Minimal residual disease monitoring in childhood B lymphoblastic leukemia with t(12;21)(p13;q22); ETV6-RUNX1: concordant results using quantitation of fusion transcript and flow cytometry

Cytogenetic abnormalities and TP53 and RAS gene profiles of childhood acute lymphoblastic leukemia in Morocco

BACKGROUND

Recurrent genetic abnormalities affecting pivotal signaling pathways are the hallmark of childhood acute lymphoblastic leukemia (ALL). The identification of these aberrations remains clinically important. Therefore, we sought to determine the cytogenetic profile and the mutational status of TP53 and RAS genes among Moroccan childhood cases of ALL.

METHODS

In total, 35 patients with childhood ALL were enrolled in the study. The diagnosis and treatment were established in the Pediatric Hematology and Oncology Center at the Children's Hospital of Rabat. Chromosome banding analysis and fluorescence in situ hybridization were used to detect genetic aberrations. Blood samples were screened for TP53 and RAS mutations using Sanger sequencing.

RESULTS

Of the 35 cases, 30 were B-lineage ALL (85.7 %). Moreover, a male predominance was observed. Cytogenetic analysis revealed chromosomal anomalies in 27 cases (77.1 %). The most frequent aberrations were high hyperdiploidy and BCR/ABL rearrangement. Interestingly, we found the rare t(15;16) and the t(8;14), which are uncommon translocations in pediatric B-ALL. The mutational analysis revealed Pro72Arg (rs1042522:C > G) and Arg213Arg (rs1800372:A > G) in TP53. In correlation with cytogenetic data, rs1042522:C > G showed a significant association with the occurrence of chromosomal translocations (p = 0.04). However, no variant was detected in NRAS and KRAS genes.

CONCLUSION

Our findings emphasize the significance of detecting chromosomal abnormalities as relevant prognostic markers. We also suggest a low occurrence of genetic variants among Moroccan children with ALL.

Fusion transcript analysis reveals slower response kinetics than multiparameter flow cytometry in childhood acute myeloid leukaemia

INTRODUCTION

Analysis of measurable residual disease (MRD) is increasingly being implemented in the clinical care of children and adults with acute myeloid leukaemia (AML). However, MRD methodologies differ and discordances in results lead to difficulties in interpretation and clinical decision-making. The aim of this study was to compare results from reverse transcription quantitative polymerase chain reaction (RT-qPCR) and multiparameter flow cytometry (MFC) in childhood AML and describe the kinetics of residual leukaemic burden during induction treatment.

METHODS

In 15 children who were treated in the NOPHO-AML 2004 trial and had fusion transcripts quantified by RT-qPCR, we compared MFC with RT-qPCR for analysis of MRD during (day 15) and after induction therapy. Eight children had RUNX1::RUNX1T1, one CBFB::MYH11 and six KMT2A::MLLT3.

RESULTS

When ≥0.1% was used as cut-off for positivity, 10 of 22 samples were discordant. The majority (9/10) were MRD positive with RT-qPCR but MRD negative with MFC, and several such cases showed the presence of mature myeloid cells. Fusion transcript expression was verified in mature cells as well as in CD34 expressing cells sorted from diagnostic samples.

CONCLUSIONS

Measurement with RT-qPCR suggests slower response kinetics than indicated from MFC, presumably due to the presence of mature cells expressing fusion transcript. The prognostic impact of early measurements with RT-qPCR remains to be determined.

Comparison of minimal residual disease measurement by multicolour flow cytometry and PCR for fusion gene transcripts in infants with acute lymphoblastic leukaemia with KMT2A gene rearrangements

This study aimed to evaluate the concordance between minimal residual disease (MRD) results obtained by multicolour flow cytometry (MFC) and polymerase chain reaction for fusion gene transcripts (FGTs) in infants with acute lymphoblastic leukaemia (ALL) associated with rearrangement of the KMT2A gene (KMT2A-r). A total of 942 bone marrow (BM) samples from 123 infants were studied for MFC-MRD and FGT-MRD. In total, 383 samples (40.7%) were concordantly MRD-negative. MRD was detected by the two methods in 441 cases (46.8%); 99 samples (10.5%) were only FGT-MRD-positive and 19 (2.0%) were only MFC-MRD-positive. A final concordance rate of 87.4% was established. Most discordance occurred if residual leukaemia was present at levels close to the sensitivity limits. Neither the type of KMT2A fusion nor a new type of treatment hampering MFC methodology had an influence on the concordance rate. The prognostic value of MFC-MRD and FGT-MRD differed. MFC-MRD was able to identify a rapid response at early time-points, whereas FGT-MRD was a reliable relapse predictor at later treatment stages. Additionally, the most precise risk definition was obtained when combining the two methods. Because of the high comparability in results, these two rather simple and inexpensive approaches could be good options of high clinical value.

