Application of cytogenetic risk factors and molecular markers, assessed by multiplex ligation-dependent probe amplification for prognosis of outcome in pediatric B-cell precursor acute lymphoblastic leukemia do not bring any advantage over detection of isolated IKZF1 deletion

The purpose of the current work was the estimation of prognostic significance of cytogenetic and molecular markers, assessed by multiplex ligation-dependent probe amplification (MLPA) in 142 cases of pediatric B-cell precursor acute lymphoblastic leukemia (BCP-ALL) patients. Good-risk genetic (GEN-GR) group consisted of 114 patients carrying either ETV6-RUNX1 or high hyperdiploidy together with normal copy-number status for all 8 genes (IKZF1, PAX5, ETV6, RB1, BTG1, EBF1, CDKN2A/2B and PAR1) or isolated deletions affecting ETV6/ PAX5/BTG1 and ETV6 deletions with a single additional deletion of BTG1/PAX5/CDKN2A/2B. All other patients (n = 28) were classified to genetic poor risk (GEN-PR) group. GEN-PR features were older age (p = 0.015), stratification to high-risk group of ALL-MB 2008 protocol (p = 0.001), higher initial WBC (p = 0.008), M3 marrow status on day 15 (p = 0.002) and lack of remission on day 36 (p = 0.039). GEN-PR patients had statistically significant lower event-free survival (EFS) (0.59 ± 0.11 vs 0.88 ± 0.03; p = 0.0008), overall survival (OS) (0.63 ± 0.15 vs 0.93 ± 0.02; p = 0.0050) and higher cumulative incidence of relapse (CIR) (0.38 ± 0.12 и 0.06 ± 0.02; p < 0.0001) in comparison to GEN-GR patients. Genetic risk group stratification retained its negative prognostic value in multivariate analysis affecting EFS (hazard ratio (HR) – 2.659; 95 % CI 1.047–6.755; p = 0.040) and CIR (HR – 3.864; 95 % CI 1.226–12.183; p = 0.021), nut did not influenced to OS (HR – 1.479; 95 % CI 0.356–6.139; p = 0.590). There was no prognostic significance of genetic risk group classifier in the “B-other ALL” group. Majority of unfavorable events (9 out of 10) and relapse (8 out of 9) in GEN-PR patients were revealed in case of IKZF1 deletion co-occurrence. Moreover all 15 patients carrying IKZF1 deletions were stratified to GEN-PR group. So when we added IKZF1 deletion as extra variable in the multivariate analysis genetic risk group classification lost its prognostic significance on EFS (HR – 0.696; 95 % CI 0.086–5.636; p = 0,735), and CIR (HR – 0.511; 95 % CI 0.053–4.924; p = 0.561), while IKZF1 deletion remained its prognostic value both to risk of unfavorable event (HR – 4.292; 95 % CI 1.521–12.911; p = 0.006) and risk of relapse (HR – 9.163; 95 % CI 3.131–26.815; p < 0.001). Thus, combination of cytogenetic risk group and MLPA markers did not bring any advantage over detection of isolated IKZF1 deletion for the estimation of prognosis in pediatric BCP-ALL. 

1. Mullighan C., Su X., Zhang J. et al.; Children’s Oncology Group. Deletion of IKZF1 and prognosis in acute lymphoblastic leukemia. N Engl J Med 2009;360(5):470–80. doi: 10.1056/NEJMoa0808253.

2. Kuiper R., Waanders E., van der Velden V. et al. IKZF1 deletions predict relapse in uniformly treated pediatric precursor B-ALL. Leukemia 2010;24(7):1258–64. doi: 10.1038/leu.2010.87.

3. Olsson L., Albitar F., Castor A. et al. Cooperative genetic changes in pediatric B-cell precursor acute lymphoblastic leukemia with deletions or mutations of IKZF1. Genes Chromosomes Cancer 2015;54(5):315–25. doi: 10.1002/ gcc.22245.

4. Boer J., van der Veer A., Rizopoulos D. et al. Prognostic value of rare IKZF1 deletion in childhood B-cell precursor acute lymphoblastic leukemia: an international collaborative study. Leukemia 2016;30(1):32–8. doi: 10.1038/leu.2015.199.

