Supervising the recurrence of pancreatic ductal adenocarcinoma using CtDNA-based MIR129-2 methylation detection

Abstract

Background: Surgery remains the primary treatment for pancreatic ductal adenocarcinoma (PDAC), which has remarkably high morbidity and mortality rates. However, recurrence is prevalent after resection. The effectiveness of circulating tumor DNA (ctDNA) in recurrence prediction has been demonstrated, and methylation has advantages over traditional biomarkers in terms of early-stage specificity. These advances indicate the need for a ctDNA-based methylation marker for PDAC prognosis, which would be valuable in clinical practice.

Methods: MIR129-2 promoter methylation markers were identified via a combination of differential methylation, differential expression, gene set enrichment analysis and survival analysis using TCGA data. A qPCR-based assay was developed to quantify MIR129-2 methylation in plasma samples with as little as 0.05% tumor DNA. Its performance in PDAC diagnosis and progression risk evaluation was evaluated using tissue (314 tumor vs. 306 normal) and plasma (187 PDAC vs. 59 normal) samples from two independent retrospective cohorts. A longitudinal cohort study (114 patients) was conducted to assess its performance in determining PDAC prognosis. Both before surgery and after surgery, plasma samples were collected.

Results: MIR129-2 methylation showed excellent performance in differentiating PDAC and normal tissues, with a sensitivity of 97.77% and a specificity of 98.71%. For the plasma samples, it had a high sensitivity of 87.20% and a specificity of 98.30%. Survival analysis revealed its ability to predict postoperative survival outcomes even in CA19-9-negative patients ( P = 0.001).

Conclusion: Postoperative measurement of ctDNA-based MIR129-2 methylation can be used to predict PDAC recurrence risk, offering a cost-effective assay to facilitate the postoperative management of PDAC patients.

Keywords: MIR129-2 methylation; ctDNA; pancreatic ductal adenocarcinoma.

Figure 1.

Flowchart of this study.

Figure 2.

MIR129-2 methylation signals in PDAC tissue and plasma samples. (A) MIR129-2 methylation signals in PDAC, MCN and SCN, SPT, pNET, IPMN and adjacent normal tissue samples; (B) MIR129-2 methylation signals in stage I–IV PDAC and adjacent normal tissue samples; (C) ROC curve discriminating PDAC tissues from normal samples; (D) MIR129-2 methylation signals from PDAC plasma samples; (E) ROC curve discriminating PDAC plasma samples from plasma samples from healthy controls.

Figure 3.

Pre- and postoperative MIR129-2 methylation and CA19-9 measurements of PDAC patients in cohort 3. (A) MIR129-2 methylation measurements; (B) CA19-9 measurements; (C) Survival analysis against preoperative MIR129-2 methylation; (D) Survival analysis against postoperative MIR129-2 methylation; (E) Survival analysis against preoperative CA19-9 measurements; (F) Survival analysis against postoperative CA19-9 measurements.

Figure 4.

Prediction of the prognosis of patients with PDAC via MIR129-2 methylation. (A) Survival analysis against postoperative MIR129-2 methylation in patients with positive CA19-9; (B) Survival analysis against postoperative MIR129-2 methylation in patients with negative CA19-9; (C–E) Trends in MIR129-2 methylation and CA19-9 over time in patients after surgery, (C) in all patients, (D) in patients with recurrence, and (E) in patients without recurrence.