- Case report
- Open Access
PAX5 fusion genes in t(7;9)(q11.2;p13) leukemia: a case report and review of the literature
© Denk et al.; licensee BioMed Central Ltd. 2014
- Received: 2 December 2013
- Accepted: 29 January 2014
- Published: 7 February 2014
B-cell precursor acute lymphoblastic leukemia (BCP-ALL) is characterized by recurrent genetic alterations including chromosomal translocations. The transcription factor PAX5, which is pivotal for B-cell commitment and maintenance, is affected by rearrangements, which lead to the expression of in-frame fusion genes in about 2.5% of the cases.
Using conventional cytogenetics, fluorescence in situ hybridization (FISH), and molecular methods, an additional case with a der(9)t(7;9)(q11.23;p13) resulting in the expression of a PAX5-ELN fusion gene was identified. Furthermore, a general review of leukemia harboring a t(7;9)(q11.2;p13) or der(9)t(7;9)(q11.2;p13), which occurs more often in children than in adults and shows a remarkably high male preponderance, is given. These cytogenetically highly similar translocations lead to the expression of one of three different in frame PAX5-fusions, namely with AUTS2 (7q11.22), ELN (7q11.23), or POM121 (7q11.23), which constitute the only currently known cluster of PAX5 partner genes.
Our report underlines the recurrent involvement of PAX5 in different fusion genes resulting either from t(7;9)(q11.2;p13) or der(9)t(7;9)(q11.2;p13), which cannot be distinguished cytogenetically and whose discrimination requires molecular analysis.
- B-cell precursor acute lymphoblastic leukemia
PAX5 rearrangements, resulting in the expression of in-frame fusion genes, account for about 2.5% of pediatric B-cell precursor acute lymphoblastic leukemia (BCP-ALL) . While several groups, including our own, have reported the incidence and diversity of PAX5 fusion genes [1–7], their occurrence in leukemia harboring a t(7;9)(q11.2;p13) or der(9)t(7;9)(q11.2;p13) has not yet been investigated in detail. Herein, we describe an additional case with a PAX5-ELN fusion and summarize the demographic and genetic data of all cases with t(7;9)(q11.2;p13)/der(9)t(7;9)(q11.2;p13) leukemia reported to date.
Demographic and genetic data of t(7;9)(q11.2;p13) and der(9)t(7;9)(q11.2;p13) positive B-ALL cases
PAX5 fusion gene
PAX5 ex7/ELN ex2
PAX5 ex7/ELN ex2
PAX5 ex7/ELN ex2
PAX5 ex7/ELN ex5
PAX5 ex6/AUTS2 ex4
PAX5 ex6/AUTS2 ex6
PAX5 ex6/AUTS2 ex5
PAX5 ex5/POM121 ex4
PAX5 ex5/POM121 ex4
So far, sixteen in-frame PAX5-fusions have been described and the fusion partners comprise a heterogeneous group of genes encoding proteins, which play distinct roles in signaling, transcription, chromatin remodeling, and cell structuring [1–7, 9, 10]. Three of the sixteen currently known PAX5 fusion partners, namely, AUTS2, ELN, and POM121, are located at the pericentromeric region of 7q and encompass roughly 3.3 Mb of genomic DNA, forming the only currently known cluster of PAX5 partner genes. Therefore, t(7;9)(q11.2;p13) translocations may give rise to three different recurrent fusion genes, i.e. PAX5-AUTS2, PAX5-POM121, and PAX5-ELN (Figure 2), which are not distinguishable at the cytogenetic level. In addition, karyotyping of five of the cases showed an unbalanced der(9)t(7;9)(q11.2;p13) with loss of the reciprocal derivative chromosome (Table 1; cases 5–7 and 11–12). One of the cases was identified by SNP array (case 4), only detecting unbalanced chromosome alterations; furthermore, most cases showed a deletion of the PAX5 3′-end by FISH, further supporting the notion that the PAX5- partner fusions, and not the reciprocal ones contribute to leukemogenesis.
t(7;9)(q11.2;p13)/der(9)t(7;9)(q11.2;p13) positive leukemia is a rare disease and only 9 cases have been collected in the Mitelman database of the cancer genome anatomy project ( accessed November 2013) (Table 1). Three of these cases were PAX5-ELN positive [2, 4] and in addition, a case with a PAX5-ELN fusion without cytogenetic data has been reported . Together, including the case described herein, five patients harboring this fusion gene have now been identified.
Other cases involving the cluster of PAX5 fusion partners include: Three patients with a PAX5-AUTS2[5, 9, 10], two with a PAX5-POM121 fusion gene [1, 4], and in two cases involvement of PAX5 has not been investigated [12, 13] (Table 1). Of note, in the PAX5-POM121 case we have previously published , cytogenetic analysis failed to identify a t(7;9)(q11.2;p13), but the chromosome quality was rather poor. Whole chromosome painting with probes specific for chromosomes 7 and 9 showed the presence of a der(7;9), on which the 3′-end of PAX5 was located, whereas the 5′-end of PAX5, generating the PAX5-POM121 fusion, was translocated to a derivative chromosome, which only partially consisted of chromosome 7 material (data not shown). Together, with the molecular data that showed an insertion of chromosome 12 sequences in the fusion, a more complex rearrangement with involvement of at least chromosomes 7, 9, and 12 generated the in-frame PAX5-POM121 fusion .
