Structure and prognostic signifi cance of 13q14 deletion in chronic lymphocytic leukemia

Introduction. 13q14 deletion is the most common chromosomal abnormality in chronic lymphocytic leukemia (CLL), and as the sole abnormality determines the most favorable prognosis of the disease. Using molecular genetic methods two subtypes of 13q14 deletion were identifi ed based on the size of the lost chromosomal material: small (type I) with the involvement of the D13S319 segment containing MIR15A/MIR16-1 and DLEU1 genes and large (type II) containing centromeric region of 13q14 involving RB1 gene. Data on the impact of type I and II deletions on the course of CLL are controversial.

Aim — to evaluate the prognostic signifi cance of different variants of 13q14 deletion in CLL.

Patients and methods. The study enrolled two cohorts of CLL patients. Cohort 1: 256 patients who were studied by FISH with DNA probes for detection of 13q14/D13S319, 11q23/ATM, 17p13/TP53 deletions, and trisomy 12 before immunochemotherapy. 101 patients with identifi ed 13q14/D13S319 deletion were analyzed with a DNA probe for RB1 locus for determination of deletion size (type I or type II). Cohort 2: 28 patients at different stages of the disease with deletion 13q14 detected by FISH were studied by using combination of standard and molecular cytogenetic methods (mFISH, mBAND, arrayCGH) to clarify the structure of 13q abnormalities.

Results. In Cohort 1 chromosomal aberrations were detected in 75 % of patients: 13q deletion — 52 % (isolated — 36 % of all cases and 48 % of cases with deletion), 11q deletion — 19 %, +12 — 13 %, 17p deletion — 6 %. 13q14 deletion type I was detected in 56 %, type II — in 44 % of patients. Type II deletion correlated with the presence of 11q deletion (p = 0.05). Isolated deletions of type I and II were found in 61 and 39 %, respectively. Biallelic deletion was identifi ed in 12.7 % of patients with 13q deletion. Statistically signifi cant differences in OS were obtained in type I and II groups of patients with isolated 13q14 deletions: median OS was not reached and made 67.5 months, respectively, p = 0.05. In Cohort 2 structural abnormalities of chromosome 13 by conventional cytogenetic analysis (CCA) were identifi ed in 50 % of cases: 13q deletion — 11 cases; translocations involving 13q14 — 6 cases. In 5 cases with biallelic deletion identifi ed by FISH, 13q14 deletion by CCA was detected in two patients, and only in one allele.

Conclusion. In general, 13q14 deletion is a cytogenetic factor of favorable prognosis for CLL but its structure is heterogeneous. Loss of tumor suppressor RB1 (type II deletion) negatively affects OS in patients treated with immunochemotherapy

1. Mayr C., Speicher M.R., Kofl er D.M., et al. Chromosomal translocations are associated with poor prognosis in chronic lymphocytic leukemia. Blood. 2006; 107(2): 742–51. DOI: 10.1182/blood-2005-05-2093.

2. Haferlach C., Dicker F., Schnittger S., et al. Comprehensive genetic characterization of CLL: A study on 506 cases analysed with chromosome banding analysis, interphase FISH, IgVHstatus and immunophenotyping. Leukemia. 2007; 21(12): 2442–51. DOI: 10.1038/sj.leu.2404935.

3. Mosca L., Fabris S., Lionetti M., et al. Integrative genomics analyses reveal molecularly distinct subgroups of B-cell chronic lymphocytic leukemia patients with 13q14 deletion. Clin Cancer Res. 2010; 16(23): 5641–53. DOI: 10.1158/1078-0432.CCR-10-0151.

4. Döhner H., Stilgenbauer S., Benner A., et al. Genomic aberrations and survival in chronic lymphocytic leukemia. N Engl J Med. 2000; 343(26): 1910–6. DOI: 10.1056/nejm200012283432602.

5. Klein U., Lia M., Crespo M., et al. The DLEU2/miR-15a/16-1 cluster controls B cell proliferation and its deletion leads to chronic lymphocytic leukemia. Cancer Cell. 2010; 17(1): 28–40. DOI: 10.1016/j.ccr.2009.11.019.

6. Klein U., Dalla-Favera R. New insights into the pathogenesis of chronic lymphocytic leukemia. Semin Cancer Biol. 2010; 20(6): 377–83. DOI: 10.1016/j.semcancer.2010.10.012.

