Set-pp2a complex as a new therapeutic target in kmt2a (mll) rearranged aml

Set-pp2a complex as a new therapeutic target in kmt2a (mll) rearranged aml

Play all audios:

Loading...

ABSTRACT _KMT2A_-rearranged (KMT2A-R) is an aggressive and chemo-refractory acute leukemia which mostly affects children. Transcriptomics-based characterization and chemical interrogation


identified kinases as key drivers of survival and drug resistance in _KMT2A_-R leukemia. In contrast, the contribution and regulation of phosphatases is unknown. In this study we uncover the


essential role and underlying mechanisms of SET, the endogenous inhibitor of Ser/Thr phosphatase PP2A, in _KMT2A_-R-leukemia. Investigation of SET expression in acute myeloid leukemia (AML)


samples demonstrated that SET is overexpressed, and elevated expression of SET is correlated with poor prognosis and with the expression of _MEIS_ and _HOXA_ genes in AML patients.


Silencing SET specifically abolished the clonogenic ability of _KMT2A_-R leukemic cells and the transcription of _KMT2A_ targets genes _HOXA9_ and _HOXA10_. Subsequent mechanistic


investigations showed that SET interacts with both KMT2A wild type and fusion proteins, and it is recruited to the _HOXA10_ promoter. Pharmacological inhibition of SET by FTY720 disrupted


SET-PP2A interaction leading to cell cycle arrest and increased sensitivity to chemotherapy in _KMT2A_-R-leukemic models. Phospho-proteomic analyses revealed that FTY720 reduced the activity


of kinases regulated by PP2A, including ERK1, GSK3β, AURB and PLK1 and led to suppression of MYC, supporting the hypothesis of a feedback loop among PP2A, AURB, PLK1, MYC, and SET. Our


findings illustrate that SET is a novel player in _KMT2A_-R leukemia and they provide evidence that SET antagonism could serve as a novel strategy to treat this aggressive leukemia. SIMILAR


CONTENT BEING VIEWED BY OTHERS DYRK1A INHIBITION RESULTS IN MYC AND ERK ACTIVATION RENDERING _KMT2A-_R ACUTE LYMPHOBLASTIC LEUKEMIA CELLS SENSITIVE TO BCL2 INHIBITION Article Open access 27


March 2025 REQUIREMENT FOR LIM KINASES IN ACUTE MYELOID LEUKEMIA Article 26 June 2020 MUTANT SETBP1 ENHANCES NRAS-DRIVEN MAPK PATHWAY ACTIVATION TO PROMOTE AGGRESSIVE LEUKEMIA Article 17 May


2021 INTRODUCTION Acute leukemias characterized by chromosomal translocations involving the _KMT2A_ gene (previously known as _MLL_, _HRX, HTRX1, or ALL1_) are a highly aggressive group of


leukemias with a poor prognosis [1, 2]. They account for over 80% of infant acute lymphoblastic leukemia (ALL), 5–10% of acute myeloid leukemia (AML), and over 70% of therapy related AML


[2]. _KMT2A_ encodes for the histone-lysine-N-methyltransferase 2A, which regulates gene transcription via methylation of histone H3 in the gene bodies [1, 3]. The N-terminal portion of


KMT2A binds to DNA, whereas the C-terminal contains the catalytic domain for histone methylation, which is essential to relax the chromatin and to drive the expression of genes during


embryogenesis and hematopoiesis [1]. _KMT2A_ chromosomal translocations give rise to chimeric oncofusion proteins that retain only the N- terminal DNA binding domain of KMT2A fused with over


hundred partner proteins [2]. These fusions impair the normal functioning of KMT2A and cause aberrant transcriptional activation by recruitment of an epigenetic multiprotein complex that


includes the histone lysine 79 (H3K79) methyltransferase DOT1L, the bromodomain proteins, the acetyltransferase HBO1 and several other proteins that acquire opportunistic oncogenic functions


[3,4,5,6,7]. The _HOX_ genes, in particular _HOXA9_ and _HOXA10_, are primary targets of _KMT2A_-fusion products and, together with the cofactor MEIS1, play an important role in the


transcriptional reprogramming of hematopoietic stem cells (HSCs) and progenitor cells harboring the _KMT2A_ translocations, leading to impairment of cellular differentiation [8,9,10] and


resistance to DNA damage inhibitors [11]. In addition, expression of the oncogene _MYC_ contributes to _KMT2A_-mediated leukemogenesis by driving cell proliferation and survival [12].


