Targeting enhancer switching overcomes non-genetic drug resistance in acute myeloid leukaemia

Abstract

Non-genetic drug resistance is increasingly recognised in various cancers. Molecular insights into this process are lacking and it is unknown whether stable non-genetic resistance can be overcome. Using single cell RNA-sequencing of paired drug naïve and resistant AML patient samples and cellular barcoding in a unique mouse model of non-genetic resistance, here we demonstrate that transcriptional plasticity drives stable epigenetic resistance. With a CRISPR-Cas9 screen we identify regulators of enhancer function as important modulators of the resistant cell state. We show that inhibition of Lsd1 (Kdm1a) is able to overcome stable epigenetic resistance by facilitating the binding of the pioneer factor, Pu.1 and cofactor, Irf8, to nucleate new enhancers that regulate the expression of key survival genes. This enhancer switching results in the re-distribution of transcriptional co-activators, including Brd4, and provides the opportunity to disable their activity and overcome epigenetic resistance. Together these findings highlight key principles to help counteract non-genetic drug resistance.

Melanoma plasticity and phenotypic diversity: therapeutic barriers and opportunities

“…Markov modeling revealed that the cell state transitions were reversible and mediated by both Lamarckian induction and nongenetic Darwinian selection of drug-tolerant states (Su et al 2017). Moreover, single-cell RNA sequencing showed that therapeutic resistance in Acute Myeloid Leukaemia (AML) emerges from a leukemia stem cell population in the form of a Lamarckian adaptive transcriptional response and, importantly, in the absence of genetic adaptation (Bell et al 2019). Note that adaptive cell state transitions are especially likely to play a major role in drug resistance in tumors with a low mutation burden.…”

A combination strategy targeting enhancer plasticity exerts synergistic lethality against BETi-resistant leukemia cells

“…7e). Indeed, using the published HiChIP data 43 , we detected significant reduction of long-range chromatin interactions between the MYC promoter and PVT1 enhancers after LSD1 inhibitor (LSD1i, GSK-LSD1) treatment in murine AF9 BETi-resistant AML cells (Fig. 7f).…”

Mutational synergy coordinately remodels chromatin accessibility, enhancer landscape and 3-Dimensional DNA topology to alter gene expression during leukemia induction

“…In further support of its role as a TSG, heterozygous deletions of the locus or rare loss-of-function mutations of PU.1 have been described in patients with AML 9,11,54 . Moreover, oncogenic translocations or point mutations involving transcription factors such as RUNX1 abrogate the activity of PU.1 55,56 and therapeutically, the anti-leukemic activity of LSD1 inhibitors has been associated with re-activation of a PU.1 driven transcriptional programme 57,58 . However, in contrast, our study identifies Spi1/PU.1 as an oncogenic transcription factor in Npm1c/Flt3-ITD AML, and is in accord with our previous work and that of others that have demonstrated PU.1 to be a vulnerability identified by CRISPR screens in certain AML subtypes 50,51,59 .…”