SETBP1 overexpression acts in the place of class-defining mutations to drive FLT3-ITD–mutant AML

Abstract

Advances in cancer genomics have revealed genomic classes of acute myeloid leukemia (AML) characterized by class-defining mutations, such as chimeric fusion genes or in genes such as NPM1, MLL, and CEBPA. These class-defining mutations frequently synergize with internal tandem duplications in FLT3 (FLT3-ITDs) to drive leukemogenesis. However, ∼20% of FLT3-ITD–positive AMLs bare no class-defining mutations, and mechanisms of leukemic transformation in these cases are unknown. To identify pathways that drive FLT3-ITD mutant AML in the absence of class-defining mutations, we performed an insertional mutagenesis (IM) screening in Flt3-ITD mice, using Sleeping Beauty transposons. All mice developed acute leukemia (predominantly AML) after a median of 73 days. Analysis of transposon insertions in 38 samples from Flt3-ITD/IM leukemic mice identified recurrent integrations at 22 loci, including Setbp1 (20/38), Ets1 (11/38), Ash1l (8/38), Notch1 (8/38), Erg (7/38), and Runx1 (5/38). Insertions at Setbp1 led exclusively to AML and activated a transcriptional program similar, but not identical, to those of NPM1-mutant and MLL-rearranged AMLs. Guide RNA targeting of Setbp1 was highly detrimental to Flt3ITD/+/Setbp1IM+, but not to Flt3ITD/+/Npm1cA/+, AMLs. Also, analysis of RNA-sequencing data from hundreds of human AMLs revealed that SETBP1 expression is significantly higher in FLT3-ITD AMLs lacking class-defining mutations. These findings propose that SETBP1 overexpression collaborates with FLT3-ITD to drive a subtype of human AML. To identify genetic vulnerabilities of these AMLs, we performed genome-wide CRISPR-Cas9 screening in Flt3ITD/+/Setbp1IM+ AMLs and identified potential therapeutic targets, including Kdm1a, Brd3, Ezh2, and Hmgcr. Our study gives new insights into epigenetic pathways that can drive AMLs lacking class-defining mutations and proposes therapeutic approaches against such cases.

High-Throughput CRISPR Screening in Hematological Neoplasms

“…Other researchers identified POLR2M or PAICS as potential therapeutic targets for this type of AML [ 46 , 47 ]. Furthermore, in FLT3 -ITD-positive AMLs, CRISPR screening has revealed Kdm1a , Brd3 , Ezh2 and Hmgcr genes as promising targets in this genetic context [ 74 ]. In another AML entity characterized by the presence of RAS mutations which have been associated with dismal prognosis [ 238 ], synthetic lethal genes involved in the maturation of the Ras and MAPK signaling pathway were required only in the context of oncogenic Ras [ 239 ].…”

Mouse Models of Frequently Mutated Genes in Acute Myeloid Leukemia

“…Further, FLT3 mutations alone are not sufficient to induce AML and need additional cooperating mutations. Collaboration mouse models show cooperation of FLT3 mutations with other mutated genes such as SMC3 [ 19 ], RUNX1 [ 20 ], NPM1 [ 21 ], DNMT3A [ 22 , 23 ], IDH2 [ 24 , 25 ], WT1 [ 26 , 27 ], TET2 [ 28 ], SETBP1 [ 29 ] and CUX1 ( Table 2 ; Supplementary Figure S3 ) [ 30 ]. FLT3 mutations also cooperate with different fusion genes such as NUP98-NSD1 [ 31 ], NUP98-HOXD13 [ 32 ], KMT2A-AF9 [ 33 ] and RUNX1-RUNX1T1 [ 34 ] to develop AML in mice.…”

“…Using the Sleeping Beauty transposon system, Pacharne et al have shown that all FLT3-ITD mice developed AML with Setbp1 being the most frequent integration site. ( Table 2 ; Supplementary Figure S3 ) [ 29 ]. It was demonstrated that Setbp1 overexpression activates the HOXA gene signature and Flt3 ITD/+ /Setbp1 IM+ AML is vulnerable to Kdm1a and Brd3 inhibition [ 29 ].…”

“…( Table 2 ; Supplementary Figure S3 ) [ 29 ]. It was demonstrated that Setbp1 overexpression activates the HOXA gene signature and Flt3 ITD/+ /Setbp1 IM+ AML is vulnerable to Kdm1a and Brd3 inhibition [ 29 ]. These studies indicate that Setbp1 contributes to leukemogenesis predominantly through the regulation of Hox genes.…”

Mannose metabolism inhibition sensitizes acute myeloid leukaemia cells to therapy by driving ferroptotic cell death

“…Regardless of the mechanism, high MPI activity appears to provide a survival advantage in several cancer types. Interestingly, MPI was amongst the top drop-out genes in our published CRISPR-Cas9 screen aiming to identify sensitizers to the clinical grade FLT3-tyrosine kinase inhibitor (TKI) AC220 (quizartinib) in AML carrying activating FLT3 internal tandem duplication (ITD) mutations 9 and more recently was identified amongst 81 United States Food and Drug Administration (FDA) druggable genetic dependencies of a murine model of FLT3 ITD AML 24 .…”