Comprehensive multi-omics analysis reveals m7G-related signature for evaluating prognosis and immunotherapy efficacy in osteosarcoma

Yiming Zhang; Wenyi Gan; Nan Ru; Zhaowen Xue; Wenjie Chen; Zihang Chen; Huajun Wang; Xiaofei Zheng

doi:10.1016/j.jbo.2023.100481

Comprehensive multi-omics analysis reveals m7G-related signature for evaluating prognosis and immunotherapy efficacy in osteosarcoma

J Bone Oncol. 2023 Apr 18:40:100481. doi: 10.1016/j.jbo.2023.100481. eCollection 2023 Jun.

Authors

Yiming Zhang¹, Wenyi Gan¹, Nan Ru¹, Zhaowen Xue¹, Wenjie Chen¹, Zihang Chen¹, Huajun Wang¹, Xiaofei Zheng¹

Affiliation

¹ Department of Sports Medicine, The First Affiliated Hospital, Jinan University, Guangzhou 510000, China.

Abstract

Background: Osteosarcoma is one of the most prevalent bone malignancies with a poor prognosis. The N7-methylguanosine (m7G) modification facilitates the modification of RNA structure and function tightly associated with cancer. Nonetheless, there is a lack of joint exploration of the relationship between m7G methylation and immune status in osteosarcoma.

Methods: With the support of TARGET and GEO databases, we performed consensus clustering to characterize molecular subtypes based on m7G regulators in all osteosarcoma patients. The least absolute shrinkage and selection operator (LASSO) method, Cox regression, and receiver operating characteristic (ROC) curves were employed to construct and validate m7G-related prognostic features and derived risk scores. In addition, GSVA, ssGSEA, CIBERSORT, ESTIMATE, and gene set enrichment analysis were conducted to characterize biological pathways and immune landscapes. We explored the relationship between risk scores and drug sensitivity, immune checkpoints, and human leukocyte antigens by correlation analysis. Finally, the roles of EIF4E3 in cell function were verified through external experiments.

Results: Two molecular isoforms based on regulator genes were identified, which presented significant discrepancies in terms of survival and activated pathways. Moreover, the six m7G regulators most associated with prognosis in osteosarcoma patients were identified as independent predictors for the construction of prognostic signature. The model was well stabilized and outperformed traditional clinicopathological features to reliably predict 3-year (AUC = 0.787) and 5-year (AUC = 0.790) survival in osteosarcoma cohorts. Patients with increased risk scores had a poorer prognosis, higher tumor purity, lower checkpoint gene expression, and were in an immunosuppressive microenvironment. Furthermore, enhanced expression of EIF4E3 indicated a favorable prognosis and affected the biological behavior of osteosarcoma cells.

Conclusions: We identified six prognostic relevant m7G modulators that may provide valuable indicators for the estimation of overall survival and the corresponding immune landscape in patients with osteosarcoma.

Keywords: EIF4E3; Immunotherapy; M7G modification; Osteosarcoma; Single-cell analysis.