MicroRNA signatures in B-cell lymphomas

Abstract

Accurate lymphoma diagnosis, prognosis and therapy still require additional markers. We explore the potential relevance of microRNA (miRNA) expression in a large series that included all major B-cell non-Hodgkin lymphoma (NHL) types. The data generated were also used to identify miRNAs differentially expressed in Burkitt lymphoma (BL) and diffuse large B-cell lymphoma (DLBCL) samples. A series of 147 NHL samples and 15 controls were hybridized on a human miRNA one-color platform containing probes for 470 human miRNAs. Each lymphoma type was compared against the entire set of NHLs. BL was also directly compared with DLBCL, and 43 preselected miRNAs were analyzed in a new series of routinely processed samples of 28 BLs and 43 DLBCLs using quantitative reverse transcription-polymerase chain reaction. A signature of 128 miRNAs enabled the characterization of lymphoma neoplasms, reflecting the lymphoma type, cell of origin and/or discrete oncogene alterations. Comparative analysis of BL and DLBCL yielded 19 differentially expressed miRNAs, which were confirmed in a second confirmation series of 71 paraffin-embedded samples. The set of differentially expressed miRNAs found here expands the range of potential diagnostic markers for lymphoma diagnosis, especially when differential diagnosis of BL and DLBCL is required.

Figure 1

Workflow. The samples were analyzed first by SAM, comparing each lymphoma type against the whole series. In parallel, a class predictor model was investigated for the 147 samples. Also, BL and DLBCL samples were compared by SAM, and then significant miRNAs were analyzed in a second series of BL and DLBCL samples.

Figure 2

Differentially expressed miRNAs in B-cell lymphomas. In all, 128 miRNAs were differentially expressed in the series (FDR <0.01 and fold change (FC) >1.5) of 147 samples. For representation, data were normalized with non-tumoral controls (tonsils, reactive lymph nodes or spleens).

Figure 3

MiRNAs differentially expressed between BL and DLBCL. In all, 43 miRNAs were significantly (FDR <0.01 and fold change (FC) >1.5) differentially expressed in a SAM analysis comparing microarray data of 12 BL vs 29 DLBCL.

Figure 4

Box plots of qRT-PCR results. A selection of significant miRNAs (BL vs DLBCL) confirmed by qRT-PCR is illustrated. Mir-146a, miR-155 and mir-29b were upregulated in the DLBCL group, whereas miR-17-3p, miR-92 and miR-663 were upregulated in the BL group. –ΔCt values are represented in log₂ scale; ^*denotes outliers.