Despite the development of new therapeutic agents, such as inhibitors of KMT2A-fusion complex [3,4,5, 13,14,15,16] and inhibitors of kinases essential for the KMT2A-signaling pathways


[17,18,19], none of these are FDA approved. Consequently, patients affected by _KMT2A-_R-leukemia are still treated with chemotherapy followed by bone marrow transplantation, with suboptimal


outcomes. Therefore, the identification of novel targets and targetable pathways for _KMT2A_-R-leukemia is of primary importance for the development of new and effective therapeutic


approaches. SET is an oncoprotein also known as template activating factor-I-β, inhibitor 2 of Ser-Thr protein phosphatase 2A and putative histocompatibility leukocyte antigen class


II-associated protein II. Originally identified as fusion gene in acute leukemia [20], it is overexpressed in several forms of solid tumors and hematological malignancies


[21,22,23,24,25,26]. In _BCR::ABL_+ chronic myeloid leukemia (CML), SET-mediated PP2A inactivation is essential for the self-renewal of CML leukemic stem cells [27]. Silencing SET


re-activates PP2A and switches the oncogenic driver kinase BCR::ABL off, highlighting its potency as a negative regulator of PP2A and a positive regulator of oncogenic cascades [21, 26, 28].


SET has also been recognized as a prognostic marker for poor overall survival in AML [22, 24], although the exact molecular mechanisms linking a SET oncoprotein pathway with aggressive AML


outcomes remain still obscure. Interestingly, SET has been reported to interact with the N-terminal region of KMT2A, that is retained in KMT2A-fusion proteins [29]. However, the role of SET


in the pathogenesis of _KMT2A_-R leukemia is unknown. Based on this and the fundamental role played by PP2A-modulated kinases on the survival and resistance of _KMT2A_-R-leukemic cells [17,


19, 30], we herein investigated the role of the PP2A endogenous inhibitor SET in _KMT2A_-R leukemia. Our overall results provide novel insights on the role of SET in _KMT2A_-R leukemia, via


modulation of _HOXA_ gene expression and MYC stability, and a proof of concept that inhibition of SET is a promising novel strategy to treat this aggressive form of acute leukemia. RESULTS


SET IS OVER-EXPRESSED IN _KMT2A_-R CELL LINES AND PRIMARY SAMPLES We used public data repositories to characterize the role of SET across various hematopoietic contexts, to analyze its mRNA


expression in human HSCs and progenitors (_n_ = 34) [31], and in multiple independent human AML primary samples (_n_ = 384) covering the main cytogenetic subsets [10]. SET was expressed at


high levels in both HSC and myeloid progenitors (MP) compared with mature monocytes and myelocytes (Fig. 1A and Supplementary Fig. 1A), thereby indicating that it is a gene expressed during


early hematopoietic development. In silico evaluation of SET mRNA expression across all AML was uniformly high and it did not show segregation with any distinct molecular group as previously


suggested (Fig. 1B and Supplementary Fig. 1A–C) [22, 24]. A PrognoScan database-based Kaplan–Meier analysis of the overall survival of 163 AML patients by high (_n_ = 57) and low (_n_ = 


106) SET levels [32], revealed that high SET expression positively correlated with poor overall survival in human AML (Fig. 1C and Supplementary Table 1), consistent with previous reports


[24]. To further substantiate the role of SET in AML, we evaluated its protein levels by western blot in a panel of _KMT2A_-R-AML (THP1, MV411, ML2, MOLM13, NOMO-1) and _KMT2A_-R-ALL (SEM,


Hb1119, KOPN8, RS411) cell lines and primary samples (PS), KMT2A wild-type (wt) cell lines (K562, _BCR::ABL_+ erythroleukemia, Kasumi1 _AML1::ETO_ + AML, REH _TEL::AML_ + ALL, U937


