Cell-free DNA 5-hydroxymethylcytosine is highly sensitive for MRD assessment in acute myeloid leukemia

Abstract

Measurable residual disease (MRD) is an important biomarker in acute myeloid leukemia (AML). However, MRD cannot be detected in many patients using current methods. We developed a highly sensitive 5-hydroxymethylcytosine (5hmC) signature in cell-free DNA by analyzing 115 AML patients and 86 controls. The 5hmC method detected MRD in 20 of 29 patients with negative MRD by multiparameter flow cytometry and 11 of 14 patients with negative MRD by molecular methods. MRD detection by the 5hmC method was significantly associated with relapse-free survival. This novel method can be used in most AML patients and may significantly impact AML patient management.

Keywords: 5-hydroxymethylcytosine; Acute myeloid leukemia; Cell-free DNA; Measurable residual disease.

Fig. 1

A cfDNA 5hmC signature differentiates AML patients from controls. A Boxplot of weighted-detection scores (wd-scores) in controls and AML samples in training, validation, and test sets. Black dashed line represents a cutoff score of 0.229. Center line represents median, bounds of box represent 25th and 75th percentiles, and whiskers are Tukey whiskers. B Receiver Operating Characteristics analysis of wd-score calculated from the 5hmC signature in the training, validation, and test sets. AUC, area under the curve. CI, 95% confidence interval

Figure. 2

The cfDNA 5hmC signature is highly sensitive for measurable residual disease detection in AML. A Boxplot of weighted-detection scores (wd-scores) in AML samples with no measurable residual disease (MRD) assessed by multiparameter flow cytometry (MFC). Black dashed line represents a cutoff score of 0.229. Center line represents median, bounds of box represent 25th and 75th percentiles, and whiskers are Tukey whiskers. B Comparison of MRD detection by the cfDNA 5hmC method and molecular methods. Molecular-, no MRD detected by molecular methods. Molecular+, MRD detected by molecular methods. The number of patients is displayed on the columns. C Kaplan–Meier analysis of relapse-free survival (RFS) of AML patients with no MRD by MFC based on the cfDNA 5hmC method. Censored patients are indicated by dots. D Timing and MRD results were assessed using the cfDNA 5hmC method for each AML patient. AML patient samples with no MRD detected by MFC are displayed. Patients were ordered by total days of clinical follow-up from registration. HSCT, hematopoietic stem cell transplant