7. Dewald G.W., Brockman S.R., Paternoster S.F., et al. Chromosome anomalies detected by interphase fl uorescence in situ hybridization: Correlation with significant biological features of B-cell chronic lymphocytic leukaemia. Br J Haematol. 2003; 121(2): 287–95. DOI: 10.1046/j.1365-2141.2003.04265.x.

8. Van Dyke D.L., Werner L., Rassenti L.Z., et al. The Dohner fl uorescence in situ hybridization prognostic classifi cation of chronic lymphocytic leukaemia (CLL): The CLL Research Consortium experience. Br J Haematol. 2016; 173(1): 105–13. DOI: 10.1111/bjh.13933.

9. O’Brien S., Jones J.A., Coutre S.E., et al. Ibrutinib for patients with relapsed or refractory chronic lymphocytic leukaemia with 17p deletion (RESONATE-17): A phase 2, open-label, multicentre study. Lancet Oncol. 2016; 17(10): 1409–18. DOI: 10.1016/S1470-2045(16)30212-1.

10. Hammarsund M., Corcoran M.M., Wilson W., et al. Characterization of a novel B-CLL candidate gene — DLEU7 — located in the 13q14 tumor suppressor locus. FEBS Lett. 2004; 556(1–3): 75–80. DOI: 10.1016/S0014-5793(03)01371-1.

11. Palamarchuk A., Efanov A., Nazaryan N., et al. 13q14 deletions in CLL involve cooperating tumor suppressors. Blood. 2010; 115(19): 3916–22. DOI: 10.1182/blood-2009-10-249367.

12. Wolf S., Mertens D., Schaffner C., et al. B-cell neoplasia associated gene with multiple splicing (BCMS): The candidate B-CLL gene on 13q14 comprises more than 560 kb covering all critical regions. Hum Mol Genet. 2001; 10(12): 1275–85. DOI: 10.1093/hmg/10.12.1275.

13. Baranova A., Hammarsund M., Ivanov D., et al. Distinct organization of the candidate tumor suppressor gene RFP2 in human and mouse: Multiple mRNA isoforms in both species- and human-specifi c antisense transcript RFP2OS. Gene. 2003; 321(1–2): 103–12. DOI: 10.1016/j.gene.2003.08.007.

14. Edelmann J., Holzmann K., Miller F., et al. High-resolution genomic profi ling of chronic lymphocytic leukemia reveals new recurrent genomic alterations. Blood. 2012; 120(24): 4783–94. DOI: 10.1182/blood-2012-04-423517.

15. Kalachikov S., Migliazza A., Cayanis E., et al. Cloning and gene mapping of the chromosome 13q14 region deleted in chronic lymphocytic leukemia. Genomics. 1997; 42(3): 369–77. DOI: 10.1006/geno.1997.4747.

16. Calin G.A., Dumitru C.D., Shimizu M., et al. Frequent deletions and downregulation of micro-RNA genes miR15 and miR16 at 13q14 in chronic lymphocytic leukemia. Proc Natl Acad Sci U S A. 2002; 99(24): 15524–9. DOI: 10.1073/pnas.242606799.

17. Parker H., Rose-Zerilli M.J.J., Parker A., et al. 13q deletion anatomy and disease progression in patients with chronic lymphocytic leukemia. Leukemia. 2011; 25(3): 489–97. DOI: 10.1038/leu.2010.288.

18. Liu Y., Corcoran M., Rasool O., et al. Cloning of two candidate tumor suppressor genes within a 10 kb region on chromosome 13q14, frequently deleted in chronic lymphocytic leukemia. Oncogene. 1997; 15(20): 2463–73. DOI: 10.1038/sj.onc.1201643.

19. Calin G.A., Dumitru C.D., Shimizu M., et al. Frequent deletions and downregulation of micro-RNA genes miR15 and miR16 at 13q14 in chronic lymphocytic leukemia. Proc Natl Acad Sci U S A. 2002; 99(24): 15524–9. DOI: 10.1073/pnas.242606799

20. Cimmino A., Calin G.A., Fabbri M., et al. miR-15 and miR-16 induce apoptosis by targeting BCL2. Proc Natl Acad Sci U S A. 2005; 102(39): 13944–9. DOI: 10.1073/pnas.0506654102.

