Chromosome 21 is the most affected chromosome in childhood acute lymphoblastic leukemia. Many of its numerical and structural abnormalities define diagnostically and clinically important subgroups. To obtain an overview about their types and their approximate genetic subgroup-specific incidence and distribution, we performed cytogenetic, FISH and array analyses in a total of 578 ALL patients (including 26 with a constitutional trisomy 21). The latter is the preferred method to assess genome-wide large and fine-scale copy number abnormalities (CNA) together with their corresponding allele distribution patterns. We identified a total of 258 cases (49%) with chromosome 21-associated CNA, a number that is perhaps lower-than-expected because ETV6-RUNX1-positive cases (11%) were significantly underrepresented in this array-analyzed cohort. Our most interesting observations relate to hyperdiploid leukemias with tetra- and pentasomies of chromosome 21 that develop in constitutionally trisomic patients. Utilizing comparative short tandem repeat analyses, we were able to prove that switches in the array-derived allele patterns are in fact meiotic recombination sites, which only become evident in patients with inborn trisomies that result from a meiosis 1 error. The detailed analysis of such cases may eventually provide important clues about the respective maldistribution mechanisms and the operative relevance of chromosome 21-specific regions in hyperdiploid leukemias.
BackgroundTranslocations of the IGH locus on 14q32.3 are present in about 8% of patients with chronic lymphocytic leukemia (CLL) and contribute to leukemogenesis by deregulating the expression of the IGH-partner genes. Identification of these genes and investigation of the downstream effects of their deregulation can reveal disease-causing mechanisms.Case presentationWe report on the molecular characterization of a novel t(12;14)(q23.2;q32.3) in CLL. As a consequence of the rearrangement ASCL1 was brought into proximity of the IGHJ-Cμ enhancer and was highly overexpressed in the aberrant B-cells of the patient, as shown by qPCR and immunohistochemistry. ASCL1 encodes for a transcription factor acting as a master regulator of neurogenesis, is overexpressed in neuroendocrine tumors and a promising therapeutic target in small cell lung cancer (SCLC). Its overexpression has also been recently reported in acute adult T-cell leukemia/lymphoma.To examine possible downstream effects of the ASCL1 upregulation in CLL, we compared the gene expression of sorted CD5+ cells of the translocation patient to that of CD19+ B-cells from seven healthy donors and detected 176 significantly deregulated genes (Fold Change ≥2, FDR p ≤ 0.01). Deregulation of 55 genes in our gene set was concordant with at least two studies comparing gene expression of normal and CLL B-lymphocytes. INSM1, a well-established ASCL1 target in the nervous system and SCLC, was the gene with the strongest upregulation (Fold Change = 209.4, FDR p = 1.37E-4).INSM1 encodes for a transcriptional repressor with extranuclear functions, implicated in neuroendocrine differentiation and overexpressed in the majority of neuroendocrine tumors. It was previously shown to be induced in CLL cells but not in normal B-cells upon treatment with IL-4 and to be overexpressed in CLL cells with unmutated versus mutated IGHV genes. Its role in CLL is still unexplored.ConclusionWe identified ASCL1 as a novel IGH-partner gene in CLL. The neural transcription factor was strongly overexpressed in the patient’s CLL cells. Microarray gene expression analysis revealed the strong upregulation of INSM1, a prominent ASCL1 target, which was previously shown to be induced in CLL cells upon IL-4 treatment. We propose further investigation of the expression and potential role of INSM1 in CLL.Electronic supplementary materialThe online version of this article (10.1186/s13039-018-0355-7) contains supplementary material, which is available to authorized users.
Background: The detailed definition of causative genomic alterations is not only an indispensable prerequisite for the predictive and prognostic subdivision of childhood acute lymphoblastic leukemia (ALL) but increasingly also one, on which individualized treatment approaches will be based on. Apart from the already well-established genetic categories, the recent identification of several new classes of potentially relevant alterations together with the increasing availability of novel therapeutic options therefore necessitates a diagnostic workflow that is able to satisfy the ensuing clinical needs in a comprehensive manner. The two most interesting changes in this context are the therapeutically targetable recurrent but rare and heterogeneous tyrosine kinase and JAK2 pathway-activating (TKA) gene fusions and the more elusive cohort of apparently relapse risk-prone cases with hitherto only vaguely defined combinations of gene region-specific copy number alterations (CNA). Despite the availability of a multitude of applicable techniques, the fast and cost-efficient identification of the entire expectable abnormality patterns still remains a challenge, especially if one needs to perform the diagnostic work-up on a single case basis. We previously proposed that these diagnostic requirements could be covered best with a systematic hierarchical FISH screening approach for the identification of gene fusions together with array (combined SNP and non-polymorphic probes) analyses of genome-wide quantitative and qualitative large- and small-scale copy number aberrations (CNAs). Material and Methods: Since June 2015 we have therefore evaluated the feasibility of such a workflow in a prospective manner and screened so far 205 patients (i.e. 184 with B- and 21 with T-ALL, including 18 relapses with 14 diagnostic/relapse pairs) that were consecutively enrolled in the Austrian AIEOP-BFM 2009 treatment study. Cytogenetic preparations served as backup, since metaphase spreads were used for further FISH clarification of otherwise unresolvable complex rearrangements or ploidy patterns if deemed necessary. All identified gene fusions were subsequently validated with single or multiplex RT-PCR analyses. Results: FISH screening was positive in 90% (184/205) of cases and provided already the most essential diagnostic clues. CNAs were present in all T-ALL and 97% (179/184) of B-ALL cases, including 13 with an IKZF1pluspattern and three with ERG deletions, which both will be used das stratifying markers in the upcoming treatment trial. Taken together, our screening strategy allowed the unambiguous classification of the vast majority of B-ALLs: 70 hyperdiploid, 3 hypodiploid, 35 ETV6-RUNX1, 6 KMT2A-rearranged, 8 TCF3-PBX1, 2 BCR-ABL1, 4 dic(9;20), 5 iAMP21, 8 IGH-rearranged, 6 P2RY8-CRLF2, 3 PAX5-rearranged, 3 ZNF384-rearranged, 2 ETV6-rearranged, 3 TKA fusion-positive and 10 so called "B-other" cases without any apparent specific abnormality. RNA-sequencing analyses of these ten cases revealed that seven of them harbored a DUX4 gene rearrangement. Conclusions: Apart from its proven practical diagnostic value, our combined FISH/array approach has also several additional advantages, especially if one considers the amount of achievable information. Both procedures require only little amount of material and are highly standardized, reproducible and robust technologies. Moreover, arrays deliver DNA-sequence-based data, the coordinates of which can be efficiently stored, processed and analyzed. As such, they not only serve as a pure diagnostic tool but also as a valuable discovery platform. Disclosures No relevant conflicts of interest to declare.
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