Molecular Diagnosis of FLT3 Mutations in Acute Myeloid Leukemia Patients

Background. FLT3 gene is an important prognostic molecular marker in acute myeloid leukemia (AML). However, the detection of FLT3 mutations presents a challenge.

Aim. To compare techniques used for the detection of FLT3 mutations, and to develop a test-system based on polymerase chain reaction (PCR) for quick and reliable determination of FLT3 mutation status.

Materials & Methods. Bone marrow samples obtained from AML patients were subjected to examination. To detect FLT3-ITD и FLT3-TKD mutations PCR was performed with subsequent agarose gel electrophoresis visualization. The results were verified by Sanger sequencing. The data obtained using our test-system were compared with widely applied commercial kit ‘FLT3 Mutation Assay for Gel Detection’ by Invivoscribe.

Results. To determine the FLT3 mutation status a PCR test was developed. This technique was validated on 22 bone marrow samples obtained from AML patients. FLT3-ITD mutation was detected in 4 patients, 3 patients showed FLT3-TKD mutation. In 1 patient both mutations were identified. These results fully corresponded to the molecular genetic analysis of FLT3, performed by ‘FLT3 Mutation Assay for Gel Detection’. The chosen technique was validated using Sanger sequencing data analysis.

Conclusion. The article offers the review of all existing FLT3 mutation screening techniques and describes the experience of developing the PCR test for FLT3-ITD and FLT3-TKD mutation detection. The chosen technique is affordable and easy to use compared with the others. The present study with its applied nature can provide guidance for both doctors and researchers.

• E.K. Zaikova VA Almazov National Medical Research Center, 2 Akkuratova str., Saint Petersburg, Russian Federation, 197341; Institute of Citology, 4 Tikhoretskii pr-t, Saint Petersburg, Russian Federation, 194064 ; ФГБУ «НМИЦ им. В.А. Алмазова» Минздрава России, ул. Аккуратова, д. 2, Санкт-Петербург, Российская Федерация, 197341; ФГБУН «Институт цитологии РАН», Тихорецкий пр-т, д. 4, Санкт-Петербург, Российская Федерация, 194064
• Ekaterina Vasil’evna Belotserkovskaya VA Almazov National Medical Research Center, 2 Akkuratova str., Saint Petersburg, Russian Federation, 197341; Institute of Citology, 4 Tikhoretskii pr-t, Saint Petersburg, Russian Federation, 194064 ; ФГБУ «НМИЦ им. В.А. Алмазова» Минздрава России, ул. Аккуратова, д. 2, Санкт-Петербург, Российская Федерация, 197341; ФГБУН «Институт цитологии РАН», Тихорецкий пр-т, д. 4, Санкт-Петербург, Российская Федерация, 194064
• D.V. Zaytsev VA Almazov National Medical Research Center, 2 Akkuratova str., Saint Petersburg, Russian Federation, 197341 ; ФГБУ «НМИЦ им. В.А. Алмазова» Минздрава России, ул. Аккуратова, д. 2, Санкт-Петербург, Российская Федерация, 197341
• A.V. Petukhov VA Almazov National Medical Research Center, 2 Akkuratova str., Saint Petersburg, Russian Federation, 197341; Institute of Citology, 4 Tikhoretskii pr-t, Saint Petersburg, Russian Federation, 194064 ; ФГБУ «НМИЦ им. В.А. Алмазова» Минздрава России, ул. Аккуратова, д. 2, Санкт-Петербург, Российская Федерация, 197341; ФГБУН «Институт цитологии РАН», Тихорецкий пр-т, д. 4, Санкт-Петербург, Российская Федерация, 194064
• O.A. Fedorova Institute of Citology, 4 Tikhoretskii pr-t, Saint Petersburg, Russian Federation, 194064 ; ФГБУН «Институт цитологии РАН», Тихорецкий пр-т, д. 4, Санкт-Петербург, Российская Федерация, 194064
• D.V. Motorin VA Almazov National Medical Research Center, 2 Akkuratova str., Saint Petersburg, Russian Federation, 197341 ; ФГБУ «НМИЦ им. В.А. Алмазова» Минздрава России, ул. Аккуратова, д. 2, Санкт-Петербург, Российская Федерация, 197341
