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Modeling IKZF1 lesions in B-ALL reveals distinct chemosensitivity patterns and potential therapeutic vulnerabilities. Blood Adv 2021; 5:3876-3890. [PMID: 34492683 DOI: 10.1182/bloodadvances.2020002408] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2020] [Accepted: 05/26/2021] [Indexed: 12/25/2022] Open
Abstract
IKAROS family zinc finger 1 (IKZF1) alterations represent a diverse group of genetic lesions that are associated with an increased risk of relapse in B-cell acute lymphoblastic leukemia. Due to the heterogeneity of concomitant lesions, it remains unclear how IKZF1 abnormalities directly affect cell function and therapy resistance, and whether their consideration as a prognostic indicator is valuable in improving outcome. CRISPR/Cas9 strategies were used to engineer multiple panels of isogeneic lymphoid leukemia cell lines with a spectrum of IKZF1 lesions to measure changes in chemosensitivity, gene expression, cell cycle, and in vivo engraftment that can be linked to loss of IKAROS protein. IKZF1 knockout and heterozygous null cells displayed relative resistance to a number of common therapies for B-cell acute lymphoblastic leukemia, including dexamethasone, asparaginase, and daunorubicin. Transcription profiling revealed a stem/myeloid cell-like phenotype and JAK/STAT upregulation after IKAROS loss. A CRISPR homology-directed repair strategy was also used to knock-in the dominant-negative IK6 isoform into the endogenous locus, and a similar drug resistance profile, with the exception of retained dexamethasone sensitivity, was observed. Interestingly, IKZF1 knockout and IK6 knock-in cells both have significantly increased sensitivity to cytarabine, likely owing to marked downregulation of SAMHD1 after IKZF1 knockout. Both types of IKZF1 lesions decreased the survival time of xenograft mice, with higher numbers of circulating blasts and increased organ infiltration. Given these findings, exact specification of IKZF1 status in patients may be a beneficial addition to risk stratification and could inform therapy.
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Martinez-Høyer S, Deng Y, Parker J, Jiang J, Mo A, Docking TR, Gharaee N, Li J, Umlandt P, Fuller M, Jädersten M, Kulasekararaj A, Malcovati L, List AF, Hellström-Lindberg E, Platzbecker U, Karsan A. Loss of lenalidomide-induced megakaryocytic differentiation leads to therapy resistance in del(5q) myelodysplastic syndrome. Nat Cell Biol 2020; 22:526-533. [PMID: 32251398 DOI: 10.1038/s41556-020-0497-9] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2019] [Accepted: 02/28/2020] [Indexed: 12/11/2022]
Abstract
Interstitial deletion of the long arm of chromosome 5 (del(5q)) is the most common structural genomic variant in myelodysplastic syndromes (MDS)1. Lenalidomide (LEN) is the treatment of choice for patients with del(5q) MDS, but half of the responding patients become resistant2 within 2 years. TP53 mutations are detected in ~20% of LEN-resistant patients3. Here we show that patients who become resistant to LEN harbour recurrent variants of TP53 or RUNX1. LEN upregulated RUNX1 protein and function in a CRBN- and TP53-dependent manner in del(5q) cells, and mutation or downregulation of RUNX1 rendered cells resistant to LEN. LEN induced megakaryocytic differentiation of del(5q) cells followed by cell death that was dependent on calpain activation and CSNK1A1 degradation4,5. We also identified GATA2 as a LEN-responsive gene that is required for LEN-induced megakaryocyte differentiation. Megakaryocytic gene-promoter analyses suggested that LEN-induced degradation of IKZF1 enables a RUNX1-GATA2 complex to drive megakaryocytic differentiation. Overexpression of GATA2 restored LEN sensitivity in the context of RUNX1 or TP53 mutations by enhancing LEN-induced megakaryocytic differentiation. Screening for mutations that block LEN-induced megakaryocytic differentiation should identify patients who are resistant to LEN.
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Affiliation(s)
- Sergio Martinez-Høyer
- Michael Smith Genome Sciences Centre, BC Cancer Research Centre, Vancouver, British Columbia, Canada.,Department of Hematology, Erasmus Medical Centre, Rotterdam, the Netherlands
| | - Yu Deng
- Michael Smith Genome Sciences Centre, BC Cancer Research Centre, Vancouver, British Columbia, Canada.,Pathology and Laboratory Medicine, University of British Columbia, Vancouver, British Columbia, Canada
| | - Jeremy Parker
- Michael Smith Genome Sciences Centre, BC Cancer Research Centre, Vancouver, British Columbia, Canada
| | - Jihong Jiang
- Michael Smith Genome Sciences Centre, BC Cancer Research Centre, Vancouver, British Columbia, Canada.,Pathology and Laboratory Medicine, University of British Columbia, Vancouver, British Columbia, Canada
| | - Angela Mo
- Michael Smith Genome Sciences Centre, BC Cancer Research Centre, Vancouver, British Columbia, Canada.,Pathology and Laboratory Medicine, University of British Columbia, Vancouver, British Columbia, Canada
| | - T Roderick Docking
- Michael Smith Genome Sciences Centre, BC Cancer Research Centre, Vancouver, British Columbia, Canada
| | - Nadia Gharaee
- Michael Smith Genome Sciences Centre, BC Cancer Research Centre, Vancouver, British Columbia, Canada.,Pathology and Laboratory Medicine, University of British Columbia, Vancouver, British Columbia, Canada
| | - Jenny Li
- Michael Smith Genome Sciences Centre, BC Cancer Research Centre, Vancouver, British Columbia, Canada
| | - Patricia Umlandt
- Michael Smith Genome Sciences Centre, BC Cancer Research Centre, Vancouver, British Columbia, Canada
| | - Megan Fuller
- Michael Smith Genome Sciences Centre, BC Cancer Research Centre, Vancouver, British Columbia, Canada
| | - Martin Jädersten
- Center for Hematology and Regenerative Medicine, Department of Medicine Huddinge, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
| | - Austin Kulasekararaj
- Department of Haematological Medicine, King's College Hospital and King's College London, London, UK
| | - Luca Malcovati
- Department of Molecular Medicine, University of Pavia & Department of Hematology, Fondazione IRCCS Policlinico San Matteo, Pavia, Italy
| | - Alan F List
- Department of Malignant Hematology, Moffitt Cancer Center, Tampa, FL, USA
| | - Eva Hellström-Lindberg
- Center for Hematology and Regenerative Medicine, Department of Medicine Huddinge, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
| | - Uwe Platzbecker
- Medical Clinic and Policlinic 1, Hematology and Cellular Therapy, University Hospital Leipzig, Leipzig, Germany
| | - Aly Karsan
- Michael Smith Genome Sciences Centre, BC Cancer Research Centre, Vancouver, British Columbia, Canada. .,Pathology and Laboratory Medicine, University of British Columbia, Vancouver, British Columbia, Canada.
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