[Comparison of prognostic significance between multiparameter flow cytometry and real-time quantitative polymerase chain reaction in the detection of minimal residual disease of Philadelphia chromosome-positive acute B lymphocytic leukemia before allogeneic hematopoietic stem cell transplantation]

目的

探讨多参数流式细胞术（MFC）与实时定量聚合酶链反应技术（RQ-PCR）两种方法检测费城染色体阳性（Ph⁺）急性B淋巴细胞白血病（B-ALL）患者异基因造血干细胞移植（allo-HSCT）前微小残留病（MRD）的预后意义。

方法

回顾性分析2014年7月至2018年2月在北京大学血液病研究所接受allo-HSCT的280例Ph⁺ B-ALL患者，同时用MFC和RQ-PCR法（检测BCR-ABL融合基因表达）检测移植前MRD。

结果

RQ-PCR与MFC检测MRD具有相关性（rs＝0.435，P<0.001）。MFC、RQ-PCR法检测移植前MRD的阳性率分别为25.7％（72/280）、60.7％（170/280）。移植前MFC-MRD阳性组患者移植后白血病3年累积复发率（CIR）明显高于MFC-MRD阴性组（23.6％对8.6％，P<0.001）。RQ-PCR检测BCR/ABL融合基因阳性组（RQ-PCR MRD阳性组）的3年CIR、非复发死亡（NRM）、无白血病生存（LFS）、总生存（OS）与BCR/ABL融合基因阴性组（RQ-PCR MRD阴性组）相比差异均无统计学意义（P>0.05）。移植前RQ-PCR MRD≥1％组比<1％组具有更高的3年CIR（23.1％对11.4％，P＝0.032）、更低的LFS率（53.8％对74.4％，P＝0.015）与OS率（57.7％对79.1％，P＝0.009）。多因素分析显示，移植前MFC-MRD阳性是影响移植后CIR的危险因素（HR＝2.488，95％CI1.216～5.088，P＝0.013），移植前RQ-PCR MRD≥1％是影响LFS（HR＝2.272，95％CI 1.225～4.215，P<0.001）、OS（HR＝2.472，95％ CI 1.289～4.739，P＝0.006）的危险因素。MFC检测MRD预测复发的敏感性、特异性、阳性预测值（PPV）、阴性预测值（NPV）分别为48.50％、77.56％、23.62％、87.16％。以RQ-PCR MRD≥1％预测复发的敏感性、特异性、PPV、NPV分别为23.00％、88.59％、17.15％、91.84％。移植前MFC-MRD阳性或RQ-PCR MRD≥1％二者任一成立为指标预测移植后复发的敏感性、特异性、PPV、NPV分别为54.29％、73.88％、45.70％、91.87％。

结论

MFC和RQ-PCR法检测移植前MRD水平均可预测Ph⁺ B-ALL患者移植预后。移植前MFC-MRD阳性是移植后复发的危险因素。联合使用两种方法（移植前MFC-MRD阳性状态或RQ-PCR MRD≥1％成立）可提高预测移植后复发的敏感性、阳性预测值与阴性预测值，有助于更好筛选出高危患者。

How I investigate minimal residual disease in acute lymphoblastic leukemia

Minimal Residual Disease (MRD) is the most important independent prognostic factor in acute lymphoblastic leukemia (ALL) and refers to the deep level of measurable disease in cases with complete remission by conventional pathologic analysis, especially by cytomorphology. MRD can be detected by multiparametric flow cytometry, molecular approaches such as quantitative polymerase chain reaction for immunoglobulin and T-cell receptor (IG/TR) gene rearrangements or fusion genes transcript, and high-throughput sequencing for IG/TR. Despite the proven clinical usefulness in detecting MRD, these methods have differences in sensitivity, specificity, applicability, turnaround time and cost. Knowing and understanding these differences, as well as the principles and limitations of each technology, is essential to laboratory standardization and correct interpretation of MRD results in line with treatment time points, therapeutic settings, and clinical trials. Here, we review the methodological approaches to measure MRD in ALL and discuss the advantages and limitations of the most commonly used techniques.

