Can miRNAs predict EFS in pediatric AML?

Children with Refractory or Relapsed (R/R) Acute Myeloid Leukemia (AML) mainly have less positive outcomes. In an article, published  in the Journal of Clinical Oncology on 25^th of October 2017, Emilia L. Lim from the Canada's Michael Smith Genome Sciences Centre, Vancouver, Canada, et al. reported results from their study, which aimed to profile pediatric AML microRNA (miRNA) in order to identify dysregulated genes and assess the prognostic value of miRNAs in pediatric AML patients.

In this study, samples were obtained in two cohorts; Discovery (DC) and Validation (VC) cohort. In the discovery cohort, primary samples obtained at diagnosis, refractory (Induction Failure [IF])and relapse from 637 patients who were enrolled in three different pediatric AML studies including the AAML0531 (n = 528), AAML03P1 (n = 71), and  CCG-2961 (n = 38) study were analyzed used in this study. For the validation cohort, samples from 666 patients who were treated in the AAML1031 trial were obtained.

Using a comprehensive sequence-based characterization of the pediatric AML miRNA landscape, miRNA sequencing was performed on 1,362 samples (1,303 primary, 22 refractory, and 37 relapse) obtained mostly from diagnostic samples from patients in the DC. Using unsupervised non-negative matrix factorization, four subgroups were identified in the DC which had distinct miRNA expression patterns, enriched cytogenetic alterations and correlated with outcome.

In order to identify specific miRNAs whose expression correlated with response, low and high expression for each expressed miRNA in the four subgroups were analyzed further and it was found that in the DC and VC, miRNAs were found to be associated with Event Free Survival (EFS) and Overall Survival (OS).

After observing that miRNAs correlated with outcomes, Lim et al. then developed a miRNA expression-based predictor of EFS model (AMLmiR36) by combining 36 miRNAs which were expressed at diagnosis and correlated with EFS. Patients in the DC were randomly divided into two further cohorts, including a discovery training cohort (n = 425) and a discovery test cohort (n = 212). A miRNA-based risk stratification was used to separate patients in the discovery training cohort into low (n = 106), intermediate (n = 211) or high (n = 108) AMLmiR36 scores.

Key Findings:

•  5-year EFS in the discovery training cohort AMLmiR36 groups
  • High; 9.26%, HR = 3.659; 95% CI, 2.77–4.83; P < 0.001
  • Low; 84.4%, HR = 0.265; 95% CI, 0.16–0.43; P < 0.001
• Using the discovery test cohort and VC, it was validated that patients with high AMLmiR36 scores had an inferior EFS compared to patients with low AMLmiR36 scores
• Patients in the high AMLmiR36 score group were characterized by high-risk cytogenetics risk group (FLT3-ITD +); P < 0.05

Lim et al. also investigated whether there were any specific miRNAs associated with IF or relapse. It was observed that two miRNAs including miR-106a-3p and miR-106a-5p which are members of the miR-106a-363 cluster were abundantly expressed in patients with IF and relapse and were significantly associated with inferior EFS.

Furthermore, miR-106a-5p target genes were found to be involved in oxidative phosphorylation (a process that is reduced in therapy resistant leukemic cells). This indicates that miR-106a-363 could contribute to therapy resistance by repressing oxidative phosphorylation and the authors suggested that this miRNA would be significant for future research on therapy resistance in pediatric AML.

In conclusion, AMLmiR36 is the first novel mutation and translocation independent miRNA-based risk stratification scheme that could identify at the time of diagnosis patients with adverse outcomes.

Abstract

Purpose

Children with acute myeloid leukemia (AML) whose disease is refractory to standard induction chemotherapy therapy or who experience relapse after initial response have dismal outcomes. We sought to comprehensively profile pediatric AML microRNA (miRNA) samples to identify dysregulated genes and assess the utility of miRNAs for improved outcome prediction.

Patients and Methods

To identify miRNA biomarkers that are associated with treatment failure, we performed a comprehensive sequence-based characterization of the pediatric AML miRNA landscape. miRNA sequencing was performed on 1,362 samples—1,303 primary, 22 refractory, and 37 relapse samples. One hundred sixty-four matched samples—127 primary and 37 relapse samples—were analyzed by using RNA sequencing.

Results

By using penalized lasso Cox proportional hazards regression, we identified 36 miRNAs the expression levels at diagnosis of which were highly associated with event-free survival. Combined expression of the 36 miRNAs was used to create a novel miRNA-based risk classification scheme (AMLmiR36). This new miRNA-based risk classifier identifies those patients who are at high risk (hazard ratio, 2.830; P ≤ .001) or low risk (hazard ratio, 0.323; P ≤ .001) of experiencing treatment failure, independent of conventional karyotype or mutation status. The performance of AMLmiR36 was independently assessed by using 878 patients from two different clinical trials (AAML0531 and AAML1031). Our analysis also revealed that miR-106a-363 was abundantly expressed in relapse and refractory samples, and several candidate targets of miR-106a-5p were involved in oxidative phosphorylation, a process that is suppressed in treatment-resistant leukemic cells.

Conclusion

To assess the utility of miRNAs for outcome prediction in patients with pediatric AML, we designed and validated a miRNA-based risk classification scheme. We also hypothesized that the abundant expression of miR-106a could increase treatment resistance via modulation of genes that are involved in oxidative phosphorylation.