21. Cory S., Adams J.M. The BCL2 family: Regulators of the cellular life-or-death switch. Nat Rev Cancer. 2002; 2(9): 647–56. DOI: 10.1038/nrc883.

22. Cory S., Adams J.M. Killing cancer cells by fl ipping the Bcl-2/Bax switch. Cancer Cell. 2005; 8(1): 5–6. DOI: 10.1016/j.ccr.2005.06.012.

23. Sánchez-Beato M., Sánchez-Aguilera A., Piris M.A. Cell cycle deregulation in B-cell lymphomas. Blood. 2003; 101(4): 1220–35. DOI: 10.1182/blood-2002-07-2009.

24. Ouillette P., Erba H., Kujawski L., et al. Integrated genomic profi ling of chronic lymphocytic leukemia identifi es subtypes of deletion 13q14. Cancer Res. 2008; 68(4): 1012–21. DOI: 10.1158/0008-5472.CAN-07-3105.

25. Ouillette P., Collins R., Shakhan S., et al. The prognostic signifi cance of various 13q14 deletions in chronic lymphocytic leukemia. Clin Cancer Res. 2011; 17(21): 6778–90. DOI: 10.1158/1078-0432.CCR-11-0785.

26. Puiggros A., Blanco G., Espinet B. Genetic abnormalities in chronic lymphocytic leukemia: Where we are and where we go. Biomed Res Int. 2014; 2014: 435983. DOI: 10.1155/2014/435983.

27. Dal Bo M., Rossi F.M., Rossi D., et al. 13q14 deletion size and number of deleted cells both infl uence prognosis in chronic lymphocytic leukemia. Genes Chromosom Cancer. 2011; 50(8): 633–43. DOI: 10.1002/gcc.20885.

28. Yi S., Li H., Li Z., et al. The prognostic signifi cance of 13q deletions of different sizes in patients with B-cell chronic lymphoproliferative disorders: A retrospective study. Int J Hematol. 2017; 106(3): 418–25. DOI: 10.1007/s12185-017-2240-2.

29. Hallek M., Cheson B.D., Catovsky D., et al. iwCLL guidelines for diagnosis, indications for treatment, response assessment, and supportive management of CLL. Blood. 2018; 131(25): 2745–60. DOI: 10.1182/blood-2017-09-806398.

30. Binet J.L., Auquier A., Dighiero G., et al. A new prognostic classifi cation of chronic lymphocytic leukemia derived from a multivariate survival analysis. Cancer. 1981; 48(1): 198–206. DOI: 10.1002/1097-0142(19810701)48:1<198::aidcncr2820480131>3.0.co;2-v.

31. International Standing Committee on Human Cytogenomic Nomenclature, McGowan-Jordan J., Simons A., et al. ISCN: An international system for human cytogenomic nomenclature (2016). Karger, 2016.

32. Zakharova A.I., Obukhova T.N, Lorie Yu.Yu., et al. Cytogenetic disorders in chronic B-cell lymphoid leukemia: Relations with clinicobiological features and prognosis of the disease. Terapevticheskiy arkhiv. 2006; 78(7): 57–62. (In Russian).

33. Stilgenbauer S., Lichter P., Döhner H. Genetic features of B-cell chronic lymphocytic leukemia. Rev Clin Exp Hematol. 2000; 4(1): 48–72. DOI: 10.1046/j.1468-0734.2000.00003.x.

34. Huang L., Lang D., Geradts J., et al. Molecular and immunochemical analyses of RB1 and cyclin D1 in human ductal pancreatic carcinomas and cell lines. Mol Carcinog. 1996; 15(2): 85–95. DOI: 10.1002/(SICI)1098-2744(199602)15:2<85::AID-MC1>3.0.CO;2-Q.

35. Bester A.C., Roniger M., Oren Y.S., et al. Nucleotide defi ciency promotes genomic instability in early stages of cancer development. Cell. 2011; 145(3): 435–46. DOI: 10.1016/j.cell.2011.03.044.

36. Decker T., Schneller F., Kronschnabl M., et al. Immunostimulatory CpG-oligonucleotides induce functional high affi nity IL-2 receptors on B-CLL cells: Costimulation with IL-2 results in a highly immunogenic phenotype. Exp Hematol. 2000; 28(5): 558–68. DOI: 10.1016/s0301-472x(00)00144-2.

