Gene Expression Signature of B-Cell Chronic Lymphocytic Leukemia with Trisomy 12.

Abstract

The prognosis of patients with B-CLL is largely determined by the karyotype of the malignant clone. Microarray technology has facilitated linkage between chromosomal aberrations and gene expression signatures. We have investigated the gene expression profile associated with trisomy 12 (+12). Expression data were obtained by microarray analysis of mRNA from unselected PBMNC of 4 patients with +12 and compared with 16 B-CLL controls. 146 genes were at least 2-fold over- or underexpressed in samples with +12. Five of the 16 genes showing the strongest correlation with +12 were selected for further analysis (HIP1R FC=3,43; MYF6 FC=3,92; P2RY14 FC=−9,59; RASGRP3 FC=−3,85; SLC2A6 FC=2,13) and validation by real time PCR: HIP1R located on chromosome 12q24, with a fold change (FC) of 3,43, MYF6 (chromosome 12q21, FC=3,92), P2RY14 (chromosome 3q21–q25, FC-9,59) RASGRP3 (chromosome 2p25.1–p24.1, FC=−3,85). SLC2A6 (chromosome 9q34, FC=2,13). Quantitative PCR was performed with mRNA from 61 patients (29 with +12, 32 B-CLL controls) and 2 healthy donors. Only 3 genes were significantly associated with +12 compared to the B-CLL-controls in this evaluation: HIP1R (3,486; p<0,0001), MYF6 (1,498; p=0,005), P2RY14 (1,216; p=0,013). (Table1). Two of these genes (HIP1R, MYF6) are located on chromosome 12 indicating a “gene dosage effect”, while P2RY14 is localized on a different chromosome suggesting trans-acting processes. We have used expression of HIP1R as a surrogate marker for trisomy 12. The predicted sensitivity was 79,3% and the predicted specifity was 90,6. Analysis of CD19+ selected B-CLL and normal B-cells revealed that MYF6 is exclusively expressed in normal or malignant B-cells in peripheral blood. We confirmed that MYF6 is highly specific for skeletal muscle, however strong expression was found in normal tonsils, DLBCL, and other B-cell malignancies. Our data link a specific gene expression signature with trisomy 12. 3 novel marker genes were identified, which could be used as diagnostic tools. The linkage with P2RY14 suggests that +12 influences the expression of genes from other chromosomes. Table 1 Mean + 12, N=29 Mean B-CLL controls, N=32 p-value Locus Fold change microarray HIP1R 0,7819 0,2243 0,000 12q24 3,43 MYF6 37,55 25,06 0,005 12q21 3,92 P2RY14 −0,2873 0,3494 0,013 3q21–q25 −9,59 RASGRP3 0,8404 1,0774 0,055 2p25.1–p24.1 −3,85 SLC2A6 29,78 22,37 0,080 9q34 2,13