5. Dorge P., Meissner B., Zimmermann M. et al. IKZF1 deletion is an independent predictor of outcome in pediatric acute lymphoblastic leukemia treated according to the ALL-BFM 2000 protocol. Haematologica 2013;98(3):428– 32. doi: 10.3324/haematol.2011.056135.

6. Chen I.M., Harvey R., Mullighan C. et al. Outcome modeling with CRLF2, IKZF1, JAK, and minimal residual disease in pediatric acute lymphoblastic leukemia: a Children’s Oncology Group Study. Blood 2012;119(15):3512–22. doi: 10.1182/blood-2011-11-394221.

7. Palmi C., Valsecchi M.G., Longinotti G. et al. What is the relevance of Ikaros gene deletions as a prognostic marker in pediatric Philadelphia-negative B-cell precursor acute lymphoblastic leukemia? Haematologica 2013;98(8):1226–31. doi: 10.3324/haematol.2012.075432.

8. Ofverholm I., Tran A.N., Heyman M. et al. Impact of IKZF1 deletions and PAX5 amplifications in pediatric B-cell precursor ALL treated according to NOPHO protocols. Leukemia 2013;27(9):1936–9. doi: 10.1038/leu.2013.92.

9. Цаур Г.А., Друй А.Е., Солодовников А.Г. и др. Делеции гена IKZF1 – независимый прогностический фактор у детей с острым лимфобластным лейкозом из B-линейных предшественников. Онкогематология 2016;11(4):33–48. [Tsaur G.A., Druy A.E., Solodovnikov A.G. et al. IKZF1 deletions are independent prognostic factor in pediatric B-cell precursor acute lymphoblastic leukemia. Onkogematologiya = Oncohematology 2016;11(4):33–48. (In Russ.)].

10. Kuiper R., Schoenmakers E., van Reijmersdal S. et al. High-resolution genomic profiling of childhood ALL reveals novel recurrent genetic lesions affecting pathways involved in lymphocyte differentiation and cell cycle progression. Leukemia 2007;21(6):1258–66. doi: 10.1038/sj.leu.2404691.

11. Mullighan C., Goorha S., Radtke I. et al. Genome-wide analysis of genetic alterations in acute lymphoblastic leukaemia. Nature 2007;446(7137):758–64. doi: 10.1038/nature05690.

12. Mullighan C., Miller C., Radtke I. et al. BCR-ABL1 lymphoblastic leukaemia is characterized by the deletion of Ikaros. Nature 2008;453(7191):110–4. doi: 10.1038/nature06866.

13. Martinelli G., Iacobucci I., Storlazzi C.T. et al. IKZF1 (Ikaros) deletions in BCR-ABL1-positive acute lymphoblastic leukemia are associated with short disease-free survival and high rate of cumulative incidence of relapse: a GIMEMA AL WP report. J Clin Oncol 2009;27(31):5202–7. doi: 10.1200/JCO.2008.21.6408.

14. Nakayama H., Ishimaru F., Avitahl N. et al. Decreases in Ikaros activity correlate with blast crisis in patients with chronic myelogenous leukemia. Cancer Res 1999;59(16):3931–4. PMID: 10463586.

15. van der Veer A., Waanders E., Pieters R. et al. Independent prognostic value of BCR-ABL1-like signature and IKZF1 deletion, but not high CRLF2 expression, in children with B-cell precursor ALL. Blood 2013;122(15):2622–9. doi: 10.1182/ blood-2012-10-462358.

16. Buitenkamp T., Pieters R., Gallimore N. et al. Outcome in children with Down’s syndrome and acute lymphoblastic leukemia: role of IKZF1 deletions and CRLF2 aberrations. Leukemia 2012;26(10):2204–11. doi: 10.1038/leu.2012.84.

17. Moorman A., Ensor H., Richards S. et al. Prognostic effect of chromosomal abnormalities in childhood B-cell precursor acute lymphoblastic leukaemia: results from the UK Medical Research Council ALL97/99 randomised trial. Lancet Oncol 2010;11(5):429–38. doi: 10.1016/S1470-2045(10)70066-8.

