Mutational analysis of DNMT3A improves the prognostic stratification of patients with acute myeloid leukemia

Nucleophosmin1 (NPM1) mutations are the most frequently detected gene mutations in acute myeloid leukemia (AML) and are considered a favorable prognostic factor. We retrospectively analyzed the prognosis of 605 Japanese patients with de novo AML, including 174 patients with NPM1-mutated AML. Although patients with NPM1-mutated AML showed a high remission rate, this was not a favorable prognostic factor for overall survival (OS); this is contrary to generally accepted guidelines. Comprehensive gene mutation analysis showed that mutations in codon R882 of DNA methyltransferase 3A (DNMT3A^R882 mutations) were a strong predicative factor indicating poor prognosis in all AML (p < 0.0001) and NPM1-mutated AML cases (p = 0.0020). Furthermore, multivariate analysis of all AML cases showed that DNMT3A^R882 mutations and the co-occurrence of internal tandem duplication in FMS-like tyrosine kinase 3 (FLT3-ITD), NPM1 mutations, and DNMT3A^R882 mutations (triple mutations) were independent factors predicting a poor prognosis related to OS, with NPM1 mutations being an independent factor for a favorable prognosis (hazard ratios: DNMT3A^R882 mutations, 1.946; triple mutations, 1.992, NPM1 mutations, 0.548). Considering the effects of DNMT3A^R882 mutations and triple mutations on prognosis and according to the classification of NPM1-mutated AML into three risk groups based on DNMT3A^R882/FLT3-ITD genotypes, we achieved the improved stratification of prognosis (p < 0.0001). We showed that DNMT3A^R882 mutations are an independent factor for poor prognosis; moreover, when confounding factors that include DNMT3A^R882 mutations were excluded, NPM1 mutations were a favorable prognostic factor. This revealed that ethnological prognostic discrepancies in NPM1 mutations might be corrected through prognostic stratification based on the DNMT3A status.     

DNMT3A、FLT3-ITD合并NPM1基因突变正常核型急性髓系白血病患者的临床特征及预后分析

目的 分析DNMT3A、FLT3-ITD合并NPM1基因突变的正常核型急性髓系白血病(AML)患者的临床特征,探讨该类患者的预后.方法 回顾性分析2005年12月至2014年6月就诊的109例正常核型AML患者的临床特征及预后.其中DNMT3A/FLT3-ITD/NPM1+AML患者共25例,单独FLT3-ITD+ AML患者共32例,单独NPM1+AML患者24例,单独DNMT3A+ AML患者28例.结果 25例DNMT3A/FLT3-ITD/NPM1+ AML患者平均年龄46岁,伴有高白细胞(81.7×109/L)及较高的骨髓原始细胞(66.3％).其中,17例选择大剂量化疗,8例行异基因造血干细胞移植,与DNMT3A+、FLT3-ITD+、NPM1+AML组比较,差异均无统计学意义.25例DNMT3A/FLT3-ITD/NPM1+患者的3年总生存率为17.65％,3年无病生存率为13.88％,与DNMT3A+、FLT3-ITD+、NPM1+AML组差异均有统计学意义(P值分别为0.049 9、0.036 1、0.013 4),3年无病生存率差异无统计学意义(均P＞ 0.05).结论 DNMT3A、FLT3-ITD合并NPM1基因突变的正常AML患者往往合并高的外周血白细胞及骨髓原始细胞,预后较差.     

Prognostic implications of the presence of FLT3 mutations in patients with acute myeloid leukemia

Several studies have shown that mutations in the FLT3 gene are common events in AML, with approximately one third of adult patients harbouring either an internal tandem duplication in the juxtramembrane domain or a D835 mutation in the kinase domain. The majority of studies in pediatric and adult AML have shown that FLT3 mutations are powerful prognostic factors predicting for increased relapse risk and adverse overall survival. Some reports have suggested that loss of the wild type allele might be associated with an even worse prognosis. Changes in the pattern of FLT3 mutations between disease presentation and relapse restrict their value as a marker of minimal residual disease, and have significant implications for therapy. The optimum treatment for patients with FLT3 mutations remains unknown and large prospective studies are warranted to evaluate the efficacy of various treatment modalities such as bone marrow transplantation and targeted therapy with tyrosine kinase inhibitors.     

FLT3、NPM1、DNMT3A及IDH基因突变对非M3型急性髓系白血病预后影响的研究进展

非M3型急性髓系白血病(AML)是一组异质性恶性血液系统疾病,无论在形态学、免疫学、细胞遗传学、分子生物学及临床特点上都存在很大差异.细胞遗传学检测结果已经成为AML精确诊断、治疗选择和预后判断的主要依据之一,但由于在分子水平上存在高度的异质性,常规细胞遗传学技术检出率不高.有40%~50%的AML患者在初诊时用标准的染色体显带分析方法检测不到克隆性染色体畸变,被称为正常核型AML.非M3型AML较常见的分子遗传学改变为FLT3、NPM1、DNMT3A、IDH基因突变.文章主要就四种基因的特点、发病机制及对非M3型AML的预后影响作一综述.     

