Global DNA Hypermethylation in Chronic Lymphocytic Leukemia Correlates with Progressive Disease.
Authors: Yu Margaret K. , Szabo Aniko , Bergonia Hector , Senina Anna , Phillips John D. 
Published: April 2020

Abstract
Global DNA hypomethylation is observed in chronic lymphocytic leukemia, but methylation has not been correlated with clinical outcome. Although patient survival correlates with factors such as the mutational status of the immunoglobulin variable genes, karyotype abnormalities, Zap-70, and CD38 expression, none of these predictors have altered the way clinicians practice. We report interim results in the assessment of global DNA methylation as a predictor of aggressive disease in patients with chronic lymphocytic leukemia. Fourteen patients with chronic lymphocytic leukemia donated blood samples for DNA studies at the same time as blooddraws for their physician visits. All the treatments occurred within one year and the follow-ups were at least within 12 months except for one patient. We thus classified patients into two groups: those who required treatment within one year and those who did not. The cutoff in methylation level providing the smallest observed prediction error was 4.125%; it correctly predicted 5/6 patients not needing treatment within a year and 5/6 patients needing treatment. These observed classification rates were adjusted for the bias resulting from the optimal selection of the cutoff using bootstrap. The adjusted sensitivity and specificity were 74% and 80%, respectively. Asymptomatic patients with chronic lymphocytic leukemia tended to have lower levels of global DNA methylation (median 3.5%) compared to symptomatic patients (median 4.5%). In other words, high levels of global DNA methylation were associated with higher disease burden, corresponding with higher lymphocyte and white blood cell numbers. Five patients without immediate need for cytoreductive therapy were enrolled on a pilot treatment trial with low-dose cladribine, by subcutaneous injection. Three out of the five patients have had a clinical response, a secondary endpoint. Two of the patients have achieved a partial response, as defined by the NCI sponsored working group, with at least a three month follow-up after discontinuation of the drug. Of the two patients with stable or progressive disease on cladribine, their global DNA methylation levels were higher, correlating with more chemotherapy resistant disease.
DNA methylation Levels in Patients with Chronic Lymphocytic Leukemia Age Sex %5-MedC Zap-70 CD-38 Rai Stage FISH Req Treatment (mos) FISH= fluorescence in situ hybridization; Zap-70 assessed by immunochemistry 51 M 5.045 positive positive 4 Del13q14 0.75 73 F 4.865 positive not assessed 4 not assessed 12+ 52 F 4.665 positive negative 2 Del13q14 2 57 M 4.62 negative negative 4 Del13q14 2 66 M 4.59 positive not assessed 4 Del13q14 (5/05) and Del 17p and Del 13q14 (7/05) 0.25 67 M 4.14 positive positive 4 Trisomy 12 10 47 M 4.055 negative negative 0 not assessed 12+ 59 M 3.9 negative negative 2 46XY 0 72 M 3.54 negative not assessed 0 not assessed 8+ 64 M 3.55 positive not assessed 1 Del13q14 12+ 70 F 3.47 not assessed negative 4 Trisomy 12 12+ 68 F 3.47 positive negative 2 not assessed 12+ 77 M 3.2 not assessed not assessed 0 not assessed 12+ DNA Methylation Levels in patients with Chronic Lymphocytic Leukemia DNA Methylation Levels in patients with Chronic Lymphocytic Leukemia