Integrated drug profiling and CRISPR screening identify BCR::ABL1-independent vulnerabilities in chronic myeloid leukemia

Shady Adnan Awad; Olli Dufva; Jay Klievink; Ella Karjalainen; Aleksandr Ianevski; Paavo Pietarinen; Daehong Kim; Swapnil Potdar; Maija Wolf; Kourosh Lotfi; Tero Aittokallio; Krister Wennerberg; Kimmo Porkka; Satu Mustjoki

doi:10.1016/j.xcrm.2024.101521

Integrated drug profiling and CRISPR screening identify BCR::ABL1-independent vulnerabilities in chronic myeloid leukemia

Cell Rep Med. 2024 Apr 10:101521. doi: 10.1016/j.xcrm.2024.101521. Online ahead of print.

Authors

Affiliations

¹ Hematology Research Unit Helsinki, University of Helsinki and Helsinki University Hospital Comprehensive Cancer Center, 00290 Helsinki, Finland; Translational Immunology Research Program and Department of Clinical Chemistry and Hematology, University of Helsinki, 00014 Helsinki, Finland; Foundation for the Finnish Cancer Institute, 00290 Helsinki, Finland; Clinical Pathology Department, National Cancer Institute, Cairo University, 11796 Cairo, Egypt. Electronic address: shady.awad@helsinki.fi.
² Hematology Research Unit Helsinki, University of Helsinki and Helsinki University Hospital Comprehensive Cancer Center, 00290 Helsinki, Finland; Translational Immunology Research Program and Department of Clinical Chemistry and Hematology, University of Helsinki, 00014 Helsinki, Finland; iCAN Digital Precision Cancer Medicine Flagship, 00014 Helsinki, Finland.
³ Hematology Research Unit Helsinki, University of Helsinki and Helsinki University Hospital Comprehensive Cancer Center, 00290 Helsinki, Finland; Translational Immunology Research Program and Department of Clinical Chemistry and Hematology, University of Helsinki, 00014 Helsinki, Finland.
⁴ Institute for Molecular Medicine Finland (FIMM), Helsinki Institute for Life Science, University of Helsinki, 00014 Helsinki, Finland.
⁵ Hematology Research Unit Helsinki, University of Helsinki and Helsinki University Hospital Comprehensive Cancer Center, 00290 Helsinki, Finland.
⁶ Department of Medical and Health Sciences, Faculty of Medicine and Health, Linköping University, 58183 Linköping, Sweden.
⁷ Foundation for the Finnish Cancer Institute, 00290 Helsinki, Finland; iCAN Digital Precision Cancer Medicine Flagship, 00014 Helsinki, Finland; Institute for Molecular Medicine Finland (FIMM), Helsinki Institute for Life Science, University of Helsinki, 00014 Helsinki, Finland; Institute for Cancer Research, Oslo University Hospital, 0424 Oslo, Norway; Oslo Centre for Biostatistics and Epidemiology, University of Oslo, 0317 Oslo, Norway.
⁸ Institute for Molecular Medicine Finland (FIMM), Helsinki Institute for Life Science, University of Helsinki, 00014 Helsinki, Finland; Biotech Research & Innovation Centre and Novo Nordisk Foundation Center for Stem Cell Biology (DanStem), University of Copenhagen, 2200 Copenhagen, Denmark.
⁹ Hematology Research Unit Helsinki, University of Helsinki and Helsinki University Hospital Comprehensive Cancer Center, 00290 Helsinki, Finland; Translational Immunology Research Program and Department of Clinical Chemistry and Hematology, University of Helsinki, 00014 Helsinki, Finland; iCAN Digital Precision Cancer Medicine Flagship, 00014 Helsinki, Finland. Electronic address: satu.mustjoki@helsinki.fi.

PMID: 38653245
DOI: 10.1016/j.xcrm.2024.101521

Abstract

BCR::ABL1-independent pathways contribute to primary resistance to tyrosine kinase inhibitor (TKI) treatment in chronic myeloid leukemia (CML) and play a role in leukemic stem cell persistence. Here, we perform ex vivo drug screening of CML CD34⁺ leukemic stem/progenitor cells using 100 single drugs and TKI-drug combinations and identify sensitivities to Wee1, MDM2, and BCL2 inhibitors. These agents effectively inhibit primitive CD34⁺CD38^- CML cells and demonstrate potent synergies when combined with TKIs. Flow-cytometry-based drug screening identifies mepacrine to induce differentiation of CD34⁺CD38^- cells. We employ genome-wide CRISPR-Cas9 screening for six drugs, and mediator complex, apoptosis, and erythroid-lineage-related genes are identified as key resistance hits for TKIs, whereas the Wee1 inhibitor AZD1775 and mepacrine exhibit distinct resistance profiles. KCTD5, a consistent TKI-resistance-conferring gene, is found to mediate TKI-induced BCR::ABL1 ubiquitination. In summary, we delineate potential mechanisms for primary TKI resistance and non-BCR::ABL1-targeting drugs, offering insights for optimizing CML treatment.

Keywords: BCR::ABL1-independent resistance; CML; CRISPR-Cas9 screening; KCTD5; TKI; drug combination; drug repurposing; drug screening; progenitor; stem cell.