• V.V. Ivanov VA Almazov National Medical Research Center, 2 Akkuratova str., Saint Petersburg, Russian Federation, 197341 ; ФГБУ «НМИЦ им. В.А. Алмазова» Минздрава России, ул. Аккуратова, д. 2, Санкт-Петербург, Российская Федерация, 197341
• A.Yu. Zaritskey VA Almazov National Medical Research Center, 2 Akkuratova str., Saint Petersburg, Russian Federation, 197341 ; ФГБУ «НМИЦ им. В.А. Алмазова» Минздрава России, ул. Аккуратова, д. 2, Санкт-Петербург, Российская Федерация, 197341
• L.L. Girshova VA Almazov National Medical Research Center, 2 Akkuratova str., Saint Petersburg, Russian Federation, 197341 ; ФГБУ «НМИЦ им. В.А. Алмазова» Минздрава России, ул. Аккуратова, д. 2, Санкт-Петербург, Российская Федерация, 197341

1. Kiyoi H, Naoe T, Yokota S, et al. Internal tandem duplication of FLT3 associated with leukocytosis in acute promyelocytic leukemia. 1997;11(9):1447–52. doi: 10.1038/sj.leu.2400756. DOI: https://doi.org/10.1038/sj.leu.2400756
2. Блау О.В. Мутации генов при острых миелоидных лейкозах. Клиническая онкогематология. 2016;9(3):245–56. doi: 10.21320/2500-2139-2016-9-3-245-256.
3. [Blau OV. Genetic Mutations in Acute Myeloid Leukemia. Clinical oncohematology. 2016;9(3):245–56. doi: 10.21320/2500-2139-2016-9-3-245-256. (In Russ)] DOI: https://doi.org/10.21320/2500-2139-2016-9-3-245-256
4. Gu T, Nardone J, Wang Y, et al. Survey of Activated FLT3 Signaling in Leukemia. PLoS ONE. 2011;6(4):e19169. doi: 10.1371/journal.pone.0019169. DOI: https://doi.org/10.1371/journal.pone.0019169
5. Deeb KK, Smonskey MT, Defedericis H-C, et al. Deletion and deletion/insertion mutations in the juxtamembrane domain of the FLT-3 gene in adult acute myeloid leukemia. Leuk Res Rep. 2014;3(2):86–9. doi: 10.1016/j.lrr.2013.09.003. DOI: https://doi.org/10.1016/j.lrr.2013.09.003
6. Sandhofer N, Bauer J, Reiter K, et al. The new and recurrent FLT3 juxtamembrane deletion mutation shows a dominant negative effect on the wild-type FLT3 receptor. Sci Rep. 2016;6(1):28032. doi: 10.1038/srep28032. DOI: https://doi.org/10.1038/srep28032
7. Thiede C, Steudel C, Mohr B, et al. Analysis of FLT3-activating mutations in 979 patients with acute myelogenous leukemia: association with FAB subtypes and identification of subgroups with poor prognosis. Blood. 2002;99(12):4326–35. doi: 10.1182/blood.v99.12.4326. DOI: https://doi.org/10.1182/blood.V99.12.4326
8. Metzeler K, Herold T, Rothenberg-Thurley M, et al. Spectrum and prognostic relevance of driver gene mutations in acute myeloid leukemia. Blood. 2016;128(5):686–98. doi: 10.1182/blood-2016-01-693879. DOI: https://doi.org/10.1182/blood-2016-01-693879
9. Schnittger S, Bacher U, Haferlach C, et al. Diversity of the juxtamembrane and TKD1 mutations (Exons 13–15) in the FLT3 gene with regards to mutant load, sequence, length, localization, and correlation with biological data. Genes Chromos Cancer. 2012;51(10):910–24. doi: 10.1002/gcc.21975. DOI: https://doi.org/10.1002/gcc.21975
10. Kottaridis P, Gale R, Frew M, et al. The presence of a FLT3 internal tandem duplication in patients with acute myeloid leukemia (AML) adds important prognostic information to cytogenetic risk group and response to the first cycle of chemotherapy: analysis of 854 patients from the United Kingdom Medical Research Council AML 10 and 12 trials. Blood. 2001;98(6):1752–9. doi: 10.1182/blood.v98.6.1752. DOI: https://doi.org/10.1182/blood.V98.6.1752
11. Moreno I, Martin G, Bolufer P, et al. Incidence and prognostic value of FLT3 internal tandem duplication and D835 mutations in acute myeloid leukemia. Haematologica. 2003;88(1):19–24.
