Acute myeloid leukemia (AML) with co-occurring NUP98-NSD1 and FLT3-ITD is associated with unfavorable prognosis and represents a particularly challenging treatment group. To identify novel effective therapies for this AML subtype, we screened patient cells and engineered cell models with over 300 compounds. We found that mouse hematopoietic progenitors co-expressing NUP98-NSD1 and FLT3-ITD had significantly increased sensitivity to FLT3 and MEK-inhibitors compared to cells expressing either aberration alone (P < 0.001). The cells expressing NUP98-NSD1 alone had significantly increased sensitivity to BCL2-inhibitors (P = 0.029). Furthermore, NUP98-NSD1+/FLT3-ITD+ patient cells were also very sensitive to BCL2-inhibitor navitoclax, although the highest select sensitivity was found to SRC/ABL-inhibitor dasatinib (mean IC50 = 2.2 nM). Topoisomerase inhibitor mitoxantrone was the least effective drug against NUP98-NSD1+/FLT3-ITD+ AML cells. Of the 25 significant hits, four remained significant also compared to NUP98-NSD1-/FLT3-ITD+ AML patients. We found that SRC/ABL-inhibitor dasatinib is highly synergistic with BCL2-inhibitor navitoclax in NUP98-NSD1+/FLT3-ITD+ cells. Gene expression analysis supported the potential relevance of dasatinib and navitoclax by revealing significantly higher expression of BCL2A1, FGR, and LCK in NUP98-NSD1+/FLT3-ITD+ patients compared to healthy CD34+ cells. Our data suggest that dasatinib–navitoclax combination may offer a clinically relevant treatment strategy for AML with NUP98-NSD1 and concomitant FLT3-ITD.
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Papaemmanuil E, Dohner H, Campbell PJ. Genomic classification in acute myeloid leukemia. N Engl J Med. 2016;375:900–1.
Gough SM, Slape CI, Aplan PD. NUP98 gene fusions and hematopoietic malignancies: common themes and new biologic insights. Blood. 2011;118:6247–57.
Soler G, Kaltenbach S, Dobbelstein S, Broccardo C, Radford I, Mozziconacci MJ, et al. Identification of GSX2 and AF10 as NUP98 partner genes in myeloid malignancies. Blood Cancer J. 2013;3:e124.
Lim HH, An GD, Woo KS, Kim KH, Kim JM, Kim SH, et al. NUP98 Rearrangement in Acute Myelomonocytic Leukemia with t(11;19)(p15; p12): The First Case Report Worldwide. Ann Lab Med. 2017;37:285–7.
Nakamura T, Largaespada DA, Lee MP, Johnson LA, Ohyashiki K, Toyama K, et al. Fusion of the nucleoporin gene NUP98 to HOXA9 by the chromosome translocation t(7;11)(p15; p15) in human myeloid leukaemia. Nat Genet. 1996;12:154–8.
Saw J, Curtis DJ, Hussey DJ, Dobrovic A, Aplan PD, Slape CI. The fusion partner specifies the oncogenic potential of NUP98 fusion proteins. Leuk Res. 2013;37:1668–73.
Wu X, Kasper LH, Mantcheva RT, Mantchev GT, Springett MJ, van Deursen JM. Disruption of the FG nucleoporin NUP98 causes selective changes in nuclear pore complex stoichiometry and function. Proc Natl Acad Sci USA. 2001;98:3191–6.
Struski S, Lagarde S, Bories P, Puiseux C, Prade N, Cuccuini W, et al. NUP98 is rearranged in 3.8% of pediatric AML forming a clinical and molecular homogenous group with a poor prognosis. Leukemia. 2017;31:565–72.
Bisio V, Zampini M, Tregnago C, Manara E, Salsi V, Di Meglio A, et al. NUP98-fusion transcripts characterize different biological entities within acute myeloid leukemia: a report from the AIEOP-AML group. Leukemia. 2017;31:974–7.
Mertens F, Johansson B, Fioretos T, Mitelman F. The emerging complexity of gene fusions in cancer. Nat Rev Cancer. 2015;15:371–81.
Jaju RJ, Fidler C, Haas OA, Strickson AJ, Watkins F, Clark K, et al. A novel gene, NSD1, is fused to NUP98 in the t (5; 11)(q35; p15. 5) in de novo childhood acute myeloid leukemia. Blood. 2001;98:1264–7.