37. Decker T., Peschel C. Effect of immunostimulatory CpG-oligonucleotides in chronic lymphocytic leukemia B cells. Leuk Lymphoma. 2001; 42(3): 301–7. DOI: 10.3109/10428190109064586.

38. Kislitsyna M.A., Obukhova T.N., Alimova G.A., et al. The effi ciency of the use of oligonucleotide DSP30 in combination with interleukin-2 for the detection of chromosomal aberrations in patients with chronic lymphocytic leukemia. Gematologiya i transfuziologiya. 2019; 64(1): 22–34. DOI: 10.35754/0234-5730-2019-64-1-21-34. (In Russian).

39. Puiggros A., Venturas M., Salido M., et al. Interstitial 13q14 deletions detected in the karyotype and translocations with concomitant deletion at 13q14 in chronic lymphocytic leukemia: Different genetic mechanisms but equivalent poorer clinical outcome. Genes Chromosomes Cancer. 2014; 53(9): 788–97. DOI: 10.1002/gcc.22188.

40. Gardiner A.C., Corcoran M.M., Oscier D.G. Cytogenetic, fl uorescence in situ hybridisation, and clinical evaluation of translocations with concomitant deletion at 13q14 in chronic lymphocytic leukaemia. Genes Chromosom Cancer. 1997; 20(1): 73–81. DOI: 10.1002/(sici)1098-2264(199709)20:1<73::aidgcc11>3.0.co;2-g.

41. Hruba M., Dvorak P., Weberova L., Subrt I. Independent coexistence of clones with 13q14 deletion at reciprocal translocation breakpoint and 13q14 interstitial deletion in chronic lymphocytic leukemia. Leuk Lymphoma. 2012; 53(10): 2054–62. DOI: 10.3109/10428194.2012.668682.

42. Edelmann J., Tausch E., Landau D., et al. Frequent evolution of copy number alterations in CLL following fi rst-line treatment with FC ( R ) is enriched with TP53 alterations: Results from the CLL8 trial. Leukemia. 2017; 31(3): 734–8. DOI: 10.1038/leu.2016.317.

43. Berkova A., Zemanova Z., Trneny M., et al. Clonal evolution in chronic lymphocytic leukemia studied by interphase fl uorescence in-situ hybridization. Neoplasma. 2009; 56(5): 455–8. DOI: 10.4149/neo_2009_05_455.

44. Wawrzyniak E., Kotkowska A., Blonski J.Z., et al. Clonal evolution in CLL patients as detected by FISH versus chromosome banding analysis, and its clinical signifi cance. Eur J Haematol. 2014; 92(2): 91–101. DOI: 10.1111/ejh.12215.

45. Mertens D., Wolf S., Tschuch C., et al. Allelic silencing at the tumor-suppressor locus 13q14.3 suggests an epigenetic tumor-suppressor mechanism. Proc Natl Acad Sci U S A. 2006; 103(20): 7741–6. DOI: 10.1073/pnas.0600494103.

46. Chena C., Avalos J.S., Bezares R.F., et al. Biallelic deletion 13q14.3 in patients with chronic lymphocytic leukemia: Cytogenetic, FISH and clinical studies. Eur J Haematol. 2008; 81(2): 94–9. DOI: 10.1111/j.1600-0609.2008.01086.x.

47. Garg R., Wierda W., Ferrajoli A., et al. The prognostic difference of monoallelic versus biallelic deletion of 13q in chronic lymphocytic leukemia. Cancer. 2012; 118(14): 3531–7. DOI: 10.1002/cncr.26593.

48. Puiggros A., Delgado J., Rodriguez-Vicente A., et al. Biallelic losses of 13q do not confer a poorer outcome in chronic lymphocytic leukaemia: analysis of 627 patients with isolated 13q deletion. Br J Haematol. 2013; 163(1): 47–54. DOI: 10.1111/bjh.12479.

49. Grygalewicz B., Woroniecka R., Rygier J., et al. Monoallelic and biallelic deletions of 13q14 in a group of CLL/SLL patients investigated by CGH Haematological Cancer and SNP array (8x60K). Mol Cytogenet. 2016; 9: 1. DOI: 10.1186/s13039-015-0212-x.