Gene expression overlap affects karyotype prediction in pediatric acute lymphoblastic leukemia

Simultaneous use of multiplex ligation-dependent probe amplification assay and flow cytometric DNA ploidy analysis in patients with acute leukemia

BACKGROUND

The aim of this work was to simultaneously use multiplex ligation-dependent probe amplification (MLPA) assay and flow cytometric DNA ploidy analysis (FPA) to detect aneuploidy in patients with newly diagnosed acute leukemia.

METHODS

MLPA assay and propidium iodide FPA were used to test samples from 53 consecutive patients with newly diagnosed acute leukemia referred to our laboratory for immunophenotyping. Results were compared by nonparametric statistics.

RESULTS

The combined use of both methods significantly increased the rate of detection of aneuploidy as compared to that obtained by each method alone. The limitations of one method are somehow countervailed by the other and vice versa.

CONCLUSIONS

MPLA and FPA yield different yet complementary information concerning aneuploidy in acute leukemia. The simultaneous use of both methods might be recommended in the clinical setting. © 2017 International Clinical Cytometry Society.

Pediatric Acute Lymphoblastic Leukemia: Is There Still a Role for Transplant?

Constant questioning of the applicability of transplant for any diagnosis is appropriate. This is particularly necessary in fields such as pediatric leukemia, in which significant progress in therapy and risk classification is being made. Outcomes with chemotherapy are constantly improving, and donor availability and transplant outcomes are also better. It is important to be aware of likely outcomes when counseling families and recommending therapy, and to consider issues of likely late side effects. Biological studies that predict prognosis, for example, array-based studies, hold hope of identifying the children destined to relapse at the outset of disease. However, a rigorous approach must be taken in determining whether transplant does improve outcome whenever this strategy is applied.

Gene expression classifiers for relapse-free survival and minimal residual disease improve risk classification and outcome prediction in pediatric B-precursor acute lymphoblastic leukemia

To determine whether gene expression profiling could improve outcome prediction in children with acute lymphoblastic leukemia (ALL) at high risk for relapse, we profiled pretreatment leukemic cells in 207 uniformly treated children with high-risk B-precursor ALL. A 38-gene expression classifier predictive of relapse-free survival (RFS) could distinguish 2 groups with differing relapse risks: low (4-year RFS, 81%, n = 109) versus high (4-year RFS, 50%, n = 98; P < .001). In multivariate analysis, the gene expression classifier (P = .001) and flow cytometric measures of minimal residual disease (MRD; P = .001) each provided independent prognostic information. Together, they could be used to classify children with high-risk ALL into low- (87% RFS), intermediate- (62% RFS), or high- (29% RFS) risk groups (P < .001). A 21-gene expression classifier predictive of end-induction MRD effectively substituted for flow MRD, yielding a combined classifier that could distinguish these 3 risk groups at diagnosis (P < .001). These classifiers were further validated on an independent high-risk ALL cohort (P = .006) and retainedindependent prognostic significance (P < .001) in the presence of other recently described poor prognostic factors (IKAROS/IKZF1 deletions, JAK mutations, and kinase expression signatures). Thus, gene expression classifiers improve ALL risk classification and allow prospective identification of children who respond or fail current treatment regimens. These trials were registered at http://clinicaltrials.gov under NCT00005603.

ETV6/RUNX1 fusion lacking prognostic effect in pediatric patients with acute lymphoblastic leukemia

A Brazilian sample of 58 patients with acute lymphoblastic leukemia has been prospectively followed up with the objective of evaluating evolution of disease. Age ranged from 6 months to 16 years. Of the 58 patients, 11 were positive and 47 were negative for the ETV6/RUNX1 fusion (previously known as TEL/AML1). After a minimum follow-up period of 57 months, 2 of the ETV6/RUNX1(+) patients had died and 11 of the ETV6/RUNX1(-), for an overall survival of 77.6%. Among the 11 ETV6/RUNX1(+) patients (age range, 2 years to 13 years 7 months), all achieved a complete remission; the average overall survival was 64.2 months and the average event-free survival was 61.7 months. Among the 47 ETV6/RUNX1(-) patients, 4 did not have a complete remission; the average overall survival was of 60.8 months and the average event-free survival was 57.2 months. No significant difference was observed between overall survival and event-free survival, nor in any of the other data comparatively analyzed. The patients had a cure rate similar to that described in literature. In this small sample population, the presence of the ETV6/RUNX1 fusion did not identify statistical difference in prognosis.

Gene expression signatures predictive of early response and outcome in high-risk childhood acute lymphoblastic leukemia: A Children's Oncology Group Study [corrected]

PURPOSE

To identify children with acute lymphoblastic leukemia (ALL) at initial diagnosis who are at risk for inferior response to therapy by using molecular signatures.

PATIENTS AND METHODS

Gene expression profiles were generated from bone marrow blasts at initial diagnosis from a cohort of 99 children with National Cancer Institute-defined high-risk ALL who were treated uniformly on the Children's Oncology Group (COG) 1961 study. For prediction of early response, genes that correlated to marrow status on day 7 were identified on a training set and were validated on a test set. An additional signature was correlated with long-term outcome, and the predictive models were validated on three large, independent patient cohorts. Results We identified a 24-probe set signature that was highly predictive of day 7 marrow status on the test set (P = .0061). Pathways were identified that may play a role in early blast regression. We have also identified a 47-probe set signature (which represents 41 unique genes) that was predictive of long-term outcome in our data set as well as three large independent data sets of patients with childhood ALL who were treated on different protocols. However, we did not find sufficient evidence for the added significance of these genes and the derived predictive models when other known prognostic features, such as age, WBC, and karyotype, were included in a multivariate analysis.

CONCLUSION

Genes and pathways that play a role in early blast regression may identify patients who may be at risk for inferior responses to treatment. A fully validated predictive gene expression signature was defined for high-risk ALL that provided insight into the biologic mechanisms of treatment failure.