Brown J, Jawad M, Twigg SR, Saracoglu K, Sauerbrey A, Thomas AE, et al. A cryptic t(5;11)(q35; p15.5) in 2 children with acute myeloid leukemia with apparently normal karyotypes, identified by a multiplex fluorescence in situ hybridization telomere assay. Blood. 2002;99:2526–31.
Hollink IH, van den Heuvel-Eibrink MM, Arentsen-Peters ST, Pratcorona M, Abbas S, Kuipers JE, et al. NUP98/NSD1 characterizes a novel poor prognostic group in acute myeloid leukemia with a distinct HOX gene expression pattern. Blood. 2011;118:3645–56.
Ostronoff F, Othus M, Gerbing RB, Loken MR, Raimondi SC, Hirsch BA, et al. NUP98/NSD1 and FLT3/ITD coexpression is more prevalent in younger AML patients and leads to induction failure: a COG and SWOG report. Blood. 2014;124:2400–7.
Akiki S, Dyer SA, Grimwade D, Ivey A, Abou-Zeid N, Borrow J, et al. NUP98-NSD1 fusion in association with FLT3-ITD mutation identifies a prognostically relevant subgroup of pediatric acute myeloid leukemia patients suitable for monitoring by real time quantitative PCR. Genes Chromosomes Cancer. 2013;52:1053–64.
Shiba N, Ichikawa H, Taki T, Park MJ, Jo A, Mitani S, et al. NUP98-NSD1 gene fusion and its related gene expression signature are strongly associated with a poor prognosis in pediatric acute myeloid leukemia. Genes Chromosomes Cancer. 2013;52:683–93.
Thanasopoulou A, Tzankov A, Schwaller J. Potent co-operation between the NUP98-NSD1 fusion and the FLT3-ITD mutation in acute myeloid leukemia induction. Haematologica. 2014;99:1465–71.
Pemovska T, Kontro M, Yadav B, Edgren H, Eldfors S, Szwajda A, et al. Individualized systems medicine strategy to tailor treatments for patients with chemorefractory acute myeloid leukemia. Cancer Discov. 2013;3:1416–29.
Pemovska T, Johnson E, Kontro M, Repasky GA, Chen J, Wells P, et al. Axitinib effectively inhibits BCR-ABL1(T315I) with a distinct binding conformation. Nature. 2015;519:102–5.
Kontro M, Kumar A, Majumder MM, Eldfors S, Parsons A, Pemovska T, et al. HOX gene expression predicts response to BCL-2 inhibition in acute myeloid leukemia. Leukemia. 2017;31:301–9.
Zhang JH, Chung TD, Oldenburg KR. A simple statistical parameter for use in evaluation and validation of high throughput screening assays. J Biomol Screen. 1999;4:67–73.
Yadav B, Pemovska T, Szwajda A, Kulesskiy E, Kontro M, Karjalainen R, et al. Quantitative scoring of differential drug sensitivity for individually optimized anticancer therapies. Sci Rep. 2014;4:5193.
Yadav B, Wennerberg K, Aittokallio T, Tang J. Searching for drug synergy in complex dose-response landscapes using an interaction potency model. Comput Struct Biotechnol J. 2015;13:504–13.
Ianevski A, He L, Aittokallio T, Tang J. SynergyFinder: a web application for analyzing drug combination dose-response matrix data. Bioinformatics. 2017;33:2413–5.
Dobin A, Davis CA, Schlesinger F, Drenkow J, Zaleski C, Jha S, et al. STAR: ultrafast universal RNA-seq aligner. Bioinformatics. 2013;29:15–21.
Robinson MD, Oshlack A. A scaling normalization method for differential expression analysis of RNA-seq data. Genome Biol. 2010;11:R25.
Kumar A, Kankainen M, Parsons A, Kallioniemi O, Mattila P, Heckman CA. The impact of RNA sequence library construction protocols on transcriptomic profiling of leukemia. BMC Genom. 2017;18:629.
Kivioja JL, Lopez Marti JM, Kumar A, Kontro M, Edgren H, Parsons A, et al. Chimeric NUP98-NSD1 transcripts from the cryptic t(5;11)(q35.2; p15.4) in adult de novo acute myeloid leukemia. Leuk Lymphoma. 2018;59:725–32.
