The role of APOBEC mutagenesis in the progression and therapeutic guidance of pancreatic cancer

Abstract

Background

APOBEC (apolipoprotein B mRNA editing enzyme, catalytic polypeptide-like) family-mediated mutagenesis is widespread in human cancers. However, we still have a limited understanding of the biological features and clinical relevance of APOBEC mutagenesis in cancer, particularly in pancreatic cancer.

Methods

In this study, we conducted a comprehensive analysis of various data, including whole-exome sequencing (WES), targeted next-generation sequencing (NGS), transcriptome analysis (both bulk RNA-seq and single-cell RNA-seq), immune profiling, immune checkpoint blockade (ICB) response, patient survival, and drug sensitivity. We used various bioinformatics and statistical methods to uncover the distributional features, microenvironmental changes, and clinical significance of APOBEC mutagenesis in pancreatic adenocarcinoma (PAAD).

Results

APOBEC mutagenesis significantly influenced mutation patterns in PAAD. Higher enrichment scores of APOBEC mutagenesis signature (APMs) were associated with survival prognosis, immune remodeling, and potential responses to immune checkpoint blockade (ICB) in PAAD patients. In pancreatic cancer, APOBEC3A and APOBEC1 played important roles in malignant progression and cell differentiation in the tumor microenvironment and mediated enhanced CAF-tumor cell communication in the microenvironment, while APMs were also involved in the formation of an immunosuppressive microenvironment in pancreatic cancer through multiple pathways. Additionally, we developed and validated a machine learning model related to APOBEC mutagenesis across various cohorts of PAAD to predict poor survival prognosis. We also conducted drug sensitivity analyses to identify irinotecan as the drug with the highest inhibitory effect on APMs. Subsequently, in vitro experiments verified that irinotecan significantly inhibited pancreatic tumor cell proliferation. Our findings showed that irinotecan significantly reduced the proliferation, metastasis, and glycolysis of pancreatic tumor cells. It also decreased the expression levels of activation markers in cancer-associated fibroblasts (CAFs), including CD73, ACTA2, and COL1A1. In vivo experiments demonstrated that irinotecan could remodel the immune microenvironment by inhibiting Tregs, and combined with Treg inhibitors, it could effectively reduce the tumor burden of PAAD.

Conclusion

Our study illustrated the characterization of APOBEC mutagenesis in multiple cancer types and highlighted its potential value as a prognostic and immunotherapeutic biomarker for PAAD, and finally demonstrated the effectiveness of irinotecan, an inhibitor of APMs, in vivo and in vitro experiments.