_CALM::AF10_ + AML), mononuclear cells isolated from the bone marrow (BM) and peripheral blood (PB) of healthy adult volunteers. SET was significantly up-regulated in all leukemic cell lines


and in all _KMT2A_-R primary samples, irrespective of tumor lineage, compared to BM controls (Fig. 1D, E). Given the poor outcomes of the _KMT2A_-R-leukemias and the relatively well


characterized cellular context driving leukemogenesis, we further investigated the mechanistic role of SET in this group. As SET oncoprotein has several distinct roles depending on its


subcellular localization [26, 33, 34], we analyzed its subcellular localization in two _KMT2A_-R-cell lines (THP1 and MV411) and one KMT2A-wt cell line (K562) by nuclear/cytoplasm


fractionation followed by western blot and we showed that SET was relatively more abundant in the cytoplasm than in the nucleus of these cells (Fig. 1F). As phosphorylation of Ser9 and Ser25


of SET inhibits its nuclear import [26, 33, 34], we also investigated the phosphorylation status of SET. As no specific antibodies against phospho-SET are commercially available, SET was


immunoprecipitated and protein samples were analyzed by western blot with anti-phospho-Ser antibodies. Consistent with the prevalent cytoplasmatic localization, our results showed that, in


_KMT2A_-R-AML cell lines, SET is phosphorylated on serine residues (Fig. 1G and Supplementary 1D–F). Overall, these data indicate that SET is over-expressed, phosphorylated on Ser residues


and abundantly localized in the cytosol in _KMT2A_-R and -wt leukemic cells. _SET_ CORRELATES WITH THE EXPRESSION OF KMT2A TARGETS _MEIS_ AND _HOXA_ GENES To understand the role of SET in


leukemic stem cells (LSC), we analyzed the expression of _SET mRNA_ in 12 high-LSC frequency mouse _KMT2A-_R AMLs and 22 low-LSC frequency _KMT2A-_R-AMLs, using a public dataset [35], as


described in material and methods. Interestingly, we found that _SET_ mRNA expression was significantly higher in high-LSC frequency _KMT2A_-R AML than in low-LSC frequency _KMT2A_-R AML


(Fig. 2A), suggesting a potential role of SET in _KMT2A_-R leukemia self-renewal. We then used cBioPortal database to explore the potential correlation between the expression of _SET_ mRNA


and genes identified as LSC markers in human AML by Gentles et al. [36]. Out of the 52 genes identified by Gentles et al., 39 were found in the cBioPortal database for all the cohorts


included in the study. Our in-silico analysis showed a significant positive correlation between _SET_ expression and some LSC genes, such as _FAIM_ and _STAR_ (Fig. 2B). In addition, we


checked whether there was a correlation between SET expression and the self-renewal associated genetic signature identified in _KMT2A_-R-AML by Krivtsov et al. [37]. In this case, out of the


34 described by Krivtsov et al., we found 29 genes in the cBioPortal database. _SET_ expression significantly correlated with some primary targets of _KMT2A_-R-AML such as _MEIS_, _HOXA5_,


_HOXA9_ and _HOXA10_ (Fig. 2C). These data indicate that SET expression is significantly higher in high-LSC frequency mouse KMT2A-R AML and that _SET_ expression significantly correlated


with the expression of some LSC marker genes and with KMT2A targets _MEIS_ and _HOXA_ genes. SET IS ESSENTIAL FOR _KMT2A_-R LEUKEMIC CELLS’ CLONOGENIC ABILITY To determine whether SET has a


functional role in _KMT2A_-R- leukemia, we knocked down _SET_ gene in human cell lines by using RNA interference. Analysis of protein by western blot (Fig. 2D) and of gene expression by


RT-qPCR (Fig. 2E) confirmed the knock down (KD) in all the cell lines investigated. We then assessed the effect of SET KD on the clonogenic ability of the cells. _SET_ KD completely


abolished the clonogenic ability of _KMT2A_-R leukemic cell lines (THP1, MV411, and SEM, Fig. 2H, I and K and Supplementary Fig. 2), whereas it had little or no effect on the colony


formation of three independent _KMT2A_-wt leukemic cell lines (K562, Kasumi1, and REH Fig. 2F, G, and J). Then, we determined the impact of SET KD on cell proliferation of KMT2A-wt leukemic


cells by monitoring GFP fluorescence and by MTS assay, as described in [38] and in Supplementary material and methods. The correlation between the GFP fluorescence and the OD values


determined for the MTS assay are reported in supplementary Fig. 3. The correlation between two assays were above 0.8, indicating that the GFP monitoring of the newly generated GFP-expressing