Yoshimoto G, Miyamoto T, Jabbarzadeh-Tabrizi S, Iino T, Rocnik JL, Kikushige Y, et al. FLT3-ITD up-regulates MCL-1 to promote survival of stem cells in acute myeloid leukemia via FLT3-ITD-specific STAT5 activation. Blood. 2009;114:5034–43.
Hayakawa F, Towatari M, Kiyoi H, Tanimoto M, Kitamura T, Saito H, et al. Tandem-duplicated Flt3 constitutively activates STAT5 and MAP kinase and introduces autonomous cell growth in IL-3-dependent cell lines. Oncogene. 2000;19:624–31.
Crescenzi B, Nofrini V, Barba G, Matteucci C, Di Giacomo D, Gorello P, et al. NUP98/11p15 translocations affect CD34+ cells in myeloid and T lymphoid leukemias. Leuk Res. 2015;39:769–72.
Rayasam GV, Wendling O, Angrand PO, Mark M, Niederreither K, Song L, et al. NSD1 is essential for early post-implantation development and has a catalytically active SET domain. EMBO J. 2003;22:3153–63.
Wang GG, Cai L, Pasillas MP, Kamps MP. NUP98-NSD1 links H3K36 methylation to Hox-A gene activation and leukaemogenesis. Nat Cell Biol. 2007;9:804–12.
Laukkanen S, Gronroos T, Polonen P, Kuusanmaki H, Mehtonen J, Cloos J, et al. In silico and preclinical drug screening identifies dasatinib as a targeted therapy for T-ALL. Blood. Cancer J. 2017;7:e604.
Deenik W, Beverloo HB, van der Poel-van de Luytgaarde SC, Wattel MM, van Esser JW, Valk PJ, et al. Rapid complete cytogenetic remission after upfront dasatinib monotherapy in a patient with a NUP214-ABL1-positive T-cell acute lymphoblastic leukemia. Leukemia. 2009;23:627–9.
Deshpande AJ, Deshpande A, Sinha AU, Chen L, Chang J, Cihan A, et al. AF10 regulates progressive H3K79 methylation and HOX gene expression in diverse AML subtypes. Cancer Cell. 2014;26:896–908.
Franks TM, McCloskey A, Shokirev MN, Benner C, Rathore A, Hetzer MW. Nup98 recruits the Wdr82-Set1A/COMPASS complex to promoters to regulate H3K4 trimethylation in hematopoietic progenitor cells. Genes Dev. 2017;31:2222–34.
Drake KM, Watson VG, Kisielewski A, Glynn R, Napper AD. A sensitive luminescent assay for the histone methyltransferase NSD1 and other SAM-dependent enzymes. Assay Drug Dev Technol. 2014;12:258–71.
Ofran Y. Concealed dagger in FLT3/ITD+AML. Blood. 2014;124:2317–9.
Fasan A, Haferlach C, Alpermann T, Kern W, Haferlach T, Schnittger S. A rare but specific subset of adult AML patients can be defined by the cytogenetically cryptic NUP98-NSD1 fusion gene. Leukemia. 2013;27:245–8.
Borkin D, He S, Miao H, Kempinska K, Pollock J, Chase J, et al. Pharmacologic inhibition of the Menin-MLL interaction blocks progression of MLL leukemia in vivo. Cancer Cell. 2015;27:589–602.
Song Y, Wu F, Wu J. Targeting histone methylation for cancer therapy: enzymes, inhibitors, biological activity and perspectives. J Hematol Oncol. 2016;9:49.
Niu X, Wang G, Wang Y, Caldwell JT, Edwards H, Xie C, et al. Acute myeloid leukemia cells harboring MLL fusion genes or with the acute promyelocytic leukemia phenotype are sensitive to the Bcl-2-selective inhibitor ABT-199. Leukemia. 2014;28:1557–60.
Konopleva M, Pollyea DA, Potluri J, Chyla B, Hogdal L, Busman T, et al. Efficacy and Biological Correlates of Response in a Phase II Study of Venetoclax Monotherapy in Patients with Acute Myelogenous Leukemia. Cancer Discov. 2016;6:1106–17.
