Integrated genome-wide genotyping and gene expression profiling reveals BCL11B as a putative oncogene in acute myeloid leukemia with 14q32 aberrations.

Acute myeloid leukemia is a neoplasm characterized by recurrent molecular aberrations traditionally demonstrated by cytogenetic analyses. We used high density genome-wide genotyping and gene expression profiling to reveal acquired cryptic abnormalities in acute myeloid leukemia. By genome-wide genotyping of 137 cases of primary acute myeloid leukemia, we disclosed a recurrent focal amplification on chromosome 14q32, which included the genes BCL11B, CCNK, C14orf177 and SETD3, in two cases. In the affected cases, the BCL11B gene showed consistently high mRNA expression, whereas the expression of the other genes was unperturbed. Fluorescence in situ hybridization on 40 cases of acute myeloid leukemia with high BCL11B mRNA expression [2.5-fold above median; 40 out of 530 cases (7.5%)] revealed 14q32 abnormalities in two additional cases. In the four BCL11B-rearranged cases the 14q32 locus was fused to different partner chromosomes. In fact, in two cases, we demonstrated that the focal 14q32 amplifications were integrated into transcriptionally active loci. The translocations involving BCL11B result in increased expression of full-length BCL11B protein. The BCL11B-rearranged acute myeloid leukemias expressed both myeloid and T-cell markers. These biphenotypic acute leukemias all carried FLT3 internal tandem duplications, a characteristic marker of acute myeloid leukemia. BCL11B mRNA expression in acute myeloid leukemia appeared to be strongly associated with expression of other T-cell-specific genes. Myeloid 32D(GCSF-R) cells ectopically expressing Bcl11b showed decreased proliferation rate and less maturation. In conclusion, by an integrated approach involving high-throughput genome-wide genotyping and gene expression profiling we identified BCL11B as a candidate oncogene in acute myeloid leukemia.

Addition of ß-mercaptoethanol is a prerequisite for high-quality RNA isolation using QIAsymphony technology as demonstrated by detection of molecular aberrations in hematologic malignancies.

The isolation of high-quality RNA and DNA from various specimens is essential to perform reliable molecular diagnostic assays. In routine diagnostics of hematologic malignancies isolation of high-quality RNA is a prerequisite. We used QIAsymphony technology (QST) using a customized RNA CT 800 V6 protocol for automated semi-high-throughput isolation of RNA from human specimens and compared the results for breakpoint cluster region-c-abl oncogene 1 (BCR-ABL1) quantification by real-time quantitative polymerase chain reaction (RQ-PCR) and detection of JAK2 V617F mutations by reverse-transcriptase PCR (RT-PCR) on QST RNA with RNA isolation performed with our routine manual method using RNA-Bee (RB). QST RNA was isolated with and without the addition of ß-mercaptoethanol (BME). Addition of BME to the lysis buffer RLT Plus resulted in consistently lower Ct values in analyses of the reference gene porphobilinogen deaminase (PBGD). Further, the BCR-ABL1 mRNA levels of the QST RNA isolation were highly consistent with RB RNA isolation, only when the lysis buffer RLT Plus in addition contained BME. Moreover, cases of myeloproliferative neoplasms (MPN) with low levels of JAK2 V617F mRNA were even missed in QST when lysis buffer RLT Plus was used, but they were readily detected after addition of BME.

High-dose imatinib versus high-dose imatinib in combination with intermediate-dose cytarabine in patients with first chronic phase myeloid leukemia: a randomized phase III trial of the Dutch-Belgian HOVON study group.

Despite the revolutionary change in the prognosis of chronic myeloid leukemia (CML) patients with the introduction of imatinib, patients with resistant disease still pose a considerable problem. In this multicenter, randomized phase III trial, we investigate whether the combination of high-dose imatinib and intermediate-dose cytarabine compared to high-dose imatinib alone, improves the rate of major molecular response (MMR) in newly diagnosed CML patients. This study was closed prematurely because of declining inclusion due to the introduction of second generation tyrosine kinase inhibitors and only one third of the initially required patients were accrued. One hundred nine patients aged 18-65 years were randomly assigned to either imatinib 800 mg (n = 55) or to imatinib 800 mg in combination with two successive cycles of cytarabine 200 mg/m(2) for 7 days (n = 54). After a median follow-up of 41 months, 67 % of patients were still on protocol treatment. The MMR rate at 12 months was 56 % in the imatinib arm and 48 % in the combination arm (p = 0.39). Progression-free survival was 96 % after 1 year and 89 % after 4 years. Four-year overall survival was 97 %. Adverse events grades 3 and 4 were more common in the combination arm. The addition of intermediate-dose of cytarabine to imatinib did not improve the MMR rate at 12 months. However, the underpowering of the study precludes any definitive conclusions. This trial is registered at www.trialregister.nl (NTR674).