Expression of myeloperoxidase and gene mutations in AML patients with normal karyotype: double CEBPA mutations are associated with high percentage of MPO positivity in leukemic blasts

Bioinformatics Analysis Identifies Key Genes and Pathways in Acute Myeloid Leukemia Associated with DNMT3A Mutation

Background

DNA methyltransferase 3 alpha (DNMT3A) mutation was one of the most frequent genetic alterations in acute myeloid leukemia (AML), which was associated with poor prognosis and appeared to be a potential biomarker. Herein, we aimed to identify the key genes and pathways involved in adult AML with DNMT3A mutations and to find possible therapeutic targets for improving treatment.

Methods

The RNA sequencing datasets of 170 adult AML patients were obtained from The Cancer Genome Atlas (TCGA) database. EdgeR of the R platform was used to identify the differentially expressed genes (DEGs). Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses were performed by Metascape and DAVID. And protein-protein interaction (PPI) network and clustering modules were analyzed with the STRING database and Cytoscape software.

Results

Mutated DNMT3A resulted in a shorter overall survival (OS) in AML patients and obviously associated with age, blast percentage in peripheral blood, and FLT3 mutation. A total of 283 DEGs were detected, of which 95 were upregulated and 188 were downregulated. GO term analysis showed that DEGs were significantly enriched in neutrophil degranulation, myeloid cell differentiation, stem cell proliferation, positive regulation of neurological system process, leukocyte migration, and tissue morphogenesis. KEGG pathway enrichment analysis indicated that the pathway of cancer, PI3K-Akt signaling pathway, and transcriptional misregulation in cancer may play a crucial role in DNMT3A mutation AML. Seven hub genes (BMP4, MPO, THBS1, APP, ELANE, HOXA7, and VWF) had a significant prognostic value.

Conclusion

Bioinformatics analysis in the present study provided novel targets for early diagnosis and new strategies for treatment for AML with DNMT3A mutation.

[Correlation between myeloperoxidase expression and gene alterations and prognosis in acute myeloid leukemia]

目的

观察髓过氧化物酶（MPO）在急性髓系白血病（AML）中的表达，探讨其与AML临床特征、基因突变、疗效和预后的关系。

方法

回顾性分析233例初诊AML患者骨髓中原始细胞MPO表达的阳性率，根据MPO表达率不同将其分为MPO低表达组（MPO≤70%）与MPO高表达组（MPO>70%），并对两组患者的临床特征、基因突变、疗效和预后进行比较。

结果

①233例AML患者中MPO低表达组121例（51.9%），MPO高表达组112例（48.1%）。NCCN预后良好组患者多为MPO高表达（χ²=32.773，P<0.001），而MPO低表达与预后不良核型相关（χ²=7.078，P=0.008）。②MPO低表达组DNMT3A基因（χ²=6.905，P=0.009）、RNA剪接复合物相关基因（SF3B1/SRSF2/U2AF1）（χ²=5.246，P=0.022）、RUNX1基因（χ²=4.577，P=0.032）、ASXL1基因（χ²=7.951，P=0.005）及TP53基因(P=0.004）突变发生率明显高于MPO高表达组，而C-KIT基因（χ²=8.936，P=0.003）及CEBPA基因（χ²=12.340，P<0.001）突变更多见于MPO高表达组，尤其CEBPA双位点突变。③MPO低表达组首次诱导治疗缓解（CR₁）率为38.8%，MPO高表达组为68.1%，差异有统计学意义（χ²=15.197，P<0.001）。多因素分析显示MPO低表达是影响患者CR₁的独立危险因素。④MPO低表达组患者的2年总生存（OS）率及无进展生存（PFS）率均明显低于高表达组（18.0%对89.4%和11.5%对56.7%），差异有统计学意义（χ²分别为15.212和17.016，P值均<0.001）。Cox模型多因素分析显示MPO低表达是影响患者OS及PFS的独立预后不良指标。⑤正常核型AML中，MPO低表达组患者OS和PFS差于MPO高表达组（2年OS率：31.1%对83.7%，χ²=2.895，P=0.089；2年PFS率：18.8%对45.8%，χ²=5.068，P=0.024）。