12. Bacher U, Haferlach C, Kern W, et al. Prognostic relevance of FLT3-TKD mutations in AML: the combination matters—an analysis of 3082 patients. Blood. 2008;111(5):2527–37. doi: 10.1182/blood-2007-05-091215. DOI: https://doi.org/10.1182/blood-2007-05-091215
13. Moore AS, Faisal A, Gonzalez de Castro D, et al. Selective FLT3 inhibition of FLT3-ITD+ acute myeloid leukaemia resulting in secondary D835Y mutation: a model for emerging clinical resistance patterns. Leukemia. 2012;26(7):1462–70. doi: 10.1038/leu.2012.52. DOI: https://doi.org/10.1038/leu.2012.52
14. Bagrintseva K, Geisenhof S, Kern R, et al. FLT3-ITD-TKD dual mutants associated with AML confer resistance to FLT3 PTK inhibitors and cytotoxic agents by overexpression of Bcl-x(L). Blood. 2005;105(9):3679–85. doi: 10.1182/blood-2004-06-2459. DOI: https://doi.org/10.1182/blood-2004-06-2459
15. Dohner H, Estey E, Grimwade D, et al. Diagnosis and management of AML in adults: 2017 ELN recommendations from an international expert panel. Blood. 2017;129(4):424–47. doi: 10.1182/blood-2016-08-733196. DOI: https://doi.org/10.1182/blood-2016-08-733196
16. O’Donnell MR, Tallman MS, Abboud CN, et al. Acute myeloid leukemia, version 3.2017, NCCN Clinical Practice Guidelines in Oncology. J Natl Compr Canc Netw. 2017;15(7):926–57. doi: 10.6004/jnccn.2017.0116. DOI: https://doi.org/10.6004/jnccn.2017.0116
17. Nakao M, Yokota S, Iwai T, et al. Internal tandem duplication of the flt3 gene found in acute myeloid leukemia. Leukemia. 1996;10(12):1911–8.
18. Kim Y, Lee GD, Park J, et al. Quantitative fragment analysis of FLT3-ITD efficiently identifying poor prognostic group with high mutant allele burden or long ITD length. Blood Cancer J. 2015;5(8):e336. doi: 10.1038/bcj.2015.61. DOI: https://doi.org/10.1038/bcj.2015.61
19. Lin PH, Lin CC, Yang HI, et al. Prognostic impact of allogeneic hematopoietic stem cell transplantation for acute myeloid leukemia patients with internal tandem duplication of FLT3. Leuk Res. 2013;37(3):287–92. doi: 10.1016/j.leukres.2012.10.005. DOI: https://doi.org/10.1016/j.leukres.2012.10.005
20. Grunwald MR, Tseng LH, Lin MT, et al. Improved FLT3 internal tandem duplication PCR assay predicts outcome after allogeneic transplant for acute myeloid leukemia. Biol Blood Marrow Transplant. 2014;20(12):1989–95. doi: 10.1016/j.bbmt.2014.08.015. DOI: https://doi.org/10.1016/j.bbmt.2014.08.015
21. Murphy KM, Levis M, Hafez MJ, et al. Detection of FLT3 internal tandem duplication and D835 mutations by a multiplex polymerase chain reaction and capillary electrophoresis assay. J Mol Diagn. 2003;5(2):96–102. doi: 10.1016/s1525-1578(10)60458-8. DOI: https://doi.org/10.1016/S1525-1578(10)60458-8
22. Stirewalt DL, Willman CL, Radich JP. Quantitative, real-time polymerase chain reactions for FLT3 internal tandem duplications are highly sensitive and specific. Leuk Res. 2001;25(12):1085–8. doi: 10.1016/s0145-2126(01)00087-x. DOI: https://doi.org/10.1016/S0145-2126(01)00087-X
