Validation of DNA Methylation Biomarkers for Diagnosis of Acute Lymphoblastic Leukemia

Abstract

BACKGROUND DNA methylation biomarkers capable of diagnosis and subtyping have been found for many cancers. Fifteen such markers have previously been identified for pediatric acute lymphoblastic leukemia (ALL). Validation of these markers is necessary to assess their clinical utility for molecular diagnostics. Substantial efficiencies could be achieved with these DNA methylation markers for disease tracking with potential to replace patient-specific genetic testing. METHODS We evaluated DNA methylation of promoter regions of TLX3 (T-cell leukemia homeobox) and FOXE3 (forkhead box E3) in bone marrow biopsies from 197 patients classified as leukemic (n = 95) or clear of the disease (n = 102) by MALDI-TOF. Using a single nucleotide extension assay (methylSABER), we tested 10 bone marrow biopsies collected throughout the course of patient chemotherapy. Using reference materials, diagnostic thresholds and limits of detection were characterized for both methods. RESULTS Reliable detection of DNA methylation of TLX3 and FOXE3 segregated ALL from those clear of disease with minimal false-negative and false-positive results. The limit of detection with MALDI-TOF was 1000–5000 copies of methylated allele. For methylSABER, the limit of detection was 10 copies of methylated TLX3, which enabled monitoring of minimal residual disease in ALL patients. CONCLUSIONS Mass spectrometry procedures can be used to regionally multiplex and detect rare DNA methylation events, establish DNA methylation loci as clinically applicable biomarkers for disease diagnosis, and track pediatric ALL.

Validation of DNA Methylation to Predict Outcome in Acute Myeloid Leukemia by Use of xMELP

“…Not surprisingly, large-scale analyses of epigenetic phenomena have shown clear correlations between epigenetic patterns and patient outcome. Correlations between DNA methylation and clinical prognosis have been observed for many cancers, including glioblastoma, acute myeloid leukemia (AML), 6 T-cell and B-cell lymphoblastic leukemia, lung carcinoma, ovarian carcinoma, and melanoma (5–16). …”

Epigenetic Biomarkers in Personalized Medicine

“…Biomarkers of minimal residual disease in pediatric acute lymphoblastic leukemia [35] Colorectal cancer DNA methylation…”

“…DIAGNOSTIC AND PROGNOSTIC EPIGENETIC APPROACHES Indeed, DNA methylation biomarkers capable of diagnosis and subtyping have been investigated in several hematopoietic tumors as well as prognostic ones [33]. A validation study of some of these markers led to a reliable detection of DNA methylation of the TLX3 and FOXE3 genes, which allowed the monitoring of minimal residual disease in pediatric ALL patients [35]. For instance, in a genome-wide association study on pediatric acute lymphoblastic leukemia (ALL) 325 genes were found to be hypermethylated and downregulated and 45 genes hypomethylated and upregulated [34].…”

Correlation between gastric carcinoma and ZAC gene-associated microsatellite instability and loss of heterozygosity

“…Genetic alterations include the mutation of the protein-coding region or loss of heterozygosity (LOH) and microsatellite instability (MSI) in the coding or non-coding regions. Epigenetic changes typically involve the methylation of promoter DNA or histone acetylation (7).…”

“…MSI is the polymorphism in the length of these microsatellite sequences; they may affect amino acid codons or the regulation of transcription (8). At present, various MSI phenotypes have been identified in a number of tumor types (7,8). The mechanism of inactivating mutations and deletions of both alleles of a tumor suppressor gene was involved in the process of carcinogenesis.…”