MicroRNAs expression signatures are associated with lineage and survival in acute leukemias

Abstract

MicroRNAs (miRNAs) are small ( approximately 22 nucleotide) non-coding RNAs whose altered expression has been associated with various types of cancers, including leukemia. In the present study, we conducted a quantitative PCR (qPCR) analysis of expression of 23 human precursor miRNAs in bone marrow specimens of 85 Chinese primary leukemia patients, including 53 acute myeloid leukemia (AML) and 32 acute lymphoblastic leukemia (ALL) cases. We show that 16 miRNAs were differentially expressed between AMLs and ALLs. Of them, eight were previously reported (i.e., miR-23a, miR-27a/b, miR-128a, miR-128b, miR-221, miR-222, miR-223, and let-7b) and eight were newly identified (i.e., miR-17, miR-20a, miR-29a/c, miR-29b, miR-146a, miR-150, miR-155, and miR-196b). More importantly, through correlating miRNA expression signatures with outcome of patients, we further show that expression signatures of a group of miRNAs are associated with overall survival of patients. Of them, three (i.e., miR-146a, miR-181a/c, and miR-221), five (i.e., miR-25, miR-26a, miR-29b, miR-146a, and miR-196b), and three (i.e., miR-26a, miR-29b, and miR-146a) miRNAs are significantly associated with overall survival (P<0.05) of the 32 ALL, 53 AML, and 40 non-M3 AML patients, respectively. Particularly, the expression signature of miR-146a is significantly inversely correlated with overall survival of both ALL and AML patients. The prognostic significance of miR-146a in AML has been confirmed further in an independent study of 61 Chinese new AML patient samples. We also identified 622 putative target genes of miR-146a that are predicted by at least three out of the five major prediction programs (i.e., TragetScan, PicTar, miRanda, miRBase Targets, and PITA). Through gene ontology analysis, we found that these genes were particularly enriched (2- to 9-fold higher than expected by chance) in the GO categories of "negative regulation of biology processes," "negative regulation of cellular processes," "apoptosis," and "cell cycle," which may be related to the association of miR-146a with poor survival.

Figure 1. Expression profiles of 16 miRNAs that were differentially expressed between ALLs and AMLs as determined by qPCR in 32 ALL and 53 AML samples

Data are presented as ΔCt, which refers here as the difference in threshold cycles for a miRNA and U6 RNA. Expression data was mean centered and the relative value for each sample is represented by a color, with red representing a high expression and green representing a low expression (scale shown in the upper right). AML-MCL, mast cell leukemia.

Figure 2. Overall survival curves for the 32 acute lymphoblastic leukemia (ALL) patients

For the purpose of display, the outcome summary value that reflects the expression levels of three miRNAs (i.e., miR-146a, miR-181a/c, and miR-221) in the 32 ALL patient samples was dichotomized on the basis of the median value to separate patients into two groups, and Kaplan–Meier curves were generated to depict outcomes. The P value was determined by log-rank test. Censored cases are those that were still alive when they were lost to follow-up or when the study ended.

Figure 3. Overall survival curves for acute myeloid leukemia (AML) patients

(a) The outcome summary value that reflects the expression levels of five miRNAs (i.e., miR-25a, miR-26a, miR-29b, miR-146a, and miR-196b) in the 53 AML patient samples was dichotomized on the basis of the median value to separate patients into two groups; (b) The outcome summary value that reflects the expression levels of three miRNAs (i.e., miR-26a, miR-29b, and miR-146a) in the 40 non-M3 AML patient samples was dichotomized on the basis of the median value to separate patients into two groups, and Kaplan–Meier curves were generated to depict outcomes. The P value was determined by log-rank test.

Figure 4. Expression signature of miR-146a probably is a potential prognostic marker

(a) The 32 ALL cases, (b) the 53 AML, and (c) the 61 additional AML patient cases were separated into two groups according on the basis of the median value of miR-146a expression, respectively. Kaplan–Meier curves were generated to depict outcomes. The P value was determined by log-rank test.

Figure 4. Expression signature of miR-146a probably is a potential prognostic marker

(a) The 32 ALL cases, (b) the 53 AML, and (c) the 61 additional AML patient cases were separated into two groups according on the basis of the median value of miR-146a expression, respectively. Kaplan–Meier curves were generated to depict outcomes. The P value was determined by log-rank test.

Figure 5. Example of 12 GO BP terms that have a significantly higher degree of enrichment of genes in the set of 622 miR-146a putative target genes than in the set of 27,901 whole putative target genes

See more details in Supplementary Table 1a.