Copy number genome alterations are associated with treatment response and outcome in relapsed childhood ETV6/RUNX1-positive acute lymphoblastic leukemia

Abstract

© F e r r a t a S t o r t i F o u n d a t i o nations are most likely required for ETV6/RUNX1-positive leukemogenesis and might be important for the differences in clinical outcome. More than 80% of initial ETV6/RUNX1-positive ALL display additional genetic alterations of the ETV6 and RUNX1 gene loci in fluorescence in situ hybridization (FISH) analyses. These include deletions of the untranslocated ETV6 gene (70%), an extra copy of RUNX1 (23%) and duplication of the derivative chromosome der(21) t(12;21) (10%). 18 At relapse, additional alterations of chromosomes 12 and 21 are often detected in leukemic cells as well (85%). 19 Current genome wide high resolution analyses of DNA copy number alterations (CNA) have identified numerous genetic alterations in childhood ALL. [20][21][22][23] In initial ETV6/RUNX1-positive ALL, genes related to B-lymphocyte development and differentiation, cell cycle regulation, tumor suppression and apoptosis are recurrently affected. 20,21,[24][25][26][27] Recent DNA copy number analyses on matched initial diagnosis and relapse ALL samples revealed that CNA acquired at relapse primarily affect genes implicated in cell cycle regulation, B-cell development, drug metabolism and drug response. 25,28,29 In the present study, leukemic cell DNA from 51 patients with a first relapse of ETV6/RUNX1-positive ALL enrolled in and treated according to the ALL-REZ BFM relapse trials were examined by whole genome array comparative genomic hybridization (CGH) for cooperating genetic lesions. This cohort represents the largest number of patients analyzed so far, enabling the investigation of an association between identified CNA and relapse-specific clinical and prognostic parameters for the first time. Methods Patients and samplesLeukemic bone marrow samples from 51 patients with first relapse of an ETV6/RUNX1-positive BCP-ALL were collected at relapse diagnosis after written informed consent was obtained from the patients, their parents or guardians in accordance with the ethical committee of the Charité and the declaration of Helsinki. All patients were enrolled in and treated according to ALL-REZ relapse trials 90, 95/96, and 2002 of the BFM study group, which were approved by the Institutional Review Boards of the Charité and the FU-Berlin, Germany. Diagnostic bone marrow samples were selected to contain >60% leukemic cells prior to further enrichment by Ficoll-density gradient separation of mononuclear cells. The presence of the ETV6/RUNX1 fusion was detected by reverse transcriptase polymerase chain reaction analysis as described previously. 9 DNA isolationLeukemic cell samples were prepared and DNA isolated from bone marrow or peripheral blood mononuclear cells of all patients and of 20 healthy controls, serving as gender-specific control DNA, as described previously. 30 All DNA samples were amplified using the GenomePlex Whole Genome Amplification Kit (SigmaAldrich Chemie GmbH, Munich, Germany) following the manufacturer's directions. Array comparative genomic hybridizationArray CGH...

Chromosomal aberrations in childhood acute lymphoblastic leukemia: 15-year single center experience

“…In our study, the frequencies of these changes (21.9% for RUNX1/ETV6 and 28% for high hyperdiploidy) were in accordance with literature. High frequency of chromosomal changes additional to RUNX1/ETV6 is also in agreement with published data (additional genetic alterations of the ETV6 and RUNX1 gene loci were detected by FISH in more than 80% of cases) [6,[23][24][25]. In our cohort of Aberrations involving chromosome 6q are common in childhood ALL occurring in 7-18% of patients [27,28].…”

“…[26][27][28][29]. 6q deletion is a recurrent aberration detected mainly in ETV6/RUNX1-positive patients and its recurrent incidence was also confirmed by studies using the array CGH method [38,39]. Its importance is primarily associated with deletion 12p where it is assumed that co-inactivation of both FOXO3A (6q21) and CDKN1B (12p13) caused by copy number losses might have adverse prognostic impact [38].…”

Pathogenesis of ETV6/RUNX1-positive childhood acute lymphoblastic leukemia and mechanisms underlying its relapse

“…The clinical heterogeneity among first relapses implies that further genetic abnormalities exist in leukemic cells. Thus, some studies compared diagnostic and relapse CNA patterns to gain further insights into the molecular mechanisms of disease recurrence in E/R -positive ALL [97, 108, 112]. …”

“…A substantial number of CNAs in relapsed E/R -positive ALL occur in recurrently affected regions (Table 2) [30, 97, 108, 109, 112]. Also, an increase in the number of CNAs per case has been reported between diagnosis and relapse [101, 108, 109].…”

Cytogenetic and immunohistochemical characterization of mammary analogue secretory carcinoma of salivary glands

“…These two cases exhibited a similar morphology and immunophenotype to the confirmed MASCs suggesting that increased ETV6 copy number may be associated with the translocation representing an 'in situ' or early stage. Copy number genome aberrations have been shown to be associated with patient outcome and treatment response in childhood ETV6/RUNX1-positive acute lymphoblastic leukaemia [19,20]. Alteration in ETV6 copy number has also been reported in infantile fibrosarcoma and cellular type of congenital mesoblastic nephroma [21].…”