purchased from the Laboratory Animal Center of Shandong University (Jinan, China). The mice were placed in the Laboratory Animal Center of Shandong University Qilu Hospital and were fed in an air-conditioned room at 23–25°C with a light-dark cycle time of 12 hours, where they had ample access to water and food. Nude mice were injected subcutaneously with 2 × 106 stably transfected HOS cells or control cells. After four weeks, all mice were sacrificed and the xenografts weighed and harvested. The animal experiments were approved by the Animal Ethics Committee of Qilu Hospital of Shandong University (No. DWLL-2023-028).
Transwell assays were performed according to previous study[32]. At the beginning, 1 × 104 cells per group were inoculated in the upper chamber. After 24 hours, cells in the bottom chamber were fixed, stained and photographed.
For wound healing assays, a sterile pipette tip was used to scratch and form a gap when cells were completely confluent in 6-well plate. Then serum-free medium was added. After incubation for 12 hours, the gap was photographed.
Apoptosis detection
Cells were seeded at a density of 1 × 104 cells/well in 24-well plate. TUNEL staining was performed using TUNEL BrightRed Apoptosis Detection Kit (Vazyme, China).
Cell suspensions were made in phosphate-buffered saline. Annexin V-FITC Apoptosis Detection Kit (Vazyme, China) and flow cytometry were used to detect apoptosis. Cells in the upper right quadrants (PI positive and Annexin V positive) were considered necrotic.
According to the product instruction, relative activity of caspase 8 was detected by Caspase 8 Activity Assay Kit (Beyotime Biotechnology, Shanghai, China).
Statistical analysis
All analyses were performed in RStudio (version 4.1.2). All experiments were carried out at least three times independently. The statistical methods were used according to the type of data. Group differences for continuous variables were investigated with 2-tailed Student t test or Wilcoxon–Mann–Whitney nonparametric tests (2-tailed). Statistical significance was set at P < 0.05.