Proteasome inhibition targets the KMT2A transcriptional complex in acute lymphoblastic leukemia
Jennifer L Kamens, Stephanie Nance, Cary Koss, Beisi Xu, Anitria Cotton, Jeannie W Lam, Elizabeth A R Garfinkle, Pratima Nallagatla, Amelia M R Smith, Sharnise Mitchell, Jing Ma, Duane Currier, William C Wright, Kanisha Kavdia, Vishwajeeth R Pagala, Wonil Kim, LaShanale M Wallace, Ji-Hoon Cho, Yiping Fan, Aman Seth, Nathaniel Twarog, John K Choi, Esther A Obeng, Mark E Hatley, Monika L Metzger, Hiroto Inaba, Sima Jeha, Jeffrey E Rubnitz, Junmin Peng, Taosheng Chen, Anang A Shelat, R Kiplin Guy, Tanja A Gruber, Jennifer L Kamens, Stephanie Nance, Cary Koss, Beisi Xu, Anitria Cotton, Jeannie W Lam, Elizabeth A R Garfinkle, Pratima Nallagatla, Amelia M R Smith, Sharnise Mitchell, Jing Ma, Duane Currier, William C Wright, Kanisha Kavdia, Vishwajeeth R Pagala, Wonil Kim, LaShanale M Wallace, Ji-Hoon Cho, Yiping Fan, Aman Seth, Nathaniel Twarog, John K Choi, Esther A Obeng, Mark E Hatley, Monika L Metzger, Hiroto Inaba, Sima Jeha, Jeffrey E Rubnitz, Junmin Peng, Taosheng Chen, Anang A Shelat, R Kiplin Guy, Tanja A Gruber
Abstract
Rearrangments in Histone-lysine-N-methyltransferase 2A (KMT2Ar) are associated with pediatric, adult and therapy-induced acute leukemias. Infants with KMT2Ar acute lymphoblastic leukemia (ALL) have a poor prognosis with an event-free-survival of 38%. Herein we evaluate 1116 FDA approved compounds in primary KMT2Ar infant ALL specimens and identify a sensitivity to proteasome inhibition. Upon exposure to this class of agents, cells demonstrate a depletion of histone H2B monoubiquitination (H2Bub1) and histone H3 lysine 79 dimethylation (H3K79me2) at KMT2A target genes in addition to a downregulation of the KMT2A gene expression signature, providing evidence that it targets the KMT2A transcriptional complex and alters the epigenome. A cohort of relapsed/refractory KMT2Ar patients treated with this approach on a compassionate basis had an overall response rate of 90%. In conclusion, we report on a high throughput drug screen in primary pediatric leukemia specimens whose results translate into clinically meaningful responses. This innovative treatment approach is now being evaluated in a multi-institutional upfront trial for infants with newly diagnosed ALL.
Conflict of interest statement
The authors declare no competing interests.
© 2023. The Author(s).
Figures
References
- Pieters R, et al. Outcome of infants younger than 1 year with acute lymphoblastic leukemia treated with the interfant-06 protocol: results from an international phase III randomized study. J. Clin. Oncol. 2019;37:2246–2256. doi: 10.1200/JCO.19.00261.
- Pui CH, et al. Treating childhood acute lymphoblastic leukemia without cranial irradiation. N. Engl. J. Med. 2009;360:2730–2741. doi: 10.1056/NEJMoa0900386.
- Meyer C, et al. The MLL recombinome of acute leukemias in 2017. Leukemia. 2018;32:273–284. doi: 10.1038/leu.2017.213.
- Andersson AK, et al. The landscape of somatic mutations in infant MLL-rearranged acute lymphoblastic leukemias. Nat. Genet. 2015;47:330–337. doi: 10.1038/ng.3230.
- Bernt KM, et al. MLL-rearranged leukemia is dependent on aberrant H3K79 methylation by DOT1L. Cancer Cell. 2011;20:66–78. doi: 10.1016/j.ccr.2011.06.010.
- Daigle SR, et al. Selective killing of mixed lineage leukemia cells by a potent small-molecule DOT1L inhibitor. Cancer Cell. 2011;20:53–65. doi: 10.1016/j.ccr.2011.06.009.
- Stein EMG-MG, et al. The DOT1L inhibitor EPZ-5676: safety and activity in relapsed/refractory patients with MLL-rearranged leukemia. Blood. 2014;124:387. doi: 10.1182/blood.V124.21.387.387.
- Pieters R, et al. Relation between age, immunophenotype and in vitro drug resistance in 395 children with acute lymphoblastic leukemia–implications for treatment of infants. Leukemia. 1998;12:1344–1348. doi: 10.1038/sj.leu.2401129.
