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Preclinical efficacy of CDK7 inhibitor-based combinations against myeloproliferative neoplasms transformed to AML
Warren Fiskus1, Christopher P Mill1, Prithviraj Bose1
1Department of Leukemia, The University of Texas MD Anderson Cancer Center, Houston, TX.
Abstract:
Rising blast percentage or secondary acute myeloid leukemia (sAML) transformation in myeloproliferative neoplasms (MPNs) leads to JAK1/2 inhibitor (JAKi) therapy resistance and poor survival. Here, we demonstrate that treatment with the CDK7 inhibitor (CDK7i) SY-5609 depletes phenotypically characterized post-MPN sAML stem/progenitor cells. In cultured post-MPN sAML SET2, HEL and patient-derived (PD) post-MPN sAML cells, SY-5609 treatment inhibited growth and induced lethality while sparing normal cells. RNA-sequencing analysis after SY-5609 treatment reduced mRNA expression of MYC, MYB, CDK4/6, PIM1, and CCND1 but increased expression of CDKN1A and BCL2L1. Mass spectrometry of SY-5609-treated MPN-sAML cells also reduced c-Myc, c-Myb, PIM1, and CDK4/6 but increased p21, caspase-9, and BAD protein levels. CRISPR-mediated CDK7 depletion also reduced cell viability of HEL cells. Cytometry by time of flight (CyTOF) analysis of SY-5609-treated PD post-MPN sAML stem/progenitor cells showed reduced c-Myc, CDK6, and PU.1 but increased protein levels of CD11b, p21, and cleaved caspase-3. Cotreatment with SY-5609 and ruxolitinib was synergistically lethal in HEL, SET2, and PD post-MPN sAML cells. A CRISPR screen in sAML cells revealed BRD4, CBP, and p300 as codependencies with CDK7i. Accordingly, cotreatment with SY-5609 and the bromodomain and extra-terminal protein inhibitor (BETi) OTX015 or pelabresib or the CBP/p300 inhibitor GNE-049 was synergistically lethal in MPN-sAML cells (including those exhibiting TP53 loss). Finally, in the HEL-Luc/GFP xenograft model, compared with each agent alone, cotreatment with SY-5609 and OTX015 reduced sAML burden and improved survival without host toxicity. These findings demonstrate promising preclinical activity of CDK7i-based combinations with BETi or CBP/p300 inhibitor against advanced MPNs, including post-MPN sAML.
Insights
The CDK7 inhibitor SY-5609 effectively targets therapy-resistant secondary acute myeloid leukemia (sAML) stem cells in myeloproliferative neoplasms (MPNs). Combinations with BET inhibitors or CBP/p300 inhibitors show promising preclinical activity against advanced MPNs.
Area of Science:
- Oncology
- Hematology
- Molecular Biology
Background:
- Myeloproliferative neoplasms (MPNs) with rising blast percentage or secondary acute myeloid leukemia (sAML) transformation exhibit resistance to JAK1/2 inhibitor (JAKi) therapy, leading to poor survival.
- Identifying novel therapeutic strategies is crucial for managing advanced MPNs and post-MPN sAML.
Purpose of the Study:
- To evaluate the efficacy of the CDK7 inhibitor (CDK7i) SY-5609, alone and in combination, against post-MPN sAML stem/progenitor cells.
- To investigate the molecular mechanisms underlying SY-5609's anti-leukemic activity.
- To assess the therapeutic potential of CDK7i-based combination therapies in preclinical models of advanced MPNs.
Main Methods:
- Treatment of cultured post-MPN sAML cells (SET2, HEL, patient-derived) with SY-5609.
- RNA-sequencing and mass spectrometry to analyze molecular changes post-SY-5609 treatment.
- CRISPR-mediated CDK7 depletion and CRISPR screen to identify genetic dependencies.
- Cytometry by time of flight (CyTOF) analysis of treated stem/progenitor cells.
- Combination studies with ruxolitinib, BET inhibitors (OTX015, pelabresib), and CBP/p300 inhibitor (GNE-049).
- In vivo efficacy assessment using a HEL-Luc/GFP xenograft model.
Main Results:
- SY-5609 treatment inhibited growth and induced lethality in post-MPN sAML cells while sparing normal cells.
- SY-5609 modulated the expression of key cell cycle regulators (MYC, MYB, CDK4/6, CDKN1A) and apoptosis-related proteins (BCL2L1, caspase-9, BAD).
- Combination therapies (SY-5609 + ruxolitinib, SY-5609 + BETi, SY-5609 + CBP/p300 inhibitor) demonstrated synergistic lethality in vitro.
- SY-5609 and OTX015 cotreatment reduced sAML burden and improved survival in vivo without host toxicity.
Conclusions:
- CDK7 inhibition represents a promising therapeutic approach for targeting therapy-resistant post-MPN sAML.
- Combination strategies involving CDK7 inhibitors with BET inhibitors or CBP/p300 inhibitors show significant preclinical potential against advanced MPNs.
- These findings support the further clinical investigation of CDK7i-based combinations for treating advanced MPNs, including those with TP53 loss.
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