Furthermore, out of the 12 cases with t(7;9)(q11.2;p13)/der(9)t(7;9)(q11.2;p13) rearrangements only one was an adult and two were young adolescents, whereas all other patients were ≤ 4 years of age (Table 1), suggesting that this subtype of leukemia occurs more frequently in pediatric than in adult cases. Remarkably, 83% (10/12) of the t(7;9)(q11.2;p13)/der(9)t(7;9)(q11.2;p13) patients were male, and thus, the male/female ratio was 5. Although the number of so far reported cases is rather low, in acute leukemia such an extreme gender bias is exceedingly rare . This finding is intriguing, but currently there is no plausible explanation why a specific subtype of leukemia is associated with one or the other gender.
Regarding the prognostic relevance of PAX5 fusion genes in general, due to their rareness no final conclusions may be drawn. However, we have recently shown that PAX5-AUTS2 leukemia may have a rather unfavorable outcome . Out of the five PAX5-ELN cases, one patient (case 4) showed high-risk features and displayed a JAK1 mutation and a BCR-ABL1-like expression signature . Furthermore, cases 1 and 2 both relapsed post allograft and died 16 months after initial diagnosis ( accessed November 2013). The PAX5-ELN positive patient presented herein is currently, eight months after initial diagnosis, in complete remission. Together, there is at least some evidence that t(7;9)(q11.2;p13)/der(9)t(7;9)(q11.2;p13) leukemia may have a rather poor prognosis. However, whether this is attributable to the specific PAX5-fusions or to coinciding mutations in, for example, tyrosine kinases, remains to be determined, and a larger cohort of patients needs to be analyzed, which, due to the low incidence of this leukemia subtype, will require an international collaborative effort.
In this report an additional case of PAX5-ELN positive leukemia is described, and, furthermore, an overview of the published cases of t(7;9)(q11.2;p13)/der(9)t(7;9)(q11.2;p13) leukemia is given, emphasizing the importance of molecular analysis to discriminate between cytogenetically identical translocations resulting in distinct fusion genes.
Cytogenetic and fluorescence in situ hybridization (FISH) analysis
Cytogenetic analysis was performed according to standard techniques. FISH analysis using PAX5- and ELN-specific probes was conducted as previously described . The PAX5 rearrangement was first detected using PAX5-flanking BAC clones RP11-220I1 and RP11-12P15 (obtained from Pieter de Jong, BACPAC Resources, Children’s Hospital and Research Center Oakland, CA, USA). Verification of the PAX5-ELN fusion was performed using the PAX5 5′-end-flanking BAC clone RP11-220I1 in combination with the ELN 3′-end-specific clone RP11-349P21 (Welcome Trust Sanger Institute; http://www.sanger.ac.uk).
RNA isolation and reverse transcription-polymerase chain reaction (RT-PCR)
RNA isolation and RT-PCR for the detection of PAX5-ELN transcripts were performed according to standard procedures using primers PAX5ex2-3-F1 (5′-TCTTGGCAGGTATTAT GAGACAGGAAG-3′) and ELNex6-R2 (5′-AGCAGCGTCAGCCACTCCAC-3′) located in exons 2–3 and 6 of PAX5 and ELN, respectively. Amplification products were directly sequenced (Microsynth AG, Austria) and sequence analysis was conducted using the CLC Main Workbench 6.0 (CLC bio, Denmark).
Reference sequences and exon nomenclature
The chromosome band positions of the genes and the exon nomenclature used correspond to that of the Ensemble database and the reference sequences for AUTS2 (ENST00000342771), ELN (ENST00000252034), POM121 (ENST00000257622), and PAX5 (ENST00000358127) (Ensembl release 73 - September 2013). A summary of all mRNA fusion sequences as well as the entire transcript and protein sequences of the putative consensus chimeras PAX5-AUTS2, PAX5-ELN, and PAX5-POM121 are provided as Additional file 1.
Within the AIEOP-BFM ALL 2009 study (ClinicalTrials.gov Identifier: NCT01117441), written informed consent - which includes the compliance that surplus material not required for diagnostic purposes may be used for research purposes - is obtained from the patients, their parents or their legal guardians. This study has exclusively been performed on material obtained for diagnostic purposes and neither any additional medical intervention nor patient recruitment was necessary.
We thank Andishe Attarbaschi, Gertrud Pass, and Klaus Fortschegger for helpful discussions. This work was supported by a grant from the Austrian Science Fund (FWF P21554-B19 to S.S.) and the St. Anna Kinderkrebsforschung e.V.