TET2合并DNMT3A突变及其他共存基因突变对急性髓系白血病患者预后的影响

  目的  探究TET2合并DNMT3A突变及其他共存基因突变对成人非M3型急性髓系白血病（acute myeloid leukemia,AML）患者预后的影响。  方法  回顾性分析2018年1月至2021年9月于南昌大学第一附属医院确诊的初治且行血液肿瘤相关突变基因外显子二代测序检测的512例成人 AML（非 M3 型）患者的临床资料,分析患者的临床特征、疗效及生存情况。  结果  本研究共纳入110例AML患者,TET2突变组64例,DNMT3A单突变组46例。男性50例（45.5%）,中位年龄54（15～79）岁。TET2基因突变频率为12.5%（64/512）,98.4%（63/64）患者突变基因数≥2个,每例患者平均合并5.2个突变基因。NPM1（43.8%）、DNMT3A（42.2%）、FLT3-ITD/TKD（40.6%）、CEBPA（26.6%）、TTN（20.3%）为TET2突变常见的共存突变基因。TET2合并DNMT3A突变患者初次诱导完全缓解（complete response,CR）率为46.2%,略低于TET2单突变患者的76.9%（P=0.077）,与DNMT3A单突变患者无显著性差异（P=0.952）。TET2合并DNMT3A突变患者的中位总生存（median overall survival,mOS）时间为9.5个月,明显低于TET2单突变患者（P=0.002）,而与DNMT3A单突变患者无显著性差异（P=0.414）。三者的中位无复发生存（median relapse- free survival,mRFS）时间无显著性差异（P>0.05）。在TET2突变背景下,合并K/NRAS突变患者的CR率为28.6%,明显低于无K/NRAS突变患者的75.0%（P=0.030）,合并FLT3-ITD突变患者的mOS明显短于无FLT3-ITD突变患者（P=0.030）。多因素分析显示年龄≥60岁、合并FLT3-ITD突变、初次诱导未达CR是影响TET2突变AML患者总生存时间（overall survival,OS）的独立危险因素,DNMT3A突变不影响TET2突变患者OS。  结论  TET2突变是AML患者常见突变,且常合并共存基因突变。共存基因突变与TET2突变共同影响AML患者预后。基于二代测序的基因突变检测对指导AML精确分层及精准治疗具有重要意义。      

Telomerase activity is prognostic in pediatric patients with acute myeloid leukemia: comparison with adult acute myeloid leukemia

BACKGROUND: Significantly elevated telomerase activity (TA) has been found in samples from patients with almost all malignant hematologic diseases. The impact of elevated TA on the course of pediatric patients with acute myeloid leukemia (P-AML) is unknown. METHODS: Using a modified polymerase chain reaction-based, telomeric repeat-amplification protocol assay, the authors measured TA in bone marrow samples from 40 patients with P-AML and, for comparison, in 65 adult patients with AML (A-AML), excluding patients with French-American-British M3 disease. The results were correlated with patient characteristics and survival. RESULTS: TA in patients with P-AML was significantly lower compared with TA in patients with A-AML (P = 0.005). Patients who had P-AML with low TA had a projected 5-year survival rate of 88%, whereas patients who had P-AML with high TA had a projected 5-year survival rate of 43% (P = 0.009). Conversely, patients who had A-AML with very high TA (upper quartile) had significantly longer survival compared with patients who had A-AML with lower TA (P = 0.03). There was no correlation between complete remission rate or disease free survival and TA in P-AML or A-AML. In the A-AML group, when patients were separated by cytogenetic findings (poor prognosis vs. others), it was found that TA was significantly lower in patients with a poor prognosis, but the prognostic value of TA was not independent of cytogenetic status. CONCLUSIONS: The current results suggest, that for patients with P-AML, bone marrow TA is a highly significant prognostic factor.     

Prognostic implications of gene mutations in acute myeloid leukemia with normal cytogenetics

In recent years, a number of somatically acquired mutational changes have been identified in patients with acute myeloid leukemia (AML). Most of these genetic alterations occur in AML exhibiting a normal karyotype, representing the largest cytogenetic subgroup (40%-50%) of AML. These molecular findings not only provide novel insights into the pathogenesis of AML but also are of clinical importance. In this review we will discuss the most relevant gene alterations, including NPM1 gene mutations, internal tandem duplications (ITD) or tyrosine kinase domain (TKD) mutations of the FLT3 gene, CEBPA gene mutations, and partial tandem duplications (PTD) of the MLL gene, as well as mutations in the NRAS and WT1 genes. In part, these gene mutations have emerged as important prognostic markers and they now allow us to dissect cytogenetically normal (CN)-AML in distinct prognostic subgroups. Furthermore, these mutant molecules represent potential targets for molecular therapies.     