- Ramakers-van Woerden NL, et al. In vitro drug-resistance profile in infant acute lymphoblastic leukemia in relation to age, MLL rearrangements and immunophenotype. Leukemia. 2004;18:521–529. doi: 10.1038/sj.leu.2403253.
- Szczepanek J, et al. Differential ex vivo activity of bortezomib in newly diagnosed paediatric acute lymphoblastic and myeloblastic leukaemia. Anticancer Res. 2010;30:2119–2124.
- Boccadoro M, Morgan G, Cavenagh J. Preclinical evaluation of the proteasome inhibitor bortezomib in cancer therapy. Cancer Cell Int. 2005;5:18. doi: 10.1186/1475-2867-5-18.
- Liu H, et al. Proteasome inhibitors evoke latent tumor suppression programs in pro-B MLL leukemias through MLL-AF4. Cancer Cell. 2014;25:530–542. doi: 10.1016/j.ccr.2014.03.008.
- Prenzel T, et al. Estrogen-dependent gene transcription in human breast cancer cells relies upon proteasome-dependent monoubiquitination of histone H2B. Cancer Res. 2011;71:5739–5753. doi: 10.1158/0008-5472.CAN-11-1896.
- Mimnaugh EG, Chen HY, Davie JR, Celis JE, Neckers L. Rapid deubiquitination of nucleosomal histones in human tumor cells caused by proteasome inhibitors and stress response inducers: effects on replication, transcription, translation, and the cellular stress response. Biochemistry. 1997;36:14418–14429. doi: 10.1021/bi970998j.
- Lee JS, et al. Histone crosstalk between H2B monoubiquitination and H3 methylation mediated by COMPASS. Cell. 2007;131:1084–1096. doi: 10.1016/j.cell.2007.09.046.
- Zhu B, et al. Monoubiquitination of human histone H2B: the factors involved and their roles in HOX gene regulation. Mol. Cell. 2005;20:601–611. doi: 10.1016/j.molcel.2005.09.025.
- McGinty RK, Kim J, Chatterjee C, Roeder RG, Muir TW. Chemically ubiquitylated histone H2B stimulates hDot1L-mediated intranucleosomal methylation. Nature. 2008;453:812–816. doi: 10.1038/nature06906.
- Wang E, et al. Histone H2B ubiquitin ligase RNF20 is required for MLL-rearranged leukemia. Proc. Natl Acad. Sci. USA. 2013;110:3901–3906. doi: 10.1073/pnas.1301045110.
- Stumpel DJ, et al. Connectivity mapping identifies HDAC inhibitors for the treatment of t(4;11)-positive infant acute lymphoblastic leukemia. Leukemia. 2012;26:682–692. doi: 10.1038/leu.2011.278.
- Ahmad K, et al. Inhibition of class I HDACs abrogates the dominant effect of MLL-AF4 by activation of wild-type MLL. Oncogenesis. 2014;3:e127. doi: 10.1038/oncsis.2014.39.
- Kikuchi J, et al. Histone deacetylases are critical targets of bortezomib-induced cytotoxicity in multiple myeloma. Blood. 2010;116:406–417. doi: 10.1182/blood-2009-07-235663.
- Carew JS, Giles FJ, Nawrocki ST. Histone deacetylase inhibitors: mechanisms of cell death and promise in combination cancer therapy. Cancer Lett. 2008;269:7–17. doi: 10.1016/j.canlet.2008.03.037.
- Dimopoulos M, et al. Vorinostat or placebo in combination with bortezomib in patients with multiple myeloma (VANTAGE 088): a multicentre, randomised, double-blind study. Lancet Oncol. 2013;14:1129–1140. doi: 10.1016/S1470-2045(13)70398-X.
- Premkumar DR, Jane EP, Agostino NR, DiDomenico JD, Pollack IF. Bortezomib-induced sensitization of malignant human glioma cells to vorinostat-induced apoptosis depends on reactive oxygen species production, mitochondrial dysfunction, Noxa upregulation, Mcl-1 cleavage, and DNA damage. Mol. Carcinog. 2013;52:118–133. doi: 10.1002/mc.21835.
- Simms-Waldrip T, et al. The aggresome pathway as a target for therapy in hematologic malignancies. Mol. Genet. Metab. 2008;94:283–286. doi: 10.1016/j.ymgme.2008.03.012.
- Catley L, et al. Aggresome induction by proteasome inhibitor bortezomib and alpha-tubulin hyperacetylation by tubulin deacetylase (TDAC) inhibitor LBH589 are synergistic in myeloma cells. Blood. 2006;108:3441–3449. doi: 10.1182/blood-2006-04-016055.
- Zhang J, Zhong Q. Histone deacetylase inhibitors and cell death. Cell Mol. Life Sci. 2014;71:3885–3901. doi: 10.1007/s00018-014-1656-6.
