Genome-wide CRISPR-Cas9 screen identifies rationally designed combination therapies for CRLF2-rearranged Ph-like ALL

• Published in: Blood Vol. 139; no. 5; pp. 748 - 760
• Main Authors: Sasaki, Kensuke, Yamauchi, Takuji, Semba, Yuichiro, Nogami, Jumpei, Imanaga, Hiroshi, Terasaki, Tatsuya, Nakao, Fumihiko, Akahane, Koshi, Inukai, Takeshi, Verhoeyen, Els, Akashi, Koichi, Maeda, Takahiro
• Format: Journal Article
• Language: English
• Published: United States Elsevier Inc 03.02.2022; American Society of Hematology
• Subjects: Animals; Antineoplastic Combined Chemotherapy Protocols - pharmacology; Cell Line, Tumor; CRISPR-Cas Systems; Gene Rearrangement - drug effects; Humans; Lymphoid Neoplasia; Mice; Nitriles - pharmacology; Philadelphia Chromosome; Precursor Cell Lymphoblastic Leukemia-Lymphoma - drug therapy; Precursor Cell Lymphoblastic Leukemia-Lymphoma - genetics; Protein Kinase Inhibitors - pharmacology; Pyrazoles - pharmacology; Pyrimidines - pharmacology; Receptors, Cytokine - genetics; Signal Transduction - drug effects
• ISSN: 0006-4971; 1528-0020
• DOI: 10.1182/blood.2021012976

Acute lymphoblastic leukemia (ALL) harboring the IgH-CRLF2 rearrangement (IgH-CRLF2-r) exhibits poor clinical outcomes and is the most common subtype of Philadelphia chromosome-like acute lymphoblastic leukemia (Ph-like ALL). While multiple chemotherapeutic regimens, including ruxolitinib monotherapy and/or its combination with chemotherapy, are being tested, their efficacy is reportedly limited. To identify molecules/pathways relevant for IgH-CRLF2-r ALL pathogenesis, we performed genome-wide CRISPR-Cas9 dropout screens in the presence or absence of ruxolitinib using 2 IgH-CRLF2-r ALL lines that differ in RAS mutational status. To do so, we employed a baboon envelope pseudotyped lentiviral vector system, which enabled, for the first time, highly efficient transduction of human B cells. While single-guide RNAs (sgRNAs) targeting CRLF2, IL7RA, or JAK1/2 significantly affected cell fitness in both lines, those targeting STAT5A, STAT5B, or STAT3 did not, suggesting that STAT signaling is largely dispensable for IgH-CRLF2-r ALL cell survival. We show that regulators of RAS signaling are critical for cell fitness and ruxolitinib sensitivity and that CRKL depletion enhances ruxolitinib sensitivity in RAS wild-type (WT) cells. Gilteritinib, a pan-tyrosine kinase inhibitor that blocks CRKL phosphorylation, effectively killed RAS WT IgH-CRLF2-r ALL cells in vitro and in vivo, either alone or combined with ruxolitinib. We further show that combining gilteritinib with trametinib, a MEK1/2 inhibitor, is an effective means to target IgH-CRLF2-r ALL cells regardless of RAS mutational status. Our study delineates molecules/pathways relevant for CRLF2-r ALL pathogenesis and could suggest rationally designed combination therapies appropriate for disease subtypes. •STAT signaling is dispensable for survival of IgH-CRLF2-r Ph-like ALL cells.•A precision medicine approach based on mutational status, namely of RAS, is key for treatment of IgH-CRLF2-r Ph-like ALL. [Display omitted]