DNA甲基化靶向药物在急性髓系白血病中的应用

DNA甲基化和组蛋白甲基化是急性髓系白血病（acute myeloid leukemia,AML）表观遗传学调控的常见模式,针对甲基化过程的靶向治疗包括DNA甲基转移酶抑制剂、甲基化调节蛋白抑制剂及组蛋白甲基化调控蛋白抑制剂,其中DNA甲基转移酶（DNA methyltransferase,DNMT）抑制剂阿扎胞苷、地西他滨已上市进入临床,针对甲基化调节蛋白IDH1/2抑制剂也已进入Ⅱ期临床研究。此外,针对组蛋白甲基化调控蛋白EZH2、LSD1抑制剂也显示出良好体外抗白血病活性,部分已进入Ⅰ期临床研究,为AML的治疗提供新的选择。      

Quantitative detection of DNMT3A R882H mutation in acute myeloid leukemia

Background

DNMT3A mutations represent one of the most frequent gene alterations detectable in acute myeloid leukemia (AML) with normal karyotype. Although various recurrent somatic mutations of DNMT3A have been described, the most common mutation is located at R882 in the methyltransferase domain of the gene. Because of their prognostic significance and high stability during disease evolution, DNMT3A mutations might represent highly informative biomarkers for prognosis and outcome of disease.

Methods

We describe an allele-specific PCR with a Blocking reagent for the quantitative detection of DNMT3A R882H mutation providing the possibility to analyze the quantitative amount of mutation during the course of disease. Next, we analyzed 62 follow-up samples from 6 AML patients after therapy and allogeneic stem cell transplantation (alloSCT).

Results

We developed an ASB-PCR assay for quantitative analysis of R882H DNMT3A mutation. After optimization of blocker concentration, a R882H-positive plasmid was constructed to enhance the accuracy of the sensitivity of quantitative detection. The assay displayed a high efficiency and sensitivity up to 10⁻³. The reproducibility of assay analyzed using follow-up samples showed the standard deviation less than 3.1 %. This assay displayed a complete concordance with sequencing and endonuclease restriction analysis. We have found persistence of DNMT3A R882H mutations in complete remission (CR) after standard cytoreduction therapy that could be indicating presence of DNMT3A mutation in early pre-leukemic stem cells that resist chemotherapy. The loss of correlation between NPM1 and DNMT3A in CR could be associated with evolution of pre-leukemic and leukemic clones. In patients with CR with complete donor chimerism after alloSCT, we have found no DNMT3A R882H. In relapsed patients, all samples showed an increasing of both NPM1 and DNMT3A mutated alleles. This suggests at least in part the presence of NPM1 and DNMT3A mutations in the same cell clone.

Conclusion

We developed a rapid and reliable method for quantitative detection of DNMT3A R882H mutations in AML patients. Quantitative detection of DNMT3A R882H mutations at different time points of AML disease enables screening of follow-up samples. This could provide additional information about the role of DNMT3A mutations in development and progression of AML.     

Genetic variations of DNA repair genes and their prognostic significance in patients with acute myeloid leukemia

Common genetic variations in genes involved in DNA repair or response to genotoxic stress may influence both cancer susceptibility and treatment response individually or interactively. However, in acute myeloid leukemia (AML), the relevance of these genetic variations remains to be fully established. In this study, we analyzed 42 genetic variations among 15 candidate genes in 307 AML patients and 560 age‐sex matched controls. Their associations with chemotherapy response were further evaluated in combination with other well‐established prognostic factors. An increased risk of AML was found in individuals heterozygous for XPD 2251A>C (rs13181) with an odds ratio (OR) of 1.637 (95% confidence interval [CI]: 1.118–2.395), and the increased risk could be attributed to C allele (OR = 1.505, 95% CI: 1.061–2.134). Postchemotherapy response analysis revealed that AML patients heterozygous for ATM 4138C>T (rs3092856) or GG homozygous for TP53 215C>G (rs1042522) were independently linked to inferior treatment outcomes. These results uncover novel prognostic factors for AML patients treated with chemotherapy and may also indicate an etiological role of XPD in this disease.     