结论

不同MPO表达的AML具有独特的基因突变谱；MPO低表达是影响AML患者CR₁、OS和PFS的独立危险因素，细胞化学染色检测MPO表达可能为评估AML疗效和预后提供一种简单而有效的手段。

Distinct gene alterations with a high percentage of myeloperoxidase-positive leukemic blasts in de novo acute myeloid leukemia

The myeloperoxidase (MPO)-positivity of blasts in bone marrow smears is an important marker for not only the diagnosis, but also the prognosis of acute myeloid leukemia (AML). To investigate the relationship between genetic alterations and MPO-positivity, we performed targeted sequencing for 51 genes and 10 chimeric gene transcripts in 164 newly diagnosed de novo AML patients; 107 and 57 patients were classified as AML with >50% MPO-positive blasts (MPO-high group) and ≤50% MPO-positive blasts, (MPO-low group), respectively. The univariate analysis revealed that RUNX1-RUNX1T1 (P < 0.001), the KIT mutation (P < 0.001), and CEBPA double mutation (P = 0.001) were more likely to be found in the MPO-high group, while the DNMT3A mutation (P = 0.001), FLT3 tyrosine kinase domain mutation (P = 0.004), and TP53 mutation (P = 0.020) were more likely to be present in the MPO-low group. Mutations in genes related to DNA hypermethylation signatures (IDH1, IDH2, TET2, and WT1 genes) were more frequent in the MPO-high group (P = 0.001) when patients with fusion genes of core-binding factors were excluded from the analysis. Our results suggest that MPO-positivity of blasts was related with the distinct gene mutation patterns among de novo AML patients.

Gene expression profiling of acute myeloid leukemia samples from adult patients with AML-M1 and -M2 through boutique microarrays, real-time PCR and droplet digital PCR

Acute myeloid leukemia (AML) is the most common and severe form of acute leukemia diagnosed in adults. Owing to its heterogeneity, AML is divided into classes associated with different treatment outcomes and specific gene expression profiles. Based on previous studies on AML, in this study, we designed and generated an AML-array containing 900 oligonucleotide probes complementary to human genes implicated in hematopoietic cell differentiation and maturation, proliferation, apoptosis and leukemic transformation. The AML-array was used to hybridize 118 samples from 33 patients with AML of the M1 and M2 subtypes of the French-American-British (FAB) classification and 15 healthy volunteers (HV). Rigorous analysis of the microarray data revealed that 83 genes were differentially expressed between the patients with AML and the HV, including genes not yet discussed in the context of AML pathogenesis. The most overexpressed genes in AML were STMN1, KITLG, CDK6, MCM5, KRAS, CEBPA, MYC, ANGPT1, SRGN, RPLP0, ENO1 and SET, whereas the most underexpressed genes were IFITM1, LTB, FCN1, BIRC3, LYZ, ADD3, S100A9, FCER1G, PTRPE, CD74 and TMSB4X. The overexpression of the CPA3 gene was specific for AML with mutated NPM1 and FLT3. Although the microarray-based method was insufficient to differentiate between any other AML subgroups, quantitative PCR approaches enabled us to identify 3 genes (ANXA3, S100A9 and WT1) whose expression can be used to discriminate between the 2 studied AML FAB subtypes. The expression levels of the ANXA3 and S100A9 genes were increased, whereas those of WT1 were decreased in the AML-M2 compared to the AML-M1 group. We also examined the association between the STMN1, CAT and ABL1 genes, and the FLT3 and NPM1 mutation status. FLT3⁺/NPM1⁻ AML was associated with the highest expression of STMN1, and ABL1 was upregulated in FLT3⁺ AML and CAT in FLT3⁻ AML, irrespectively of the NPM1 mutation status. Moreover, our results indicated that CAT and WT1 gene expression levels correlated with the response to therapy. CAT expression was highest in patients who remained longer under complete remission, whereas WT1 expression increased with treatment resistance. On the whole, this study demonstrates that the AML-array can potentially serve as a first-line screening tool, and may be helpful for the diagnosis of AML, whereas the differentiation between AML subgroups can be more successfully performed with PCR-based analysis of a few marker genes.