Prognostic Value and Outcome for ETV6/RUNX1-Positive Pediatric Acute Lymphoblastic Leukemia: A Report From the South China Children's Leukemia Group

PURPOSE

To analyzed the outcome of ETV6/RUNX1-positive pediatric acute B lymphoblastic leukemia (B-ALL) with the aim of identifying prognostic value.

METHOD

A total of 2,530 pediatric patients who were diagnosed with B-ALL were classified into two groups based on the ETV6/RUNX1 status by using a retrospective cohort study method from February 28, 2008, to June 30, 2020, at 22 participating ALL centers.

RESULTS

In total, 461 (18.2%) cases were ETV6/RUNX1-positive. The proportion of patients with risk factors (age <1 year or ≥10 years, WB≥50×10⁹/L) in ETV6/RUNX1-positive group was significantly lower than that in negative group (P<0.001), while the proportion of patients with good early response (good response to prednisone, D15 MRD < 0.1%, and D33 MRD < 0.01%) in ETV6/RUNX1-positive group was higher than that in the negative group (P<0.001, 0.788 and 0.004, respectively). Multivariate analysis of 2,530 patients found that age <1 or ≥10 years, SCCLG-ALL-2016 protocol, and MLL were independent predictor of outcome but not ETV6/RUNX1. The EFS and OS of the ETV6/RUNX1-positive group were significantly higher than those of the negative group (3-year EFS: 90.11 ± 4.21% vs 82 ± 2.36%, P<0.0001, 3-year OS: 91.99 ± 3.92% vs 88.79 ± 1.87%, P=0.017). Subgroup analysis showed that chemotherapy protocol, age, prednisone response, and D15 MRD were important factors affecting the prognosis of ETV6/RUNX1-positive children.

CONCLUSIONS

ETV6/RUNX1-positive pediatric ALL showed an excellent outcome but lack of independent prognostic significance in South China. However, for older patients who have the ETV6/RUNX1 fusion and slow response to therapy, to opt for more intensive treatment.

Exploring a potential mechanistic role of DNA methylation in the relationship between in utero and post-natal environmental exposures and risk of childhood acute lymphoblastic leukaemia

The aetiology of childhood acute lymphoblastic leukaemia (ALL) is unclear. Genetic abnormalities have been identified in a number of ALL cases, although these alone are not sufficient for leukaemic transformation. Various in utero and post-natal environmental exposures have been suggested to alter risk of childhood ALL. DNA methylation patterns can be influenced by environmental exposures, and are reported to be altered in ALL, suggesting a potential mediating mechanism between environment and ALL disease risk. To investigate this, we used a 'meet in the middle' approach, investigating the overlap between exposure-associated and disease-associated methylation change. Genome-wide DNA methylation changes in response to possible ALL-risk exposures (i.e. breast feeding, infection history, day care attendance, maternal smoking, alcohol, caffeine, folic acid, iron and radiation exposure) were investigated in a sub-population of the Avon Longitudinal Study of Parents and Children (ALSPAC) cohort using an epigenome-wide association study (EWAS) approach (n = 861-927), and compared to a list of ALL disease-associated methylation changes compiled from published data. Hypergeometric probability tests suggested that the number of directionally concordant gene methylation changes observed in ALL disease and in response to the following exposures; maternal radiation exposure (p = 0.001), alcohol intake (p = 0.006); sugary caffeinated drink intake during pregnancy (p = 0.045); and infant day care attendance (p = 0.003), were not due to chance. Data presented suggests that DNA methylation may be one mediating mechanism in the multiple hit pathway needed for ALL disease manifestation.

High sensitivity and clonal stability of the genomic fusion as single marker for response monitoring in ETV6-RUNX1-positive acute lymphoblastic leukemia

BACKGROUND

Assessment of minimal residual disease (MRD) is an integral component for response monitoring and treatment stratification in acute lymphoblastic leukemia (ALL). We aimed to evaluate the genomic ETV6-RUNX1 fusion sites as a single marker for MRD quantification.

PROCEDURE

In a representative, uniformly treated cohort of pediatric relapsed ALL patients (n = 52), ETV6-RUNX1 fusion sites were compared to the current gold standard, immunoglobulin/T-cell receptor (Ig/TCR) gene rearrangements.