- Bai B, et al. Deep multilayer brain proteomics identifies molecular networks in Alzheimer’s disease progression. Neuron. 2020;105:975–991 e977. doi: 10.1016/j.neuron.2019.12.015.
- Zhang X, et al. Proteome-wide identification of ubiquitin interactions using UbIA-MS. Nat. Protoc. 2018;13:530–550. doi: 10.1038/nprot.2017.147.
- Twarog NR, Stewart E, Hammill CV, Shelat AA. BRAID: a unifying paradigm for the analysis of combined drug action. Sci. Rep. 2016;6:25523. doi: 10.1038/srep25523.
- Parker C, et al. Effect of mitoxantrone on outcome of children with first relapse of acute lymphoblastic leukaemia (ALL R3): an open-label randomised trial. Lancet. 2010;376:2009–2017. doi: 10.1016/S0140-6736(10)62002-8.
- Messinger Y, et al. Phase I study of bortezomib combined with chemotherapy in children with relapsed childhood acute lymphoblastic leukemia (ALL): a report from the therapeutic advances in childhood leukemia (TACL) consortium. Pediatr. Blood Cancer. 2010;55:254–259. doi: 10.1002/pbc.22456.
- Messinger YH, et al. Bortezomib with chemotherapy is highly active in advanced B-precursor acute lymphoblastic leukemia: Therapeutic Advances in Childhood Leukemia & Lymphoma (TACL) Study. Blood. 2012;120:285–290. doi: 10.1182/blood-2012-04-418640.
- Kaspers GJ, et al. Improved outcome in pediatric relapsed acute myeloid leukemia: results of a randomized trial on liposomal daunorubicin by the International BFM Study Group. J. Clin. Oncol. 2013;31:599–607. doi: 10.1200/JCO.2012.43.7384.
- Koss C, et al. Targeted inhibition of the MLL transcriptional complex by proteosome inhibitors elicits a high response rate in relapsed/refractory MLL rearranged leukemia. Blood. 2014;124:972–972. doi: 10.1182/blood.V124.21.972.972.
- Cheung LC, et al. Preclinical evaluation of carfilzomib for infant KMT2A-rearranged acute lymphoblastic leukemia. Front Oncol. 2021;11:631594. doi: 10.3389/fonc.2021.631594.
- Walters BJ, Zovkic IB. Building up and knocking down: an emerging role for epigenetics and proteasomal degradation in systems consolidation. Neuroscience. 2015;300:39–52. doi: 10.1016/j.neuroscience.2015.05.005.
- Harned TM, Gaynon P. Relapsed acute lymphoblastic leukemia: current status and future opportunities. Curr. Oncol. Rep. 2008;10:453–458. doi: 10.1007/s11912-008-0070-3.
- Horton TM, et al. Toxicity assessment of molecularly targeted drugs incorporated into multiagent chemotherapy regimens for pediatric acute lymphocytic leukemia (ALL): review from an international consensus conference. Pediatr. Blood Cancer. 2010;54:872–878. doi: 10.1002/pbc.22414.
- Ko RH, et al. Outcome of patients treated for relapsed or refractory acute lymphoblastic leukemia: a Therapeutic Advances in Childhood Leukemia Consortium study. J. Clin. Oncol. 2010;28:648–654. doi: 10.1200/JCO.2009.22.2950.
- Horton TM, et al. Bortezomib interactions with chemotherapy agents in acute leukemia in vitro. Cancer Chemother. Pharmacol. 2006;58:13–23. doi: 10.1007/s00280-005-0135-z.
- Van der Velden VH, et al. Prognostic significance of minimal residual disease in infants with acute lymphoblastic leukemia treated within the Interfant-99 protocol. Leukemia. 2009;23:1073–1079. doi: 10.1038/leu.2009.17.
- Hadley, W. Ggplot2 (Springer Science+Business Media, LLC, 2016).
- Shechter D, Dormann HL, Allis CD, Hake SB. Extraction, purification and analysis of histones. Nat. Protoc. 2007;2:1445–1457. doi: 10.1038/nprot.2007.202.
- Ritchie ME, et al. limma powers differential expression analyses for RNA-sequencing and microarray studies. Nucleic Acids Res. 2015;43:e47. doi: 10.1093/nar/gkv007.
- Andersson AK, et al. The landscape of somatic mutations in infant MLL-rearranged acute lymphoblastic leukemias. Nat. Genet. 2015;47:330. doi: 10.1038/ng.3230.
- Frank SR, Schroeder M, Fernandez P, Taubert S, Amati B. Binding of c-Myc to chromatin mediates mitogen-induced acetylation of histone H4 and gene activation. Genes Dev. 2001;15:2069–2082. doi: 10.1101/gad.906601.
- Orlando DA, et al. Quantitative ChIP-Seq normalization reveals global modulation of the epigenome. Cell Rep. 2014;9:1163–1170. doi: 10.1016/j.celrep.2014.10.018.