18. Moorman A., Enshaei A., Schwab C. et al A novel integrated cytogenetic and genomic classification refines risk stratification in pediatric acute lymphoblastic leukemia. Blood 2014;124(9):1434–44. doi: 10.1182/blood-2014-03-562918.

19. Stanulla M., Dagdan E., Zaliova M. et al. IKZF1plus defines a new minimal residual disease-dependent very poor prognostic profile in pediatric B cell precursor acute lymphoblastic leukemia. JCO [Accepted for publication].

20. Литвинов Д.В., Карелин А.Ф., Романова К.И. и др. Лечение острого лимфобластного лейкоза у детей: современные возможности и нерешенные проблемы. Доктор.Ру 2015;(10):30–7. [Litvinov D.V., Karelin A.F., Romanova K.I. et al. Treatment of acute lymphoblastic leukemia in children: current possibilities and unsolved problems. Doctor.ru 2015;(10): 30–7. (In Russ.)].

21. Цаур Г.А., Попов А.М., Фечина Л.Г., Румянцев С.А. Методические основы диагностики и мониторинга минимальной остаточной болезни при острых лейкозах у детей первого года жизни. Онкогематология 2016;11(1):62–74. [Tsaur G.A., Popov A.M., Fechina L.G., Rumyantsev S.A. Methodological aspects of diagnostics and minimal residual disease monitoring in infant acute leukemias. Onkogematologia = Oncohematology 2016;11(1):62–74. (In Russ.)].

22. Попов А.М., Вержбицкая Т.Ю., Цаур Г.А. и др. Алгоритм применения проточной цитометрии для мониторинга минимальной остаточной болезни при CD10-негативном остром лимфобластном лейкозе из В-линейных предшественников. Вопросы диагностики в педиатрии 2012;5:31–5. [Popov A.M., Verzhbitskaya T.Yu., Tsaur G.A. et al. Methodology of flow cytometry application for minimal residual disease monitoring in childhood CD10-negative B-cell precursor acute lymphoblastic leukemia. Voprosy diagnostiki v pediatrii = Diagnostics in Pediatrics 2012;5:31–5. (In Russ.)].

23. Попов А.М., Вержбицкая Т.Ю., Цаур Г.А. и др. Применение проточной цитометрии для определения минимальной остаточной болезни у детей с острым лимфобластным лейкозом, получающих терапию по протоколам со сниженной интенсивностью. Онкогематология 2015;10(4):44–55. [Popov А.M.,Verzhbitskaya Т.Yu., Tsaur G.A. et al. Flow cytometric minimal residual disease monitoring in children with acute lymphoblastic leukemia treated by regimens with reduced intensity. Onkogematologia = Oncohematology 2015;10(4): 44–55. (In Russ.)].

24. Patel S., Mason C., Glenn M. et al Genomic analysis of adult B-ALL identifies potential markers of shorter survival. Leuk Res 2017;56:44–51. doi: 10.1016/j.leukres.2017.01.034.

25. Caye A., Beldjord Kh., Mass-Malo K. et al. Breakpoint-specific multiplex polymerase chain reaction allows the detection of IKZF1 intragenic deletions and minimal residual disease monitoring in B-cell precursor acute lymphoblastic leukemia. Haematologica 2013;98(4):597–601. doi: 10.3324/haematol.2012.073965.

26. Schwab C., Jones L., Morrison H. et al. Evaluation of multiplex ligation-dependent probe amplification as a method for the detection of copy number abnormalities in B-cell precursor acute lymphoblastic leukemia. Genes Chromosomes Cancer 2010;49(12):1104–13. doi: 10.1002/gcc.20818.

27. Moorman A., Richards S., Robinson H. et al. Prognosis of children with acute lymphoblastic leukaemia (ALL) and intrachromosomal amplification of chromosome 21 (iAMP21). Blood 2007;109(6):2327–30. doi: 10.1182/blood-2006-08-040436.