Pan-cancer analysis for APOBEC3C can comprehensively reveal its functional significance with abnormal expressions between tumor tissues and normal ones, providing new insights into the pathogenesis and prevention of cancer21. In this study, we utilized multiple public databases to perform comprehensive bioinformatics analysis of the expression of the APOBEC3C gene in normal tissues and different types of tumors. In addition, we examined the association between APOBEC3C expression and survival outcomes (OS and DSS) and found that APOBEC3C expression levels had different prognostic impacts across the different cancer types. APOBEC3C was associated with immune features (including immune infiltration, immune checkpoints, TMB, and MSI), MMR Gene Mutation, and epigenetic modification methylation. Finally, we conducted several in vitro experiments with GBM cells to further explore the biological functions of APOBEC3C in tumor progression.
APOBEC3C belongs to the cytidine deaminase (APOBEC) family that can convert cytosine to uracil or thymine (C-to-U or T)22. Recent studies have shown that APOBEC3C may be involved in the occurrence and development of human cancer11. However, its role in most types of cancer is still quite unclear. By analyzing 27 cancer data sets, we found that the expression of APOBEC3C was significantly different in several new tumor types, such as CHOL, GBM, and LGG. OS and DSS are important prognostic indicators in survival analysis. Through the analysis of these 2 prognostic indices, we found that the expression of APOBEC3C can be regarded as a tumor marker for predicting unfavorable prognosis, especially in glioma. Therefore, our studies strongly suggest that APOBEC3C may provide a new sight for tumor prognosis and treatment.
The tumor microenvironment, including neoplastic cells, non-cancerous cells, and some non-cellular components, is a key factor in conducting complex interactions with tumor cells, such as assisting malignant cells to escape from immune clearance, and promoting tumor inflammation, invasion and metastasis. With in-depth studies, therapies targeted against the TME have become an ingenious choice23. Increasing evidence suggests that tumor-infiltrating lymphocytes (T and B cell lineage) and other immune cells (dendritic cells, macrophages, and neutrophils) play an indispensable role in the tumor immune response. At present, there are few studies on the relationship between APOBEC3C expression levels and immune infiltration. As shown in this research, the expression of APOBEC3C was significantly correlated with the level of immune cell infiltration in BRCA, KIRC, LGG, LIHC, LUAD, and PAAD. The immune score, which is composed of the immune cell type, density, and location, is considered to be a simple, quantitative and standardized routine tool for evaluating the immune environment, showing great potential in predicting the prognosis of immune or matrix components and evaluating the value of biomarkers24. Similarly, we calculated matrix scores, immune scores, and estimated scores of APOBEC3C gene expression in different cancers. Our results suggested that APOBEC3C expression positively correlated with the matrix and immune components in LGG and GBM. Immune checkpoint inhibitors (ICIs) have emerged as a new pillar of cancer treatment, pointing to new directions for tumor immunotherapy25. Patients with high TMB or MSI are more likely to receive the better efficacy of immunotherapy. TMB and MSI can be used as predictors of immunotherapy for cancer patients26, 27. Previous studies have shown that APOBEC3 was abnormally expressed in many malignant tumors and led to genome instability and idiosyncratic DNA mutations by the deamination of cytosine to thymine (C-to-T)28–31. Jiang et al. reported that APOBEC3C was upregulated in myeloproliferative neoplasm (MPN) patients, and the burden of C-to-T mutations increased, subsequently inducing the proliferation of human pre-leukemia stem cells (pre-LSCs) and facilitating the transformation into acute myeloid leukemia stem cells (LSCs)11. With this in mind, our work examined the correlation between APOBEC3C expression and TMB and MSI in all TCGA patients. The results suggested that APOBEC3C expression was associated with TMB and MSI respectively.
Mismatch repair can correct errors missed by the proofreading function of DNA polymerase, thereby ensuring the stability of DNA replication, while MMR gene mutations lead to defects in the mismatch repair function (dMMR), subsequently resulting in genome or microsatellite instability32. A body of evidence showed that mismatch repair defects (dMMR) could be used to predict the efficacy of immune checkpoint inhibitors (ICI)33. Abnormal methylation plays important role in the development and metastasis of tumors34. In our research, we found that APOBEC3C was linked with the expression of 5 MMR genes and 4 DNA methyltransferases in human cancer. These results indicate that the aberrant APOBEC3C expression may play an essential role in oncogenesis by regulating MMR activity and methylation. Based on the above bioinformatics analysis results, we also carried out IHC and in vitro cell experiments to study the biological functions of APOBEC3C in GBM cell lines. The results suggested that higher APOBEC3C level was paralleled with higher malignancy in glioma and the upregulation of APOBEC3C promoted the proliferation, migration ability as well as invasion of glioblastoma. There are studies indicating that APOBEC3B triggers DNA replication stress and chromosomal instability through incomplete replication of genomic DNA35. Therefore, we speculate that APOBEC3C may play an important role in malignancy in glioma by APOBEC3C-mediated mutagenesis.
Although we used multiple databases to perform pan-cancer analysis on APOBEC3C, there is still much room for improvement in our research. First of all, we have not conducted a comprehensive analysis of mutational signatures, especially in glioma. Due to this, our understanding of the biological process of mutation is limited, which means that more detailed studies are needed. Secondly, this study only conducted limited experiments, we will conduct more experiments in vivo or in vitro, especially in glioma. Third, our work proved that APOBEC3C expression was associated with tumor immunity and disease prognosis, but how APOBEC3C regulates tumor microenvironment and immune-related pathways to influence clinical survival and prognosis requires further mechanism research. Future research on the APOBEC3C gene may solve these scientific problems.