lines can be used as a readout of cell proliferation in these experimental conditions. SET KD attenuated the proliferation of K562 (Fig. 2L, Supplementary Fig. 3 and Supplementary Table 2),


in line with a previous report [21]. SET KD had a stronger impact on _KMT2A_-wt AML cell line Kasumi1 (Fig. 2M, Supplementary Fig. 3 and Supplementary Table 2) and on _KMT2A_-wt ALL cell


line REH (Fig. 2N, Supplementary Fig. 3 and Supplementary Table 2). Interestingly, whereas the GFP monitoring indicates that eGFP-Kasumi1-shSET proliferate significantly more slowly than


eGFP-Kasumi1-shScramble, the MTS assay indicates that eGFP-Kasumi-shSET are still metabolically active. The discrepancy between these results might be due to the emergence of growth arrested


cells that are still highly metabolically active [39]. Overall, these data indicate that SET-KD specifically abolishes the clonogenic ability in _KMT2A_-R-leukemic cells and it attenuates


the proliferation of _KMT2A-_wt leukemic cells; whereas in K562 the effect on proliferation is mild, in Kasumi1 and REH SET KD induces a significant arrest in proliferation. THE SET


INHIBITOR FTY720 INDUCES CELL CYCLE ARREST AND DRIVES CELL DEATH IN _KMT2A_-R LEUKEMIC CELLS We next tested pharmacological modulation of SET by FTY720 (Fingolimod) [40], a FDA-approved


immunosuppressive drug that has gained further attention as anti-cancer and PP2A activating drug, due to its ability to disrupt the binding between SET and PP2A [28, 41,42,43]. We first


carried out a dose-response titration assay and determined that the half maximal inhibitory concentration of FTY720 in vitro ranged between 1 and 5 μM (Supplementary Fig. 4A), which were


reported as non-toxic to healthy bone marrow mononuclear cells [27, 28]. We then assessed the effect of FTY720 on proliferation, cell cycle and cell death of _KMT2A_-wt (K562, Kasumi1 and


REH) and _KMT2A_-R-leukemic cells (THP1, MV411 Hb119, and SEM) (Fig. 3A–G and Supplementary Fig. 3 and Table 2). We observed that 5 µM FTY720 had a variable but significant effect on the


proliferation of all the analyzed cell lines, ranging from modest for the _KMT2A_-wt-cell lines K562 and Kasumi1 to severe for eGFP-REH (Fig. 3G and Supplementary Fig. 3 and Table 2), as


reported [28, 44, 45]. In addition, FTY720 severely halted the proliferation of all the _KMT2A_-R-cell lines. Cell cycle analyses revealed that treatment with FTY720 for 48 h induced a


significant increase of cells in G1 and a reduction in S and G2-M phase, in _KMT2A_-R-cells (Fig. 3H and Supplementary Fig. 4B), indicating cell cycle failure. Moreover, we investigated the


fraction of leukemic cells undergoing cell death upon FTY720 treatment by FACS, by gating the GFP negative (GFP-) cells, as described previously [38] and in the Supplementary material and


methods. FTY720 induced a statistically significant increase in cell death in two _KMT2A_-wt-cell lines K562 and REH whereas this was not significant for the _KMT2A-_wt cell line


eGFP-Kasumi1. In contrast, FTY720 induced a consistent and statistically significant increase in cell death in _KMT2A_-R-cells (Fig. 3I and Supplementary Fig. 4C). These results indicate


that the SET inhibitor FTY720 induces heterogenous effects in leukemic cells; in K562 FTY720 has a modest effect on proliferation and cell death; in Kasumi1 FTY720 has a modest effect on


proliferation and it does not induce cell death; in REH, FTY720 significantly impairs the proliferation and it induces cell death; in _KMT2A_-R-leukemic cells, FTY720 significantly impairs


the proliferation, causes cell cycle arrest in G1 and increases the rate of cell death. THE EFFECT OF FTY720 IS DEPENDENT ON PP2A ACTIVATION FTY720 is a SET inhibitor able to rescue the


activity of PP2A towards its target pathways [40, 46]. By immunoprecipitation, we showed that FTY720 treatment for 24 hours disrupted the binding between SET and PP2A in _KMT2A_-R cells,


confirming the molecular mechanism reported in other leukemic models (Fig. 4A) [28, 41,42,43]. To investigate whether the observed effects of FTY720 on _KMT2A_-R cells were due to the


