Microrna-34a As a Marker for Fludarabine Resistance and Impairment of p53-Pathway in Chronic Lymphocytic Leukemia

MicroRNAs (miRNAs) are known to be involved in the pathogenesis of chronic lymphocytic leukemia (CLL) and affect its clinical course (Calin et al. NEJM, 2005; Mraz et al. Blood, 2012). Moreover, we and others have shown that several miRNAs are down-regulated in the aggressive CLL subtype harboring p53 aberration (Mraz et al. Leukemia, 2009). The role of miRNAs in primary or acquired resistance to therapy in CLL, however, is poorly understood.

In this study, we screened for miRNAs that are induced by fludarabine-mediated apoptosis in vitro, and we suggested that differences in the expression of one of the identified miRNAs (miR-34a) can be used to distinguish patients with impairment of the p53-apoptotic pathway.

Ten primary CLL B-cell samples (purity>95% of CD5+19+ cells) were treated in vitro with fludarabine dose (IC50 dose of 3.5 ug/mL, 48hrs), and the expression of 750 miRNAs was subsequently profiled (TaqMan miRNA Cards, ABI). In comparison with untreated control samples, 15 miRNAs were induced by fludarabine (fold change>1.5, SAM FDR<0.05). The most prominently up-regulated miRNA was miR-34a (fold change 3.7, P=0.003), which is a known p53 down-stream target (He et al. Nature, 2007). We then compared miR-34a up-regulation post fludarabine treatment to the decrease in cell viability (wt-p53 samples, N=20). This revealed that miR-34a induction was significantly higher in CLL samples more sensitive to fludarabine and suggested its role in the apoptotic effects of fludarabine in B-cells. Moreover, the up-regulation of miR-34a was also observed in vivo in samples obtained from fifty FCR-treated CLL patients (fold change 2.2, P<0.0001, analyzed at day 0 and 3 of FCR). These data encouraged us to develop an assay for absolute quantification of miR-34a which would allow determining the copy numbers of miR-34a, defining precise cut-offs, and comparing miR-34a levels during the course of the disease in one patient. We designed synthetic RNA oligos that were used to construct standard curves for both miR-34a and a normalization gene (RNU48). Using this assay, we profiled the expression of miR-34a in a cohort of CLL patients (N=200) to define a cut-off value that would discriminate therapy resistant cases. The distribution of miR-34a expression in the cohort ranged from 1 to 81820 molecules (per 10e6 copies of RNU48). Significantly, miR-34a levels below 2500 copies (N=47) were correlated with shorter overall survival (9.6 years vs. not-reached, HR 2.2 [CI 1.1–4.5], P=0.03). Subsequently, the expression of miR-34a was compared in samples stratified by known prognostic markers: chromosomal aberrations (del17p13, del11q23, tris.12, and del13q14), IgHV status, expression of CD38, CD49d, age, gender, and Rai stage. The lower miR-34a levels were only associated with the deletion of 17p13 locus that includes the p53 gene (N=18, fold change −3.4, P=0.003). Remarkably, CLL samples with sole p53 mutation not accompanied by p53 deletion (N=13) also expressed low levels of miR-34a compared to wt-p53 (P=0.005, fold change −2.7). Most notably, 77% (10/13) of these samples had miR-34a levels below the cut-off of 2500 copies. We further validated our observations and assay by analyzing miR-34a expression in paired samples from 12 CLL cases that acquired p53 aberration during the course of the disease. This emphasized that miR-34a expression decreased in all cases after occurrence of p53 mutation (P=0.0008, fold change −6.1). Additionally, the effect of miR-34a up-regulation on therapy response is currently being investigated in a cohort of FCR-treated patients (N=50).

Our data provide complex evidence for the use of miR-34a as a marker of fludarabine-resistant disease. MicroRNA-34a quantification can identify p53 mutated cases that would not be recognized by FISH (mutation not accompanied by del17p13), and miR-34a down-regulation can be used as a sensor for acquisition of p53 abnormality during the course of the disease. This can be accomplished without treatment of cells with gamma-irradiation, which was previously used to identify functional impairment of the p53-pathway (Pettitt et al. Blood, 2001; Mous et al. Leukemia, 2009; Lin et al. CCR, 2012). The described assay for absolute quantification of miR-34a encourages further inter-laboratory validation.

IGA MZCR NT11218–6/2010, CZ.1.07/2.3.00/20.0045, CZ.1.05/1.1.00/02.0068

No relevant conflicts of interest to declare.