N6-methyladenosine methylation modification patterns reveal immune profiling in pancreatic adenocarcinoma

Identification of TNFRSF21 as an inhibitory factor of osteosarcoma based on a necroptosis-related prognostic gene signature and molecular experiments

BACKGROUND

Osteosarcoma is one of the most common malignant bone tumors with bad prognosis. Necroptosis is a form of programmed cell death. Recent studies showed that targeting necroptosis was a new promising approach for tumor therapy. This study aimed to establish a necroptosis-related gene signature to evaluated prognosis and explore the relationship between necroptosis and osteosarcoma.

METHODS

Data from The Cancer Genome Atlas was used for developing the signature and the derived necroptosis score (NS). Data from Gene Expression Omnibus served as validation. Principal component analysis (PCA), Cox regression, receiver operating characteristic (ROC) curves and Kaplan-Meier survival analysis were used to assess the performance of signature. The association between the NS and osteosarcoma was analyzed via gene set enrichment analysis, gene set variation analysis and Pearson test. Single-cell data was used for further exploration. Among the genes that constituted the signature, the role of TNFRSF21 in osteosarcoma was unclear. Molecular experiments were used to explore TNFRSF21 function.

RESULTS

Our data revealed that lower NS indicated more active necroptosis in osteosarcoma. Patients with lower NS had a better prognosis. PCA and ROC curves demonstrated NS was effective to predict prognosis. NS was negatively associated with immune infiltration levels and tumor microenvironment scores and positively associated with tumor purity and stemness index. Single-cell data showed necroptosis heterogeneity in osteosarcoma. The cell communication pattern of malignant cells with high NS was positively correlated with tumor progression. The expression of TNFRSF21 was down-regulated in osteosarcoma cell lines. Overexpression of TNFRSF21 inhibited proliferation and motility of osteosarcoma cells. Mechanically, TNFRSF21 upregulated the phosphorylation levels of RIPK1, RIPK3 and MLKL to promote necroptosis in osteosarcoma.

CONCLUSIONS

The necroptosis prognostic signature and NS established in this study could be used as an independent prognostic factor, TNFRSF21 may be a necroptosis target in osteosarcoma therapy.

Metastasis-Related Signature for Clinically Predicting Prognosis and Tumor Immune Microenvironment of Osteosarcoma Patients

Osteosarcoma is the most prevalent clinical malignant bone tumor in adolescents. The prognosis of metastatic osteosarcoma is still very poor. The aim of our study was to investigate the clinical diagnosis and prognostic significance of metastasis related genes (MRGs) in patients with osteosarcoma. Clinical information and RNA sequencing data with osteosarcoma patients were obtained and set as the training set from UCSC databases. GSE21257 were downloaded and chosen as the verification cohort. An eight gene metastasis related risk signature including MYC, TAC4, ABCA4, GADD45GIP1, TNFRSF21, HERC5, MAGEA11, and PDE1B was built to predict the overall survival of osteosarcoma patients. Based on risk assessments, patients were classified into high- and low-risk groups. The high-risk patients had higher risk score and shorter survival time. ROC curves revealed that this risk signature can accurately predict survival times of osteosarcoma patients at the 1-, 2-, 3-, 4- and 5- year. GSEA revealed that MYC targets, E2F targets, mTORC1 signaling, Wnt /β-catenin signaling and cell cycle were upregulated, and cell adhesion molecules, and primary immunodeficiency were decreased in high-risk group. MRGs were highly linked with the tumor immune microenvironment and ICB response. These results identified that MRGs as a novel prognostic and diagnostic biomarker in osteosarcoma.

Focus on Therapeutic Options for Surgically Resectable Pancreatic Adenocarcinoma Based on Novel Biomarkers

Pancreatic ductal adenocarcinoma remains associated with a poor prognosis, even when diagnosed at an early stage. Consequently, it is imperative to carefully consider the available therapeutic options and tailor them based on clinically relevant biomarkers. In our comprehensive review, we specifically concentrated on the identification of novel predictive and prognostic markers that have the potential to be integrated into multiparametric scoring systems. These scoring systems aim to accurately predict the efficacy of neoadjuvant chemotherapy in surgically resectable pancreatic cancer cases. By identifying robust predictive markers, we can enhance our ability to select patients who are most likely to benefit from neoadjuvant chemotherapy. Furthermore, the identification of prognostic markers can provide valuable insights into the overall disease trajectory and inform treatment decisions. The development of multiparametric scoring systems that incorporate these markers holds great promise for optimizing the selection of patients for neoadjuvant chemotherapy, leading to improved outcomes in resectable pancreatic neoplasia. Continued research efforts are needed to validate and refine these markers and scoring systems, ultimately advancing the field of personalized medicine in pancreatic adenocarcinoma management.

Identification of Nine M6A-Related Long Noncoding RNAs as Prognostic Signatures Associated with Oxidative Stress in Oral Cancer Based on Data from The Cancer Genome Atlas

Objective

Although the expression of long noncoding RNAs (lncRNAs) and N6-methyladenosine (M6A) is correlated with different tumors, it remains unclear how M6A-related lncRNA functioning affects the initiation and progression of oral squamous cell carcinoma (OSCC).

Materials and Methods

Gene expression and clinical data were retrieved from The Cancer Genome Atlas. The prognostic value of M6A-related lncRNAs was determined using univariate Cox regression analyses. Gene set enrichment analysis of OSCC patient clusters revealed the pathways that elucidate the mechanism. Furthermore, a risk-based model was established. The difference in the overall survival (OS) between groups, including low-/high-risk groups, was determined by Kaplan-Meier analysis. Relationships among immune cells, clusters, clinicopathological characteristics, and risk scores were explored.

Results

Among 1,080 M6A-related lncRNAs, 36 were prognosis-related. Patients with OSCC were divided into two clusters. T stage and the pathological grade were noticeably lower in cluster 2 than in cluster 1. Epithelial-mesenchymal transition showed greater enrichment in cluster 1. Nine hub M6A-related lncRNAs were identified for the model of risk score for predicting OSCC prognosis. The OS was longer in patients with a low-risk score than in patients with a high-risk score. The risk score was an independent prognostic factor of OSCC and was associated with the infiltration of different immune cells. T stages and the American Joint Committee on Cancer (AJCC) stages were more advanced in the high-risk score group than in the low-risk score group. Finally, expression correlation analysis showed that the risk score is associated with the expression of oxidative stress markers.

Conclusion

M6A-related lncRNAs play an important role in OSCC progression. Immune cell infiltration was related to the risk score model in OSCC and could accurately predict OSCC prognosis.