Comparative examination of various PCR-based methods for DNMT3A and IDH1/2 mutations identification in acute myeloid leukemia

Background

Mutations in epigenetic modifiers were reported in patients with acute myeloid leukaemia (AML) including mutations in DNA methyltransferase 3A gene (DNMT3A) in 20%-30% patients and mutations in isocitrate dehydrogenase 1/2 gene (IDH1/2) in 5%-15% patients. Novel studies have shown that mutations in DNMT3A and IDH1/2 influence prognosis, indicating an increasing need to detect these mutations during routine laboratory analysis. DNA sequencing for the identification of these mutations is time-consuming and cost-intensive. This study aimed to establish rapid screening tests to identify mutations in DNMT3A and IDH1/2 that could be applied in routine laboratory procedures and that could influence initial patient management.

Methods

In this study we developed an endonuclease restriction method to identify the most common DNMT3A mutation (R882H) and an amplification-refractory mutation system (ARMS) to analyse IDH2 R140Q mutations. Furthermore, we compared these methods with HRM analysis and evaluated the latter for the detection of IDH1 mutations.

Results

Of 230 samples from patients with AML 30 (13%) samples had DNMT3A mutations, 16 (7%) samples had IDH2 R140Q mutations and 36 (16%) samples had IDH1 mutations. Sensitivity assays performed using serial dilutions of mutated DNA showed that ARMS analysis had a sensitivity of 4.5%, endonuclease restriction had a sensitivity of 0.05% and HRM analysis had a sensitivity of 5.9%–7.8% for detecting different mutations. HRM analysis was the best screening method to determine the heterogeneity of IDH1 mutations. Furthermore, for the identification of mutations in IDH2 and DNMT3A, endonuclease restriction and ARMS methods showed a perfect concordance (100%) with Sanger sequencing while HRM analysis showed a near-perfect concordance (approximately 98%).

Conclusion

Our study suggested that all the developed methods were rapid, specific and easy to use and interpret. HRM analysis is the most timesaving and cost-efficient method to rapidly screen all the 3 genes at diagnosis in samples obtained from patients with AML. Endonuclease restriction and ARMS assays can be used separately or in combination with HRM analysis to obtain more reliable results. We propose that early screening of mutations in patients with AML having normal karyotype could facilitate risk stratification and improve treatment options.     

The prognostic significance of trisomy 8 in patients with acute myeloid leukemia

Recent therapeutic outcomes for patients with acute myeloid leukemia and trisomy 8 (+8) who were seen at our institution were investigated. Complete remission was achieved in 85% with isolated +8, 100% with +8 and chromosomal abnormalities predictive of a favorable outcome, and 47% of patients with +8 and other, mostly complex chromosomal abnormalities. Median relapse-free and overall survivals in months were 5.5 and 12 (isolated +8), 20 and 25 (+8 and favorable karyotype), and 7.5 and 6 (+8 and unfavorable karyotype). Despite an encouraging rate of complete remission, the relapse-free and overall survivals for patients with isolated +8 were not significantly different from those of patients with +8 and unfavorable karyotypes. The presence of +8 did not appear to adversely affect the outcome of patients with favorable karyotypes.     

Aberrant DNA methylation in pediatric patients with acute lymphocytic leukemia

BACKGROUND: Aberrant methylation of promoter-associated cystosine-guanine (CpG) islands is an epigenetic modification of DNA frequently observed in adult patients with acute lymphocytic leukemia (ALL). This epigenetic modification has been associated with gene silencing, malignant transformation, and aging. It is not known whether there are epigenetic differences between pediatric patients and adult patients with ALL. METHODS: To investigate the methylation characteristics of pediatric patients with ALL and to determine whether DNA methylation can explain prognostic or biologic differences between pediatric and adult patients, the authors analyzed the methylation status of 7 promoter-associated CpG islands in 16 pediatric patients with ALL and compared them with the methylation characteristics of a cohort of adult patients with ALL. The genes analyzed included the estrogen receptor gene (ER), multidrug resistance gene 1 (MDR1), p15, C-ABL, CD10, p16, and p73. RESULTS: The mean methylation densities of ER, MDR1, CD10, p15, and C-ABL were 25.4%, 16.4%, 5.23%, 4.24%, and 4%, respectively. P16 was methylated in 11.7% of patients, and p73 was methylated in 17.6% of patients. One patient (6.2%) had methylation of 0 genes, 15 patients (93.7%) had methylation of >/= 1 gene, and 4 patients (25%) had methylation of 3-4 genes. Methylation of all these genes was < 2% (or methylation specific polymerase chain reaction negative) in nonneoplastic tissues. A significant inverse correlation was observed between methylation of CD10 and CD10 expression. No differences were observed between the methylation characteristics of pediatric patients and adult patients. CONCLUSIONS: The results indicate that DNA methylation is common in pediatric patients with ALL and that methylation of the genes studied does not account for prognostic differences between pediatric patients and adult patients with ALL.