23. Beretta C, Gaipa G, Rossi V, et al. Development of a quantitative-PCR method for specific FLT3/ITD monitoring in acute myeloid leukemia. Leukemia. 2004;18(8):1441–4. doi: 10.1038/sj.leu.2403409. DOI: https://doi.org/10.1038/sj.leu.2403409
24. Daver N, Schlenk RF, Russell NH, et al. Targeting FLT3 mutations in AML: review of current knowledge and evidence. Leukemia. 2019;33(2):299–312. doi: 10.1038/s41375-018-0357-9. DOI: https://doi.org/10.1038/s41375-018-0357-9
25. Patnaik MM. The importance of FLT3 mutational analysis in acute myeloid leukemia. Leuk Lymphoma. 2018;59(10):2273–86. doi: 10.1080/10428194.2017.1399312. DOI: https://doi.org/10.1080/10428194.2017.1399312
26. Kamps R, Brandao RD, Bosch BJ, et al. Next-generation sequencing in oncology: genetic diagnosis, risk prediction and cancer classification. Int J Mol Sci. 2017;18(2):308. doi: 10.3390/ijms18020308. DOI: https://doi.org/10.3390/ijms18020308
27. Chin EL, da Silva C, Hegde M. Assessment of clinical analytical sensitivity and specificity of next-generation sequencing for detection of simple and complex mutations. BMC Genet. 2013;14(1):6. doi: 10.1186/1471-2156-14-6. DOI: https://doi.org/10.1186/1471-2156-14-6
28. Bibault JE, Figeac M, Helevaut N, et al. Next-generation sequencing of FLT3 internal tandem duplications for minimal residual disease monitoring in acute myeloid leukemia. Oncotarget. 2015;6(26):22812–21. doi: 10.18632/oncotarget.4333. DOI: https://doi.org/10.18632/oncotarget.4333
29. Spencer DH, Abel HJ, Lockwood CM, et al. Detection of FLT3 Internal Tandem Duplication in Targeted, Short-Read-Length, Next-Generation Sequencing Data. J Mol Diagn. 2013;15(1):81–93. doi: 10.1016/j.jmoldx.2012.08.001. DOI: https://doi.org/10.1016/j.jmoldx.2012.08.001
30. Au CH, Wa A, Ho DN, et al. Clinical evaluation of panel testing by next-generation sequencing (NGS) for gene mutations in myeloid neoplasms. Diagn Pathol. 2016;11(1):11. doi: 10.1186/s13000-016-0456-8. DOI: https://doi.org/10.1186/s13000-016-0456-8
31. Abdelhamid E, Preudhomme C, Helevaut N, et al. Minimal residual disease monitoring based on FLT3 internal tandem duplication in adult acute myeloid leukemia. Leuk Res. 2012;36(3):316–23. doi: 10.1016/j.leukres.2011.11.002. DOI: https://doi.org/10.1016/j.leukres.2011.11.002
32. Schranz K, Hubmann M, Harin E, et al. Clonal heterogeneity of FLT3-ITD detected by high-throughput amplicon sequencing correlates with adverse prognosis in acute myeloid leukemia. Oncotarget. 2018;9(53):30128–45. doi: 10.18632/oncotarget.25729. DOI: https://doi.org/10.18632/oncotarget.25729
33. Thiede C, Prior T, Lavorgna S, et al. FLT3 mutation Assay Laboratory Cross Validation: Results from the CALGB 10603/Ratify Trial in Patients with Newly Diagnosed FLT3-Mutated Acute Myeloid Leukemia (AML). Blood. 2018;132(Suppl_1):2800. doi: 10.1182/blood-2018-99-112127. DOI: https://doi.org/10.1182/blood-2018-99-112127
34. Сабурова И.Ю., Горбунова А.В., Слободнюк К.Ю. и др. Выявление внутренних тандемных дупликаций и мутации D835Y в гене FLT3 у пациентов с острым миелобластным лейкозом. Ученые записки Санкт-Петербургского государственного медицинского университета имени академика И.П. Павлова. 2010;XVII(3):48–51.
