BACKGROUND: The BCR::ABL1 is a hallmark of chronic myeloid leukemia (CML) and is also found in acute lymphoblastic leukemia (ALL). Most genomic breaks on the BCR side occur in two regions - Major and minor - leading to p210 and p190 fusion proteins, respectively. METHODS: By multiplex long-distance PCR or next-generation sequencing technology we characterized the BCR::ABL1 genomic fusion in 971 patients (adults and children, with CML and ALL: pediatric ALL: n = 353; pediatric CML: n = 197; adult ALL: n = 166; adult CML: n = 255 patients) and designed "Break-App" web tool to allow visualization and various analyses of the breakpoints. Pearson's Chi-Squared test, Kolmogorov-Smirnov test and logistic regression were used for statistical analyses. RESULTS: Detailed analysis showed a non-random distribution of breaks in both BCR regions, whereas ABL1 breaks were distributed more evenly. However, we found a significant difference in the distribution of breaks between CML and ALL. We found no association of breakpoints with any type of interspersed repeats or DNA motifs. With a few exceptions, the primary structure of the fusions suggests non-homologous end joining being responsible for the BCR and ABL1 gene fusions. Analysis of reciprocal ABL1::BCR fusions in 453 patients showed mostly balanced translocations without major deletions or duplications. CONCLUSIONS: Taken together, our data suggest that physical colocalization and chromatin accessibility, which change with the developmental stage of the cell (hence the difference between ALL and CML), are more critical factors influencing breakpoint localization than presence of specific DNA motifs.

Children's Cancer Institute Randwick Australia

CLIP Childhood Leukaemia Investigation Prague Prague Czech Republic

Department of Paediatric Haematology and Oncology 2nd Faculty of Medicine Charles University University Hospital Motol Prague Czech Republic

Department of Pediatrics University Hospital Schleswig Holstein Kiel Germany

Division of Hematology Department of Translational and Precision Medicine Sapienza University of Rome Rome Italy

Hematology laboratory AP HP Saint Louis hospital Université Paris Cité Paris France

Institute of Hematology and Blood Transfusion Prague Czech Republic

Institute of Pharmaceutical Biology Diagnostic Center of Acute Leukemia Goethe University Frankfurt Germany

Kids Cancer Centre Sydney Children's Hospital Randwick Sydney Australia

Medical Genetics School of Medicine and Surgery Univ Milano Bicocca Monza Italy

Pediatric Oncology and Hematology Department of Pediatrics and Adolescent Medicine University Hospital Erlangen Germany

School of Women's and Children's Health School of Medicine University of NSW Sydney Australia

Tettamanti Center Fondazione IRCCS San Gerardo dei Tintori Monza Italy

Zobrazit více v PubMed

Burmeister T, Groger D, Kuhn A, Hoelzer D, Thiel E, Reinhardt R. Fine structure of translocation breakpoints within the major breakpoint region in BCR-ABL1-positive leukemias. DNA Repair (Amst) 2011;10(11):1131–7. doi: 10.1016/j.dnarep.2011.08.010. PubMed DOI

Score J, Calasanz MJ, Ottman O, Pane F, Yeh RF, Sobrinho-Simoes MA, et al. Analysis of genomic breakpoints in p190 and p210 BCR-ABL indicate distinct mechanisms of formation. Leukemia. 2010;24(10):1742–50. doi: 10.1038/leu.2010.174. PubMed DOI

Krumbholz M, Goerlitz K, Albert C, Lawlor J, Suttorp M, Metzler M. Large amplicon droplet digital PCR for DNA-based monitoring of pediatric chronic myeloid leukaemia. J Cell Mol Med. 2019;14(10):14321. PubMed PMC

Ross DM, O’Hely M, Bartley PA, Dang P, Score J, Goyne JM, et al. Distribution of genomic breakpoints in chronic myeloid leukemia: analysis of 308 patients. Leukemia. 2013;27(10):2105–7. doi: 10.1038/leu.2013.116. PubMed DOI

