Haploinsufficiency of ETV6 and CDKN1B in patients with acute myeloid leukemia and complex karyotype

Abstract

BackgroundAcute myeloid leukemia with complex karyotype (CK-AML) is a distinct biological entity associated with a very poor outcome. Since complex karyotypes frequently contain deletions of the chromosomal region 12p13 encompassing the tumor suppressor genes ETV6 and CDKN1B, we aimed to unravel their modes of inactivation in CK-AML.ResultsTo decipher deletions, mutations and methylation of ETV6 and CDKN1B, arrayCGH, SNP arrays, direct sequencing of all coding exons and pyrosequencing of the 5′UTR CpG islands of ETV6 and CDKN1B were performed. In total, 39 of 79 patients (49%) showed monoallelic deletions of 12p13 according to karyotypic data and 20 of 43 patients (47%) according to genomic profiling. Genomic profiling led to the minimal deleted region covering the 3′-UTR of ETV6 and CDKN1B. Direct sequencing revealed one novel monoallelic frameshift mutation in ETV6 while no mutations in CDKN1B were identified. Furthermore, methylation levels of ETV6 and CDKN1B did not indicate transcriptional silencing of any of these genes. ETV6 and CDKN1B had reduced expression levels in CK-AML patients with deletion in 12p13 as compared to CK-AML without deletion in 12p13, while the other genes (BCL2L14, LRP6, DUSP16 and GPRC5D) located within the minimal deleted region in 12p13 had very low or missing expression in CK-AML irrespective of their copy number status.ConclusionsETV6 and CDKN1B are mainly affected by small monoallelic deletions, whereas mutations and hypermethylation play a minor role in CK-AML. Reduced gene dosage led to reduced gene expression levels, pointing to haploinsufficiency as the relevant mechanism of inactivation of ETV6 and CDKN1B in CK-AML.Electronic supplementary materialThe online version of this article (doi:10.1186/1471-2164-15-784) contains supplementary material, which is available to authorized users.

Phenotypic and molecular insights into CASK-related disorders in males

“…Labelling and hybridization of genomic DNA were performed according to the protocol provided by Agilent without enzymatic restriction. Data visualization and analysis was performed as described [ 13 ]. Copy number profiling for patient 8 was performed on a 60K oligonucleotide array (Agilent Technologies, Diegem, Belgium) according to the manufacturer’s instructions with minor modifications as described [ 14 ].…”

A 14.8 Mb 12p Deletion Disrupting ETV6 in a Patient with Myelodysplastic Syndrome

“…It can be guessed that this partial deletion results in a decreased expression of this gene [11]. These authors demonstrated that levels of ETV6 were significantly decreased in cases with 12p13 deletions encompassing the entire gene or at least the 3'UTR, like in the present case, whereas expression of other genes in the deleted region, like BCL2L14, LRP6, DUSP16 and GPRC5D, did not show any variation, independently of their copy number status.…”

“…Other genes within the minimal deleted region like CDKN1B, BCL2L14, LRP6, DUSP16 and GPRC5D may play an additional role in tumorigenesis and leukemogenesis [11]. All these genes are deleted in the case here presented; his deletion extends to band p11.23 where the oncogene KRAS2 is harbored.…”

“…12p deletions are detected in a broad spectrum of hematological malignancies in acute myeloid leukemia (AML) they are usually associated with complex karyotypes, whereas in myelodysplastic syndromes these anomalies are often seen along with monosomy 7 [8][9][10][11]. Rucker et al showed that about half of the AML with complex karyotype (CK-AML) presented 12p13 deletions, when analyzed by high-resolution arrays [12].…”

Germline ETV6 mutations and predisposition to hematological malignancies

“…Likewise, somatic ETV6 mutations in AML are rare but recurrent events [7,9]. Deletions involving the cytogenetic region 12p13 are common in hematopoietic malignancies of both lymphoid and myeloid origin, notably in MDS with monosomy 7 [10] and AML with complex karyotypes [11][12][13][14].…”