Prognostic nomogram for previously untreated adult patients with acute myeloid leukemia

This study was designed to perform an acceptable prognostic nomogram for acute myeloid leukemia. The clinical data from 311 patients from our institution and 165 patients generated with Cancer Genome Atlas Research Network were reviewed. A prognostic nomogram was designed according to the Cox's proportional hazard model to predict overall survival (OS). To compare the capacity of the nomogram with that of the current prognostic system, the concordance index (C-index) was used to validate the accuracy as well as the calibration curve. The nomogram included 6 valuable variables: age, risk stratifications based on cytogenetic abnormalities, status of FLT3-ITD mutation, status of NPM1 mutation, expression of CD34, and expression of HLA-DR. The C-indexes were 0.71 and 0.68 in the primary and validation cohort respectively, which were superior to the predictive capacity of the current prognostic systems in both cohorts. The nomogram allowed both patients with acute myeloid leukemia and physicians to make prediction of OS individually prior to treatment.

[Expression of cMPO in 502 cases of acute myeloid leukemia (AML) and its diagnosis significance in AML subtypes]

目的

探讨髓过氧化物酶（cMPO）在急性髓系白血病（AML）患者中的表达及其在诊断分型中的意义。

方法

采用CD45/SSC双参数散点图设门方法对502例AML患者进行八色流式细胞术免疫表型分析，观察患者白血病细胞cMPO表达的阳性率和阳性强度。

结果

502例AML患者cMPO总体阳性率为58.0%，其中阳性占21.5%，弱阳性占34.1%，部分阳性占2.4%；阴性占42.0%。各亚型中，AML伴t(15;17）（q22;q12）/PML-RARα的cMPO阳性率最高，为100%，阳性强度多数接近正常粒细胞水平；其次为AML伴t(8;21）（q22;q22）/RUNX1-RUNX1T1，阳性率为91.4%，阳性强度多为弱阳性；AML微分化型和急性巨核细胞白血病患者cMPO表达皆为阴性；余各亚型阳性率在22.7%~76.2%。

结论

各亚型AML cMPO的阳性率及阳性强度存在显著差异。

Expression of myeloperoxidase in acute myeloid leukemia blasts mirrors the distinct DNA methylation pattern involving the downregulation of DNA methyltransferase DNMT3B

Myeloperoxidase (MPO) has been associated with both a myeloid lineage commitment and favorable prognosis in patients with acute myeloid leukemia (AML). DNA methyltransferase inhibitors (decitabine and zeburaline) induced MPO gene promoter demethylation and MPO gene transcription in AML cells with low MPO activity. Therefore, MPO gene transcription was directly and indirectly regulated by DNA methylation. A DNA methylation microarray subsequently revealed a distinct methylation pattern in 33 genes, including DNA methyltransferase 3 beta (DNMT3B), in CD34-positive cells obtained from AML patients with a high percentage of MPO-positive blasts. Based on the inverse relationship between the methylation status of DNMT3B and MPO, we found an inverse relationship between DNMT3B and MPO transcription levels in CD34-positive AML cells (P=0.0283). In addition, a distinct methylation pattern was observed in five genes related to myeloid differentiation or therapeutic sensitivity in CD34-positive cells from AML patients with a high percentage of MPO-positive blasts. Taken together, the results of the present study indicate that MPO may serve as an informative marker for identifying a distinct and crucial DNA methylation profile in CD34-positive AML cells.