Pre-clinical activity of combined LSD1 and mTORC1 inhibition in MLL-translocated acute myeloid leukaemia

Abstract

The histone demethylase lysine-specific demethylase 1 (LSD1 or KDM1A) has emerged as a candidate therapeutic target in acute myeloid leukaemia (AML); tranylcypromine-derivative inhibitors induce loss of clonogenic activity and promote differentiation, in particular in the MLL-translocated molecular subtype of AML. In AML, the use of drugs in combination often delivers superior clinical activity. To identify genes and cellular pathways that collaborate with LSD1 to maintain the leukaemic phenotype, and which could be targeted by combination therapies, we performed a genome-wide CRISPR-Cas9 dropout screen. We identified multiple components of the amino acid sensing arm of mTORC1 signalling-RRAGA, MLST8, WDR24 and LAMTOR2-as cellular sensitizers to LSD1 inhibition. Knockdown of mTORC1 components, or mTORC1 pharmacologic inhibition, in combination with LSD1 inhibition enhanced differentiation in both cell line and primary cell settings, in vitro and in vivo, and substantially reduced the frequency of clonogenic primary human AML cells in a modelled minimal residual disease setting. Synergistic upregulation of a set of transcription factor genes associated with terminal monocytic lineage differentiation was observed. Thus, dual mTORC1 and LSD1 inhibition represents a candidate combination approach for enhanced differentiation in MLL-translocated AML which could be evaluated in early phase clinical trials.

Superior efficacy of co-targeting GFI1/KDM1A and BRD4 against AML and post-MPN secondary AML cells

“…Notably, a dual class I HDACi and LSD1 inhibitor was shown to exert synergistic lethality in AML as well as in tumor models other than AML 30 , 57 , 58 . CRISPR-Cas9 screens in AML cells expressing MLL-fusion gene showed superior efficacy of co-targeting mTORC1 with LSD1, which was not revealed by our screen 59 . This difference is because our domain-focused CRISPR-Cas9 screen involved AML cells without MLL fusion gene-expression, and utilized gRNAs targeting chromatin regulators not mTORC1.…”

Combined epigenetic and metabolic treatments overcome differentiation blockade in acute myeloid leukemia

“…Beyond these metabolic drugs though, it would be interesting to compare the efficiency of differentiation induction and proliferation reduction from treatment with the LSD1i, 6MP, and CER triple combination to other published epigenetic-based strategies. Examples of such strategies include combining LSD1 inhibitors with RAD001 (mTORC1 inhibitor), SYC-522 (DOT1L inhibitor), all-trans retinoic acid, and azacytidine, where the latter two combinations are currently being evaluated in clinical trials ( Deb et al., 2020 ) ( Feng et al., 2016 ) ( Wass et al., 2020 ) ( Buesa et al., 2019 ). As transcriptional programs are clarified in AML differentiation blockade, such as the IRX3-HOXA9 axis, and additional new pathways that cooperate with LSD1 inhibition are characterized, such studies may uncover the relative contributions, if any, of LSD1 catalytic activity and LSD1 interactions with binding partners such as GFI1 in bypassing the AML differentiation blockade in specific subtypes ( Maiques-Diaz et al., 2018 ) ( Somerville et al., 2018 ).…”

Clinical Responsiveness to All-trans Retinoic Acid Is Potentiated by LSD1 Inhibition and Associated with a Quiescent Transcriptome in Myeloid Malignancies

“…Low RARA expression has previously been proposed as the reason why non-APL AML patients are resistant to ATRA therapy (13,14); however, we found that non-responders had higher levels of RARA expression compared to responders (Figure S2D) in agreement with previous reports (40) that ATRA alone fails to show efficacy in RARA-high models. Non-responders were enriched for genes in the mTOR signaling pathway, which may confer resistance to ATRA-TCP and supports the rationale for combining LSD1 and mTOR inhibitors in AML (41). Non-responders also expressed higher levels of XPO1, which codes for an exportin that regulates the cytoplasmic localization of nuclear receptors like RARs, preventing their transcriptional activity, and is associated with poor outcomes in AML (32,42).…”