A copy number repeat polymorphism in the transactivation domain of the CEPBA gene is possibly associated with a protective effect against acquired CEBPA mutations: an analysis in 1135 patients with AML and 187 healthy controls

The Wilms Tumor-1 (WT1) rs2234593 variant is a prognostic factor in normal karyotype acute myeloid leukemia

The single-nucleotide polymorphism (SNP) within Wilms tumor-1 (WT1) exon 7, rs16754, has been arguably reported to be implicated in acute myeloid leukemia (AML) prognosis. We assessed the potential association of selected WT1 SNPs as well as WT1 mutations in normal karyotype (NK)-AML and evaluated the prognostic value of these normal gene variants. Diagnostic samples from a series of 474 young adult NK-AML patients were used to genotype five WT1 SNPs using TaqMan assays and to directly sequence WT1 exons 7 and 9. Analysis of five WT1 gene variants showed an association of rs2234593 allele C with WT1 Ex7 mutation. Prognostic study of the same variants identified rs2234593 significantly associated with relapse and overall survival (OS). Patients with rs2234593AA/AC showed significantly higher 10-year OS (50 vs 36 %, hazard ratio (HR) = 0.69 (0.52–0.90), p = 0.006) and lower cumulative incidence of relapse (CIR) (36 vs 51 %, HR = 0.62 (0.45–0.86), p = 0.004) compared to those with rs2234593CC. The effect of AA genotype on CIR remained significant after adjustment for basic covariates including FLT3 internal-tandem duplication (FLT3-ITD) and nucleophosmin 1 (NPM1) mutations (HR = 0.60 (0.41–0.89), p = 0.009), with some evidence of improved survival (HR = 0.75 (0.55–1.03), p = 0.07). A multivariate analysis showed WT1 Ex7-mutant as the major relapse predictor, with a tendency for rs2234593-A effect after allowing for Ex7 mutation (p = 0.07). No adjusted risk benefit was found for previously reported rs16754-G. In conclusion, WT1 normal gene variant rs2234593 is associated with mutational status of WT1 Ex7 and is a further prognostic marker independent from FLT3-ITD and NPM1 mutations in NK-AML.

A novel hierarchical prognostic model of AML solely based on molecular mutations

The karyotype is so far the most important prognostic parameter in acute myeloid leukemia (AML). Molecular mutations have been analyzed to subdivide AML with normal karyotype into prognostic subsets. The aim of this study was to develop a prognostic model for the entire AML cohort solely based on molecular markers. One thousand patients with cytogenetic data were investigated for the following molecular alterations: PML-RARA, RUNX1-RUNX1T1, CBFB-MYH11, FLT3-ITD, and MLL-PTD, as well as mutations in NPM1, CEPBA, RUNX1, ASXL1, and TP53. Clinical data were available in 841 patients. Based on Cox regression and Kaplan-Meier analyses, 5 distinct prognostic subgroups were identified: (1) very favorable: PML-RARA rearrangement (n = 29) or CEPBA double mutations (n = 42; overall survival [OS] at 3 years: 82.9%); (2) favorable: RUNX1-RUNX1T1 (n = 35), CBFB-MYH11 (n = 31), or NPM1 mutation without FLT3-ITD (n = 186; OS at 3 years: 62.6%); (3) intermediate: none of the mutations leading to assignment into groups 1, 2, 4, or 5 (n = 235; OS at 3 years: 44.2%); (4) unfavorable: MLL-PTD and/or RUNX1 mutation and/or ASXL1 mutation (n = 203; OS at 3 years: 21.9%); and (5) very unfavorable: TP53 mutation (n = 80; OS at 3 years: 0%; P < .001). This comprehensive molecular characterization provides a more powerful model for prognostication than cytogenetics.

Molecular evaluation of CEBPA gene mutation in normal karyotype acute myeloid leukemia: a comparison of two methods and report of novel CEBPA mutations from Indian acute myeloid leukemia patients

BACKGROUND AND AIM

Mutation in the CAAT/enhancer binding protein-α (CEBPA) gene has been reported as being one of the common genetic abnormalities in acute myeloid leukemia (AML) and is associated with a good clinical outcome. We intend to explore the prevalence of CEBPA mutations and evaluate the efficacy of fragment and sequencing analysis methods for CEBPA mutation detection in Indian AML patients.