RESULTS

Primer/probe sets designed to ETV6-RUNX1 fusions achieved significantly more frequent a sensitivity and a quantitative range of at least 10^-4 compared to the gold standard with 100% and 73% versus 76% and 47%, respectively. The breakpoint sequence was identical at diagnosis and relapse in all tested cases. There was a high degree of concordance between quantitative MRD results assessed using ETV6-RUNX1 and the highest Ig/TCR marker (Spearman's 0.899, P < .01) with differences >½ log-step in only 6% of patients. A high proportion of ETV6-RUNX1-positive ALL relapses (40%) in our cohort showed a poor response to induction treatment at relapse, and therefore had an indication for hematopoietic stem cell transplantation, demonstrating the need of accurate identification of this subgroup.

CONCLUSIONS

ETV6-RUNX1 fusion sites are highly sensitive and reliable MRD markers. Our data confirm that they are unaffected by clonal evolution and selection during front-line and second-line chemotherapy in contrast to Ig/TCR rearrangements, which require several markers per patient to compensate for the observed loss of target clones. In future studies, the genomic ETV6-RUNX1 fusion can be used as single MRD marker.

Quantitative monitoring of minimal residual disease in childhood acute lymphoblastic leukemia using TEL-AML1 fusion transcript as a marker

IMPORTANCE

By demonstrating with TEL-AML1, this study indicated that mRNAs transcribed from fusion genes are ideal targets for minimal residual disease (MRD) monitoring in childhood acute lymphoblastic leukemia, and that different thresholds are needed to apply them into the risk stratification.

OBJECTIVE

TEL-AML1 expression was measured at three time points to 1) determine cut-off values for predicting acute lymphoblastic leukemia (ALL) relapse; 2) investigate the prognostic value of this method and how well the results at these time points correlated; 3) determine the correlation between MRD levels assessed using this marker and that determined by immunoglobulin/T-cell receptor (Ig/TCR) rearrangement detection.

METHODS

TEL- AML1 expression in 62 children with ALL was quantitated by real-time quantitative PCR at day 15, day 33, and month 3. The relationship between patient outcome and TEL-AML1 level was analyzed at each time point. The correlation between the MRD levels determined by TEL-AML1 or Ig/TCR rearrangements was also analyzed.

RESULTS

For day 33, 6.68 TEL-AML1 copies/104 ABL copies was determined to be the best cut-off value. Higher levels were correlated with relapse (P = 0.001). For day 15 and month 3, the best cut-off values were 336.5 and 0.85 copies/104 ABL copies respectively; patients with higher expression levels had lower RFSs (day 15: P = 0.027; month 3: P = 0.023). For days 15 and 33, MRD levels assessed using TEL-AML1 or Ig/TCR rearrangements were strongly correlated [Spearman rank correlation coefficient (ρ) = 0.729 (day 15), 0.719 (day 33); P < 0.001 (both)], and both methods were equally effective at predicting relapse. At month 3, there was moderate correlation between the results derived from the two markers (ρ = 0.418, P = 0.003); however, receiver operating characteristic curve analysis showed that TEL-AML1 was a better prognostic marker.

INTERPRETATION

TEL-AML1 is an effective marker for MRD assessment and relapse prediction in children with ALL.

A QA Program for MRD Testing Demonstrates That Systematic Education Can Reduce Discordance Among Experienced Interpreters

BACKGROUND

Minimal residual disease (MRD) in B lymphoblastic leukemia (B-ALL) by flow cytometry is an established prognostic factor used to adjust treatment in most pediatric therapeutic protocols. MRD in B-ALL has been standardized by the Children's Oncology Group (COG) in North America, but not routine clinical labs. The Foundation for National Institutes of Health sought to harmonize MRD measurement among COG, oncology groups, academic, community and government, laboratories.

METHODS

Listmode data from post-induction marrows were distributed from a reference lab to seven different clinical FCM labs with variable experience in B-ALL MRD. Labs were provided with the COG protocol. Files from 15 cases were distributed to the seven labs. Educational sessions were implemented, and 10 more listmode file cases analyzed.

RESULTS

Among 105 initial challenges, the overall discordance rate was 26%. In the final round, performance improved considerably; out of 70 challenges, there were five false positives and one false negative (9% discordance), and no quantitative discordance. Four of six deviations occurred in a single lab. Three samples with hematogones were still misclassified as MRD.

CONCLUSIONS

Despite the provision of the COG standardized analysis protocol, even experienced laboratories require an educational component for B-ALL MRD analysis by FCM. Recognition of hematogones remains challenging for some labs when using the COG protocol. The results from this study suggest that dissemination of MRD testing to other North American laboratories as part of routine clinical management of B-ALL is possible but requires additional educational components to complement standardized methodology. © 2017 International Clinical Cytometry Society.