activation of PP2A, we analyzed the phosphorylation of some of PP2A targeted pathways [47] by western blot. In K562 cells, we observed reduction in phospho-ERK1/2 (Thr202/Tyr204), which was


instead unchanged in Kasumi1; in these two cell lines, phospho- GSK3β (Ser9) expression decreased, upon FTY720 treatment. Notably, in _KMT2A_-R-leukemic cells, we observed a dramatic and


stable decrement in the expression of the PP2A target phospho- ERK1/2 (Fig. 4B). In addition, we observed a sustained reduction in the abundance of phospho-AKT1(Ser473), a phosphosite


identified as marker of active AKT1 (Fig. 4B). To confirm that the effect of FTY720 was specifically dependent on PP2A activation, we performed the same experiments by pre-treating cells


with the phosphatase inhibitor okadaic acid (OA). We first tested OA in K562 cells and confirmed that the range of concentrations used did not impact the cell proliferation (Supplementary


Fig. 5A). Treatment with 5 nM OA for 2 hours induced a significant increase in pAKT Ser473, a phosphosite that is not reported as regulated by PP2A (PhosphositePlus), indicating that this


concentration might alter the activity of other phosphatases. At lower concentrations, equal to 2.5 nM, OA caused a significant increase in three PP2A targets, phospho-GSK3β Ser9,


phospho-ERK1 (Thr202/Tyr204) and phospho-AKT Thr308 with maximal expression after 2–4 hours of treatment (Supplementary Fig. 5B, C), indicating that, at this concentration, OA preferentially


inactivates PP2A. We therefore used this concentration of OA for our combination experiments with FTY720. Western blot analysis of PP2A targets in the cells pre-treated with OA for 4 h and


then treated with FTY720 for 20 hours, revealed that pre-treatment with OA restored phospho-AKT and phospho-ERK1/2 levels in KMT2A-R- leukemic cells (Fig. 4C). Whereas pre-treatment with OA


did not have any effect on the percentage of dead cells in eGFP-K562 and eGFP-Kasumi1, it significantly decreased the percentage of cell death in _KMT2A_-R-cells (Fig. 4D and Supplementary


Fig. 6), suggesting that OA rescues the effect of FTY720 in _KMT2A_-R-leukemic cells. A similar effect was obtained by knocking down _PPP2CA_, the gene encoding for the catalytic α subunit


of PP2A (Fig. 4E, F). These data indicate that the effects of FTY720 on _KMT2A_-R cells are dependent on PP2A activation. THE PHOSPHO-PROTEOME REVEALS FTY720-MEDIATED EFFECTS ON CELL


DIVISION, APOPTOSIS AND GENE TRANSCRIPTION To reveal the global impact of FTY720 on leukemic cells, we performed a phospho-proteomic analysis on two _KMT2A_-R cell lines (eGFP-THP1 and


eGFP-MV411) treated with FTY720, using in gel digestion and liquid chromatography–tandem mass spectrometry (LC–MS/MS) [48]. LC–MS/MS analysis showed a differential pattern of phospho-protein


abundance in eGFP-THP1 and eGFP-MV411 cells, with 2276 phosphosites up-regulated and 1862 phosphosites down-regulated (>2 fold and _p_ < 0.01) in eGFP-THP1, and with 1428 phosphosites


up-regulated and 743 phosphosites down-regulated (>2 fold and <0.01) in eGFP-MV411 (Fig. 5A and B and Supplementary Fig. 7), in comparison to vehicle-treated cells. The complete list


of identified proteins and phospho-peptides are provided in Supplementary Table 3. To gain deeper biological insights, we categorized the phospho-proteins using Gene Ontology (GO) (Fig. 5C),


revealing that treatment with FTY720 led to a robust decrease in cell division and an increase in apoptosis-related kinase signaling in eGFP-THP1 (Fig. 5C and Supplementary Fig. 7E). In


contrast, the data indicate a strong decrease in cell division-related kinase signaling, but a subtler increase in apoptosis eGFP-MV411 (Fig. 5C and Supplementary Fig. 7F). In addition,


FTY720-modulated phosphosites implicated in transcription regulation, chromatin organization, DNA damage repair, mRNA processing, microtubule and actin cytoskeletal organization (Fig. 5C).