- Li H, Durbin R. Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics. 2009;25:1754–1760. doi: 10.1093/bioinformatics/btp324.
- Tischler G, Leonard S. biobambam: tools for read pair collation based algorithms on BAM files. Source Code Biol. Med. 2014;9:13. doi: 10.1186/1751-0473-9-13.
- Li H, et al. The sequence alignment/map format and SAMtools. Bioinformatics. 2009;25:2078–2079. doi: 10.1093/bioinformatics/btp352.
- Landt SG, et al. ChIP-seq guidelines and practices of the ENCODE and modENCODE consortia. Genome Res. 2012;22:1813–1831. doi: 10.1101/gr.136184.111.
- Yang X, et al. Differentiation of human pluripotent stem cells into neurons or cortical organoids requires transcriptional co-regulation by UTX and 53BP1. Nat. Neurosci. 2019;22:362–373. doi: 10.1038/s41593-018-0328-5.
- Kharchenko PV, Tolstorukov MY, Park PJ. Design and analysis of ChIP-seq experiments for DNA-binding proteins. Nat. Biotechnol. 2008;26:1351–1359. doi: 10.1038/nbt.1508.
- Ramírez F, et al. deepTools2: a next generation web server for deep-sequencing data analysis. Nucleic Acids Res. 2016;44:W160–W165. doi: 10.1093/nar/gkw257.
- Guenther MG, et al. Aberrant chromatin at genes encoding stem cell regulators in human mixed-lineage leukemia. Genes Dev. 2008;22:3403–3408. doi: 10.1101/gad.1741408.
- Law CW, Chen Y, Shi W, Smyth GK. voom: precision weights unlock linear model analysis tools for RNA-seq read counts. Genome Biol. 2014;15:R29. doi: 10.1186/gb-2014-15-2-r29.
- Bai B, et al. Deep profiling of proteome and phosphoproteome by isobaric labeling, extensive liquid chromatography, and mass spectrometry. Methods Enzymol. 2017;585:377–395. doi: 10.1016/bs.mie.2016.10.007.
- Wang X, et al. JUMP: a tag-based database search tool for peptide identification with high sensitivity and accuracy. Mol. Cell Proteom. 2014;13:3663–3673. doi: 10.1074/mcp.O114.039586.
- Gong J, et al. The C. elegans taste receptor homolog LITE-1 is a photoreceptor. Cell. 2017;168:325. doi: 10.1016/j.cell.2016.12.040.
- Tan H, et al. Integrative proteomics and phosphoproteomics profiling reveals dynamic signaling networks and bioenergetics pathways underlying T cell activation. Immunity. 2017;46:488–503. doi: 10.1016/j.immuni.2017.02.010.
- Nesvizhskii AI, Aebersold R. Interpretation of shotgun proteomic data: the protein inference problem. Mol. Cell Proteom. 2005;4:1419–1440. doi: 10.1074/mcp.R500012-MCP200.
- Warlick ED, Cao Q, Miller J. Bortezomib and vorinostat in refractory acute myelogenous leukemia and high-risk myelodysplastic syndromes: produces stable disease but at the cost of high toxicity. Leukemia. 2013;27:1789–1791. doi: 10.1038/leu.2013.61.
- Garcia-Manero G, et al. SWOG S1203: a randomized phase III study of standard cytarabine plus daunorubicin (7+3) therapy versus idarubicin with high dose cytarabine (IA) with or without vorinostat (IA+V) in younger patients with previously untreated acute myeloid leukemia (AML) Blood. 2016;128:901–901. doi: 10.1182/blood.V128.22.901.901.
- Waldschmidt JM, et al. Safety and efficacy of vorinostat, bortezomib, doxorubicin and dexamethasone in a phase I/II study for relapsed or refractory multiple myeloma (VERUMM study: vorinostat in elderly, relapsed and unfit multiple myeloma) Haematologica. 2018;103:e473–e479. doi: 10.3324/haematol.2018.189969.
- Keller A, et al. Vorinostat (V), bortezomib (B), doxorubicin (Dox) and dexamethasone (Dex, VBDD) in relapsed or refractory multiple myeloma patients (pts): results of an open, non-comparative, phase I/II investigator initiated trial (IIT) Clin. Lymphoma Myeloma Leuk. 2015;15:e276–e277. doi: 10.1016/j.clml.2015.07.572.
- Deutsch, E. W. et al. The ProteomeXchange consortium at 10 years: 2023 update. Nucleic Acids Res.51, D1539–D1548 (2023).
- Perez-Riverol Y, et al. The PRIDE database resources in 2022: a hub for mass spectrometry-based proteomics evidences. Nucleic Acids Res. 2022;50:D543–D552. doi: 10.1093/nar/gkab1038.
Source: PubMed