Prognostic methylation markers for overall survival in cytogenetically normal patients with acute myeloid leukemia treated on SWOG trials

Abstract

Background Aberrant DNA methylation is known to occur in acute myeloid leukemia (AML), while methylation signatures and prognostic markers have been proposed. This study aimed to evaluate all CpG sites of the genome and identify prognostic methylation markers for overall survival in AML patients with normal cytogenetics (AML-NK). Methods AML-NK samples from seven SWOG trials were analyzed using a novel genome-wide approach “CHARMcox”: the comprehensive high-throughput array-based relative methylation analysis combined with the Cox proportional hazard model controlling for known clinical covariates. CHARMcox was applied to a phase I discovery cohort (n=72) to identify survival associated methylation regions (SAMRs). Subsequently, using bisulfite pyrosequencing, SAMRs were studied in phase II model building (n=65) and phase III validation (n=65) cohorts. An independent external cohort from the TCGA AML study (LAML) was used for further validation (n=93). Results Two SAMRs, located at the CpG island shores of LZTS2 and NR6A1, respectively, were identified. Multivariable analyses demonstrated that hypomethylation of either LZTS2 or NR6A1 was associated with worse overall survival in the SWOG cohort (P < 0.001). The prognosis was validated in AML-NK patients from the TCGA-LAML cohort. Methylation values below median at both markers predicted worse overall survival (SWOG, HR 1.89, P <0.001; TCGA-LAML, HR 2.08, P=0.006). The C-statistics was 0.71 for both cohorts, and the impact was independent of the FLT3-ITD status. Conclusions The two methylation markers, measurable by clinically applicable assays such as bisulfite pyrosequencing, are promising for risk stratification among AML patients with normal karyotype.

Acidic leucine-rich nuclear phosphoprotein-32A expression contributes to adverse outcome in acute myeloid leukemia

“…To date, cytogenetic analysis has been one of the most useful prognostic methods to classify AML Original Article patients into different prognostic risk groups (favorable, intermediate, unfavorable) (3). The cytogenetically normal AML (CN-AML), representing 40-50% AML patients, is the largest subset of de-novo AML cases (4,5). Although CN-AML constitutes the main body of the intermediaterisk group, yet different molecular subtypes of CN-AML diverged in transcription and DNA methylation profiles (6).…”

Impact of Specimen Heterogeneity on Biomarkers in Repository Samples from Patients with Acute Myeloid Leukemia: A SWOG Report

“…These findings are consistent with previous observations of genomic mutations in MDS and methylation markers in AML. 65,66 We acknowledge that researchers will continue to rely on specimens collected through cooperative group repositories to obtain statistical power and patient heterogeneity for many types of studies, including biomarker discovery and validation. In some cases, these samples have been collected over a large period from multiple trials.…”

Targeted methylation sequencing of plasma cell-free DNA for cancer detection and classification

“…Methylation profiling of cfDNA has been investigated in cancer diagnostics and assessment of therapeutic outcomes [18][19][20][21][22][23][24]. Guo et al have shown that identifying methylation patterns from cfDNA can be used to map tissue-of-origin in lung and colorectal cancer patients [25].…”

“…more than 9000 CpG sites while using a simplified workflow and commercially available reagents. Whole-genome bisulfite sequencing can provide a more comprehensive methylation profile; however, the cost may preclude advances to the clinic in the short-term [22]. On the other hand, PCR-based approaches are less expensive, though, their utility may be limited by the small number of CpG sites assessed [25].…”