MATERIALS AND METHODS

The coding region of the CEBPA gene was screened in 36 normal karyotype AML patients by fragment analysis and direct sequencing.

RESULTS

We identified five CEBPA sequence variations in three patient samples (8.3%) by direct sequencing analysis, of which three were novel mutations. These mutations were clustered mostly in the TAD1 and basic region leucine zipper region of the CEBPA protein. Six cases demonstrated a previously reported polymorphism. Two of the three positive cases showed double mutations, and one case had a single mutation. All five mutations were also detected by fragment analysis, indicating a sensitivity of 100% (5/5). No correlation with clinical parameters including age, sex, white blood cell count, hemoglobin, and platelet count between patients with and without mutation was observed. Interestingly, CEBPA mutations were significantly higher in patients with WT1 mutation, while no correlation with FLT3 and NPM1 was observed.

CONCLUSION

We report for the first time the frequency of CEBPA mutation from an Indian patients (8.3%). The identification of novel CEBPA mutations added new insights into the genetic heterogeneity of AML. Our result suggests that the optimal approach for detecting CEBPA mutations in AML can be a combination of fragment analysis and direct sequencing.

Whole-exome sequencing identifies somatic mutations of BCOR in acute myeloid leukemia with normal karyotype

Among acute myeloid leukemia (AML) patients with a normal karyotype (CN-AML), NPM1 and CEBPA mutations define World Health Organization 2008 provisional entities accounting for approximately 60% of patients, but the remaining 40% are molecularly poorly characterized. Using whole-exome sequencing of one CN-AML patient lacking mutations in NPM1, CEBPA, FLT3-ITD, IDH1, and MLL-PTD, we newly identified a clonal somatic mutation in BCOR (BCL6 corepressor), a gene located on chromosome Xp11.4. Further analyses of 553 AML patients showed that BCOR mutations occurred in 3.8% of unselected CN-AML patients and represented a substantial fraction (17.1%) of CN-AML patients showing the same genotype as the AML index patient subjected to whole-exome sequencing. BCOR somatic mutations were: (1) disruptive events similar to the germline BCOR mutations causing the oculo-facio-cardio-dental genetic syndrome; (2) associated with decreased BCOR mRNA levels, absence of full-length BCOR, and absent or low expression of a truncated BCOR protein; (3) virtually mutually exclusive with NPM1 mutations; and (4) frequently associated with DNMT3A mutations, suggesting cooperativity among these genetic alterations. Finally, BCOR mutations tended to be associated with an inferior outcome in a cohort of 422 CN-AML patients (25.6% vs 56.7% overall survival at 2 years; P = .032). Our results for the first time implicate BCOR in CN-AML pathogenesis.

Presence of FLT3-ITD and high BAALC expression are independent prognostic markers in childhood acute myeloid leukemia

Mutation status of FLT3, NPM1, CEBPA, and WT1 genes and gene expression levels of ERG, MN1, BAALC, FLT3, and WT1 have been identified as possible prognostic markers in acute myeloid leukemia (AML). We have performed a thorough prognostic evaluation of these genetic markers in patients with pediatric AML enrolled in the Nordic Society of Pediatric Hematology and Oncology (NOPHO) 1993 or NOPHO 2004 protocols. Mutation status and expression levels were analyzed in 185 and 149 patients, respectively. Presence of FLT3-internal tandem duplication (ITD) was associated with significantly inferior event-free survival (EFS), whereas presence of an NPM1 mutation in the absence of FLT3-ITD correlated with significantly improved EFS. Furthermore, high levels of ERG and BAALC transcripts were associated with inferior EFS. No significant correlation with survival was seen for mutations in CEBPA and WT1 or with gene expression levels of MN1, FLT3, and WT1. In multivariate analysis, the presence of FLT3-ITD and high BAALC expression were identified as independent prognostic markers of inferior EFS. We conclude that analysis of the mutational status of FLT3 and NPM1 at diagnosis is important for prognostic stratification of patients with pediatric AML and that determination of the BAALC gene expression level can add valuable information.