title: 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 patients with acute myeloid leukemia (AML), whereas methylation signatures and prognostic markers have been proposed. The objective of the current study was to evaluate all CpG sites of the genome and identify prognostic methylation markers for overall survival in patients with AML with normal karyotype (AML-NK).
  
  
  METHODS
  AML-NK samples from 7 SWOG trials were analyzed using a novel genome-wide approach called "CHARMcox" (comprehensive high-throughput array-based relative methylation analysis combined with the Cox proportional hazards model) controlling for known clinical covariates. CHARMcox was applied to a phase 1 discovery cohort (72 patients) to identify survival-associated methylation regions (SAMRs). Subsequently, using bisulfite pyrosequencing, SAMRs were studied in phase 2 model-building (65 patients) and phase 3 validation (65 patients) cohorts. An independent external cohort from The Cancer Genome Atlas (TCGA) AML study (LAML) was used for further validation (93 patients).
  
  
  RESULTS
  Two SAMRs, located at the CpG island shores of leucine zipper tumor suppressor 2 (LZTS2) and nuclear receptor subfamily 6 group a member 1 (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<.001). The prognosis was validated in patients with AML-NK from the TCGA-LAML cohort. Methylation values below the median at both markers predicted worse overall survival (SWOG: hazard ratio, 1.89 [P<.001]; and TCGA-LAML: hazard ratio, 2.08 [P=.006]). The C-statistic was 0.71 for both cohorts, and the impact was independent of the Fms-related tyrosine kinase 3 internal tandem duplication (FLT3-ITD) status.
  
  
  CONCLUSIONS
  The 2 methylation markers, measurable by clinically applicable assays such as bisulfite pyrosequencing, are promising for risk stratification among patients with AML-NK. Cancer 2017;123:2472-81. © 2017 American Cancer Society.
authors.affiliation: Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, Washington.|Seattle Cancer Care Alliance, Seattle, Washington.
authors.forename: Xiaoyu
authors.initials: X
authors.lastname: Qu
authors.affiliation: Public Health Sciences Research Division, Fred Hutchinson Cancer Research Center, Seattle, Washington.|SWOG Leukemia Committee, Portland, Oregon.
authors.forename: Megan
authors.initials: M
authors.lastname: Othus
authors.affiliation: Public Health Sciences Research Division, Fred Hutchinson Cancer Research Center, Seattle, Washington.
authors.forename: Jerry
authors.initials: J
authors.lastname: Davison
authors.affiliation: Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, Washington.
authors.forename: Yu
authors.initials: Y
authors.lastname: Wu
authors.affiliation: EpigenDx Inc, Boston, Massachusetts.
authors.forename: Liying
authors.initials: L
authors.lastname: Yan
authors.affiliation: Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, Washington.
authors.forename: Soheil
authors.initials: S
authors.lastname: Meshinchi
authors.affiliation: Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, Washington.
authors.forename: Fabiana
authors.initials: F
authors.lastname: Ostronoff
authors.affiliation: Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, Washington.|Seattle Cancer Care Alliance, Seattle, Washington.|Department of Medicine, University of Washington, Seattle, Washington.
authors.forename: Elihu H
authors.initials: EH
authors.lastname: Estey
authors.affiliation: Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, Washington.|Seattle Cancer Care Alliance, Seattle, Washington.
authors.forename: Jerry P
authors.initials: JP
authors.lastname: Radich
authors.affiliation: SWOG Leukemia Committee, Portland, Oregon.|Division of Hematology & Oncology, University of Alabama at Birmingham, Birmingham, Alabama.
authors.forename: Harry P
authors.initials: HP
authors.lastname: Erba
authors.affiliation: Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, Washington.|Seattle Cancer Care Alliance, Seattle, Washington.|SWOG Leukemia Committee, Portland, Oregon.|Department of Medicine, University of Washington, Seattle, Washington.
authors.forename: Frederick R
authors.initials: FR
authors.lastname: Appelbaum
authors.affiliation: Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, Washington.|Seattle Cancer Care Alliance, Seattle, Washington.|SWOG Leukemia Committee, Portland, Oregon.|Department of Pathology, University of Washington, Seattle, Washington.
authors.forename: Min
authors.initials: M
authors.lastname: Fang
mesh_terms: D000293:Adolescent; D000328:Adult; D000368:Aged; D000369:Aged, 80 and over; D002423:Cause of Death; D018797:Cell Cycle Proteins / Q000235:genetics*; D018899:CpG Islands / Q000235:genetics; D019175:DNA Methylation / Q000235:genetics*; D004268:DNA-Binding Proteins / Q000235:genetics*; D005260:Female; D006801:Humans; D015470:Leukemia, Myeloid, Acute / Q000235:genetics* / Q000401:mortality / Q000628:therapy; D008297:Male; D008875:Middle Aged; D015999:Multivariate Analysis; D057136:Nuclear Receptor Subfamily 6, Group A, Member 1 / Q000235:genetics*; D011379:Prognosis; D016016:Proportional Hazards Models; D015996:Survival Rate; D025521:Tumor Suppressor Proteins / Q000235:genetics*; D055815:Young Adult
chemical_list: D018797:Cell Cycle Proteins; D004268:DNA-Binding Proteins; C440108:LZTS2 protein, human; C539950:NR6A1 protein, human; D057136:Nuclear Receptor Subfamily 6, Group A, Member 1; D025521:Tumor Suppressor Proteins
keywords: leucine zipper tumor suppressor 2 (LZTS2); leukemia; methylation; nuclear receptor subfamily 6 group a member 1 (NR6A1); survival