35. [Saburova IYu, Gorbunova AV, Slobodnyuk KYu, et al. Detection of FLT3 internal tandem duplications and D835Y mutation in patients with acute myeloid leukemia. Uchenye zapiski Sankt-Peterburgskogo gosudarstvennogo meditsinskogo universiteta imeni akademika I.P. Pavlova. 2010;XVII(3):48–51. (In Russ)]
36. Петрова Е.В., Мартынкевич И.С., Полушкина Л.Б. и др. Клинические, гематологические и молекулярно-генетические особенности острых миелобластных лейкозов с мутациями в генах FLT3, CKIT, NRAS и NPM1. Гематология и трансфузиология. 2016;61(2):72–80. doi: 10.18821/0234-5730-2016-61-2-72-80.
37. [Petrova EV, Martynkevich IS, Polushkina LB, et al. Clinical, hematological and molecular-genetic features of acute myeloid leukemia with mutations in FLT3, CKIT, NRAS and NPM1. Russian journal of hematology and transfusiology. 2016;61(2):72–80. doi: 10.18821/0234-5730-2016-61-2-72-80. (In Russ)]
38. Гук Л.В., Савицкая Т.В., Домнинский Д.А. и др. Анализ частоты и прогностического значения мутаций генов FLT3, c-KIT и NPM1 у детей с острым миелобластным лейкозом. Онкогематология. 2009;4(4):27–32.
39. [Guk LV, Savitskaya TV, Domninskii DA, et al. Analysis of incidence and prognostic value of FLT3, c-KIT and NPM1 genes mutations in children with acute myeloid leukemia. Onkogematologiya. 2009;4(4):27–32. (In Russ)]
40. Виноградов А.В. Разработка технологии детекции мутаций генов CDKN2A/ARF, FLT3, KIT, NPM1, NRAS, TET2, TP53, WT1 при острых миелоидных лейкозах. Российский онкологический журнал. 2013;4:34–5. DOI: https://doi.org/10.17816/onco40036
41. [Vinogradov AV. Development of the technique for CDKN2A/ARF, FLT3, KIT, NPM1, NRAS, TET2, TP53, WT1 genes mutation detection in acute myeloid leukemia. Rossiiskii onkologicheskii zhurnal. 2013;4:34–5. (In Russ)]
42. Kiyoi H, Naoe T, Nakano Y, et al. Prognostic implication of FLT3 and N-RAS gene mutations in acute myeloid leukemia. Blood. 1999;93(9):3074–80.
43. Gari M, Abuzenadah A, Chaudhary A, et al. Detection of FLT3 oncogene mutations in acute myeloid leukemia using conformation sensitive gel electrophoresis. Int J Mol Sci. 2008;9(11):2194–204. doi: 10.3390/ijms9112194. DOI: https://doi.org/10.3390/ijms9112194
44. Sly N, Gaspar K. Midostaurin for the management of FLT3-mutated acute myeloid leukemia and advanced systemic mastocytosis. Am J Health-Syst Pharm. 2019;76(5):268–74. doi: 10.1093/ajhp/zxy050. DOI: https://doi.org/10.1093/ajhp/zxy050
45. Bazarbachi AH, Hamed RA, Malard F, et al. Allogeneic transplant for FLT3-ITD mutated AML: a focus on FLT3 inhibitors before, during, and after transplant. Ther Adv Hematol. 2019;10:1–14. doi: 10.1177/2040620719882666. DOI: https://doi.org/10.1177/2040620719882666
46. Levis M. FLT3 mutations in acute myeloid leukemia: what is the best approach in 2013? Hematology Am Soc Hematol Educ Program. 2013;2013:220–6. doi: 10.1182/asheducation-2013.1.220. DOI: https://doi.org/10.1182/asheducation-2013.1.220