Benito JM, Godfrey L, Kojima K, Hogdal L, Wunderlich M, Geng H, et al. MLL-Rearranged Acute Lymphoblastic Leukemias Activate BCL-2 through H3K79 Methylation and Are Sensitive to the BCL-2-Specific Antagonist ABT-199. Cell Rep. 2015;13:2715–27.
Xu H, Valerio DG, Eisold ME, Sinha A, Koche RP, Hu W, et al. NUP98 Fusion Proteins Interact with the NSL and MLL1 Complexes to Drive Leukemogenesis. Cancer Cell. 2016;30:863–78.
Lindauer M, Hochhaus A. Dasatinib. Recent Results Cancer Res. 2014;201:27–65.
Larrosa-Garcia M, Baer MR. FLT3 Inhibitors in acute myeloid leukemia: current status and future directions. Mol Cancer Ther. 2017;16:991–1001.
Kurtz SE, Eide CA, Kaempf A, Khanna V, Savage SL, Rofelty A, et al. Molecularly targeted drug combinations demonstrate selective effectiveness for myeloid- and lymphoid-derived hematologic malignancies. Proc Natl Acad Sci USA. 2017;114:E7554–63.
Tromp JM, Geest CR, Breij EC, Elias JA, van Laar J, Luijks DM, et al. Tipping the Noxa/Mcl-1 balance overcomes ABT-737 resistance in chronic lymphocytic leukemia. Clin Cancer Res. 2012;18:487–98.
Leonard JT, Rowley JS, Eide CA, Traer E, Hayes-Lattin B, Loriaux M, et al. Targeting BCL-2 and ABL/LYN in Philadelphia chromosome-positive acute lymphoblastic leukemia. Sci Transl Med. 2016;8:354ra114.
Goff DJ, Court Recart A, Sadarangani A, Chun HJ, Barrett CL, Krajewska M, et al. A Pan-BCL2 inhibitor renders bone-marrow-resident human leukemia stem cells sensitive to tyrosine kinase inhibition. Cell Stem Cell. 2013;12:316–28.
Kohl TM, Hellinger C, Ahmed F, Buske C, Hiddemann W, Bohlander SK, et al. BH3 mimetic ABT-737 neutralizes resistance to FLT3 inhibitor treatment mediated by FLT3-independent expression of BCL2 in primary AML blasts. Leukemia. 2007;21:1763–72.
Minami Y, Yamamoto K, Kiyoi H, Ueda R, Saito H, Naoe T. Different antiapoptotic pathways between wild-type and mutated FLT3: insights into therapeutic targets in leukemia. Blood. 2003;102:2969–75.
Hewitt SM, Hamada S, McDonnell TJ, Rauscher FJ 3rd, Saunders GF. Regulation of the proto-oncogenes bcl-2 and c-myc by the Wilms’ tumor suppressor gene WT1. Cancer Res. 1995;55:5386–9.
Morrison DJ, English MA, Licht JD. WT1 induces apoptosis through transcriptional regulation of the proapoptotic Bcl-2 family member Bak. Cancer Res. 2005;65:8174–82.
Dohner H, Estey E, Grimwade D, Amadori S, Appelbaum FR, Buchner T, et al. Diagnosis and management of AML in adults: 2017 ELN recommendations from an international expert panel. Blood. 2017;129:424–47.
Arber DA, Orazi A, Hasserjian R, Thiele J, Borowitz MJ, Le Beau MM, et al. The 2016 revision to the World Health Organization classification of myeloid neoplasms and acute leukemia. Blood. 2016;127:2391–405.
We thank the patients and healthy donors who participated in this study. We would also like to thank staff at the FIMM High-Throughput Biomedicine Unit for their expert technical assistance with the drug screening experiments and the FIMM Sequencing Unit for their assistance with sequence analysis. We are grateful to laboratory technicians Alun Parsons, Minna Suvela, and Siv Knaappila for sample processing. We acknowledge personnel at the Biomedicum Helsinki FACS core and Functional Genomics Unit for their help with flow cytometry and RCV-tests. This work was supported by grants from Finnish Funding Agency for Technology and Innovation (grant number 40336/09). Personal grant support was received from the Väre Foundation for Pediatric Cancer Research, Ida Montin Foundation, the Cancer Society of Finland, and Finnish Hematology Association (JK). JS and AT were supported by grants from the Swiss Cancer League (KFS-3487-08-2014).