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

• Published in: Cell reports. Medicine 2024-05, Vol.5 (5), p.101521-101521, Article 101521
• Main Authors: Adnan Awad, Shady, Dufva, Olli, Klievink, Jay, Karjalainen, Ella, Ianevski, Aleksandr, Pietarinen, Paavo, Kim, Daehong, Potdar, Swapnil, Wolf, Maija, Lotfi, Kourosh, Aittokallio, Tero, Wennerberg, Krister, Porkka, Kimmo, Mustjoki, Satu
• Format: Article
• Language: English
• Subjects: BCR::ABL1-independent resistance; Cell Line, Tumor; CML; CRISPR-Cas Systems - genetics; CRISPR-Cas9 screening; drug combination; drug repurposing; Drug Resistance, Neoplasm - drug effects; Drug Resistance, Neoplasm - genetics; drug screening; Fusion Proteins, bcr-abl - antagonists & inhibitors; Fusion Proteins, bcr-abl - genetics; Fusion Proteins, bcr-abl - metabolism; Humans; KCTD5; Leukemia, Myelogenous, Chronic, BCR-ABL Positive - drug therapy; Leukemia, Myelogenous, Chronic, BCR-ABL Positive - genetics; Leukemia, Myelogenous, Chronic, BCR-ABL Positive - metabolism; Leukemia, Myelogenous, Chronic, BCR-ABL Positive - pathology; progenitor; Protein Kinase Inhibitors - pharmacology; Proto-Oncogene Proteins c-abl - antagonists & inhibitors; Proto-Oncogene Proteins c-abl - genetics; Proto-Oncogene Proteins c-abl - metabolism; stem cell; TKI
• ISSN: 2666-3791; 2666-3791
• DOI: 10.1016/j.xcrm.2024.101521

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. [Display omitted] •Ex vivo drug screening finds sensitivities to Wee1, MDM2, and BCL2 inhibitors in CML•Mepacrine induces differentiation of primitive CD34+CD38− CML cells•CRISPR screen identifies common BCR::ABL1-independent TKI-resistance mechanisms•Downregulation of the ubiquitination regulator KCTD5 mediates TKI resistance Adnan Awad et al. investigate the BCR::ABL1-independent resistance mechanisms in chronic myeloid leukemia (CML) with integrated ex vivo drug screening and genome-wide CRISPR screening. Discovered drugs targeting leukemia stem and progenitor cells, along with resistance mechanisms to tyrosine kinase inhibitors, offer therapeutic options for CML patients.