- Nebral K, Denk D, Attarbaschi A, Konig M, Mann G, Haas OA, Strehl S: Incidence and diversity of PAX5 fusion genes in childhood acute lymphoblastic leukemia. Leukemia 2009, 23: 134–143. 10.1038/leu.2008.306View ArticlePubMedGoogle Scholar
- Bousquet M, Broccardo C, Quelen C, Meggetto F, Kuhlein E, Delsol G, Dastugue N, Brousset P: A novel PAX5-ELN fusion protein identified in B-cell acute lymphoblastic leukemia acts as a dominant negative on wild-type PAX5. Blood 2007, 109: 3417–3423. 10.1182/blood-2006-05-025221View ArticlePubMedGoogle Scholar
- Cazzaniga G, Daniotti M, Tosi S, Giudici G, Aloisi A, Pogliani E, Kearney L, Biondi A: The paired box domain gene PAX5 is fused to ETV6/TEL in an acute lymphoblastic leukemia case. Cancer Res 2001, 61: 4666–4670.PubMedGoogle Scholar
- Coyaud E, Struski S, Prade N, Familiades J, Eichner R, Quelen C, Bousquet M, Mugneret F, Talmant P, Pages MP, et al.: Wide diversity of PAX5 alterations in B-ALL: a groupe francophone de cytogenetique hematologique study. Blood 2010, 115: 3089–3097. 10.1182/blood-2009-07-234229View ArticlePubMedGoogle Scholar
- Kawamata N, Ogawa S, Zimmermann M, Niebuhr B, Stocking C, Sanada M, Hemminki K, Yamatomo G, Nannya Y, Koehler R, et al.: Cloning of genes involved in chromosomal translocations by high-resolution single nucleotide polymorphism genomic microarray. Proc Natl Acad Sci U S A 2008, 105: 11921–11926. 10.1073/pnas.0711039105PubMed CentralView ArticlePubMedGoogle Scholar
- Lee ST, Ji Y, Kim HJ, Ki CS, Jung CW, Kim JW, Kim SH: Sequential array comparative genomic hybridization analysis identifies copy number changes during blastic transformation of chronic myeloid leukemia. Leuk Res 2012, 36: 418–421. 10.1016/j.leukres.2011.12.021View ArticlePubMedGoogle Scholar
- Mullighan CG, Goorha S, Radtke I, Miller CB, Coustan-Smith E, Dalton JD, Girtman K, Mathew S, Ma J, Pounds SB, et al.: Genome-wide analysis of genetic alterations in acute lymphoblastic leukaemia. Nature 2007, 446: 758–764. 10.1038/nature05690View ArticlePubMedGoogle Scholar
- Mullighan CG, Zhang J, Harvey RC, Collins-Underwood JR, Schulman BA, Phillips LA, Tasian SK, Loh ML, Su X, Liu W, et al.: JAK mutations in high-risk childhood acute lymphoblastic leukemia. PNAS Supplements 2009, 106: 9414–9418. 10.1073/pnas.0811761106View ArticleGoogle Scholar
- Coyaud E, Struski S, Dastugue N, Brousset P, Broccardo C, Bradtke J: PAX5-AUTS2 fusion resulting from t(7;9)(q11.2;p13.2) can now be classified as recurrent in B cell acute lymphoblastic leukemia. Leuk Res 2010, 34: e323-e325. 10.1016/j.leukres.2010.07.035View ArticlePubMedGoogle Scholar
- Denk D, Nebral K, Bradtke J, Pass G, Moricke A, Attarbaschi A, Strehl S: PAX5-AUTS2: a recurrent fusion gene in childhood B-cell precursor acute lymphoblastic leukemia. Leuk Res 2012, 36: e178-e181. 10.1016/j.leukres.2012.04.015View ArticlePubMedGoogle Scholar
- Mitelman F, Johansson B, Mertens F: Mitelman database of chromosome aberrations and gene fusions in cancer. 2013.http://cgap.nci.nih.gov/Chromosomes/Mitelman Google Scholar
- Raimondi SC, Zhou Y, Mathew S, Shurtleff SA, Sandlund JT, Rivera GK, Behm FG, Pui CH: Reassessment of the prognostic significance of hypodiploidy in pediatric patients with acute lymphoblastic leukemia. Cancer 2003, 98: 2715–2722. 10.1002/cncr.11841View ArticlePubMedGoogle Scholar
- van Zutven LJ, van Drunen E, de Bont JM, Wattel MM, Den Boer ML, Pieters R, Hagemeijer A, Slater RM, Beverloo HB: CDKN2 deletions have no prognostic value in childhood precursor-B acute lymphoblastic leukaemia. Leukemia 2005, 19: 1281–1284. 10.1038/sj.leu.2403769View ArticlePubMedGoogle Scholar
- Cartwright RA, Gurney KA, Moorman AV: Sex ratios and the risks of haematological malignancies. Br J Haematol 2002, 118: 1071–1077. 10.1046/j.1365-2141.2002.03750.xView ArticlePubMedGoogle Scholar
- Bousquet M, Dastugue N, Brousset P: t(7;9)(q11;p13). 2007.http://AtlasGeneticsOncology.org/Anomalies/t0709q11p13ID1195.html Google Scholar
This article is published under license to BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.