Krumbholz M, Karl M, Tauer JT, Thiede C, Rascher W, Suttorp M, et al. Genomic BCR-ABL1 breakpoints in pediatric chronic myeloid leukemia. Genes Chromosomes Cancer. 2012;51(11):1045–53. doi: 10.1002/gcc.21989. PubMed DOI

Mattarucchi E, Guerini V, Rambaldi A, Campiotti L, Venco A, Pasquali F, et al. Microhomologies and interspersed repeat elements at genomic breakpoints in chronic myeloid leukemia. Genes Chromosomes Cancer. 2008;47(7):625–32. doi: 10.1002/gcc.20568. PubMed DOI

Hovorkova L, Zaliova M, Venn NC, Bleckmann K, Trkova M, Potuckova E, et al. Monitoring of childhood ALL using BCR-ABL1 genomic breakpoints identifies a subgroup with CML-like biology. Blood. 2017;129(20):2771–81. doi: 10.1182/blood-2016-11-749978. PubMed DOI

Linhartova J, Hovorkova L, Soverini S, Benesova A, Jaruskova M, Klamova H, et al. Characterization of 46 patient-specific BCR-ABL1 fusions and detection of SNPs upstream and downstream the breakpoints in chronic myeloid leukemia using next generation sequencing. Mol Cancer. 2015;14:89. doi: 10.1186/s12943-015-0363-8. PubMed DOI PMC

Machova Polakova K, Zizkova H, Zuna J, Motlova E, Hovorkova L, Gottschalk A, et al. Analysis of chronic myeloid leukaemia during deep molecular response by genomic PCR: a traffic light stratification model with impact on treatment-free remission. Leukemia. 2020;34(8):2113–24. doi: 10.1038/s41375-020-0882-1. PubMed DOI

Zaliova M, Fronkova E, Krejcikova K, Muzikova K, Mejstrikova E, Stary J, et al. Quantification of fusion transcript reveals a subgroup with distinct biological properties and predicts relapse in BCR/ABL-positive ALL: implications for residual disease monitoring. Leukemia. 2009;23(5):944–51. doi: 10.1038/leu.2008.386. PubMed DOI

Zuna J, Hovorkova L, Krotka J, Koehrmann A, Bardini M, Winkowska L, et al. Minimal residual disease in BCR::ABL1-positive acute lymphoblastic leukemia: different significance in typical ALL and in CML-like disease. Leukemia. 2022;36(12):2793–801. doi: 10.1038/s41375-022-01668-0. PubMed DOI

Zuna J, Hovorkova L, Krotka J, Winkowska L, Novak Z, Sramkova L, et al. Posttreatment positivity of BCR::ABL1 in acute lymphoblastic leukemia: should we keep track? Am J Hematol. 2023;98(10):E269–71. doi: 10.1002/ajh.27022. PubMed DOI

Lukes J Jr., Winkowska L, Zwyrtkova M, Starkova J, Sramkova L, Stary J et al. Identification of Fusion Gene breakpoints is feasible and facilitates accurate sensitive minimal residual disease monitoring on genomic level in patients with PML-RARA, CBFB-MYH11, and RUNX1-RUNX1T1. Hemasphere. 2020;4(6). PubMed PMC

Zaliova M, Zuna J, Winkowska L, Janotova I, Skorepova J, Lukes J, et al. Genomic DNA-based measurable residual disease monitoring in pediatric acute myeloid leukemia: unselected consecutive cohort study. Leukemia. 2024;38(1):21–30. doi: 10.1038/s41375-023-02083-9. PubMed DOI PMC

Venn NC, Huang L, Hovorkova L, Muskovic W, Wong M, Law T, et al. Measurable residual disease analysis in paediatric acute lymphoblastic leukaemia patients with ABL-class fusions. Br J Cancer. 2022;127(5):908–15. doi: 10.1038/s41416-022-01806-6. PubMed DOI PMC