We then used Kinase-Substrate Enrichment Analysis (KSEA) for the characterization of kinase activity from the phospho-proteomic dataset. The mitosis-regulating kinase Aurora kinase B (AURB),


a critical regulator of MYC protein stability and transcriptional activity [49], was the kinase most significantly impacted by FTY720 in both cell lines (Fig. 5D, E). Indeed, FTY720


decreased the phosphorylation of several AURB targets, including PLK1 (Thr210) (Fig. 5F, G, H). As expected, FTY720 inhibited MAPK3 (ERK1) and phosphorylation of ERK1 on Thr202 and Tyr204


was significantly reduced in both cell lines (Supplementary Fig. 7G); furthermore, FTY720 significantly inhibited Abl1 and CDK2 in eGFP-MV411 (Fig. 5I and Supplementary Fig. 7I). Although


the overall effect of FTY720 resulted in a significant increase in GSK3β activity, the analysis of the phosphosites regulated by this kinase indicated that this effect was mostly due to the


increased phosphorylation of a single target RCAN1 (Ser163), whereas GSK3β-dependent phosphorylation of MYC on Thr58 was significantly inhibited by FTY720 (Fig. 5J and Supplementary Fig.


7J). FTY720 significantly increased the activity of DNA damage kinase ATM, with an overall activation of targets implicated in DNA repair by non-homologous end joining (NHEJ), such as PRKDC


(DNA-PK), and inhibition of sensors involved in transcription and DNA repair by homologous recombination (HR), such as BRCA1 (Fig. 5K, L and Supplementary Fig. 7K). Taken together, these


data indicate that FTY720 reduced the activity of phospho-signaling associated to cell division and MYC stability and increased apoptosis-related and DNA damage kinase signaling in _KMT2A_-R


cells. FTY720 AFFECTS THE CORE TRANSCRIPTOME OF _KMT2A_-R LEUKEMIA As the phospho-proteomics indicated phosphorylation changes in targets involved in transcription (Fig. 5C), we performed


RNA-seq analysis of _KMT2A_-R cell line THP1 treated with FTY720 for 24 h, to capture early changes in genetic expression, preceding cell cycle arrest and apoptosis driven by FTY720 over


48–72 h. Volcano plot filtering was used to identify differentially expressed genes between vehicle control group and FTY720 -treated group (Fig. 6A). 980 genes were significantly


upregulated and 898 genes were significantly downregulated by FTY720 (fold change >1.3, _p_adj < 0.05). Functional annotation clustering of these differentially expressed genes using


the Gene ontology (GO), Kyoto Encyclopedia of gene and genomes (KEGG) and Reactome annotation databases indicated that sets of down-regulated genes were highly enriched in functional groups


that related to ribosome biogenesis and rRNA processing (Supplementary Fig. 8A), whereas up-regulated genes were highly enriched in functional groups that related to myeloid cell activation


(Supplementary Fig. 8B). In addition, upon treatment with FTY720, genes involved in autophagy, intrinsic apoptotic signaling pathway, extrinsic apoptotic signaling pathway and cell cycle


arrest resulted upregulated (Supplementary Fig. 8B). Thus, these data corroborate our previous findings on cell cycle arrest and apoptosis and also indicate that FTY720 can induce cell death


by multiple mechanisms, as reported in other models [44, 45, 50, 51]. To investigate whether there was any overlap between the phospho-proteomic data and the RNA-seq data, we intersected


the two datasets. The results indicate that 59 out of 980 genes upregulated by FTY720, code for proteins that undergo changes in phosphorylation and 98 out of 898 genes downregulated by


FTY720, code for protein that undergo changes in phosphorylation (Supplementary Fig. 8C, D and Supplementary Tables 4 and 5). Among the genes down-regulated by FTY720 and that encode for


proteins that are also hypo-phosporylated by FTY720, we validated PLK1, a downstream target of Aurora kinase B and mediator of MYC stability [49, 52, 53] (Fig. 6B). The western blot analysis


indicates that PLK1 is downregulated in Kasumi1, THP1, and MV411 upon FTY720 treatment (Fig. 6B). Phospho-PLK1 (T210), a phosphosite regulated by AURB, which was identified in our


phospho-proteomics, was undetectable in these cell lines. In K562, PLK1 expression and phosphorylation on T210 did not change upon treatment with FTY720 or when SET was KD (Supplementary


Fig. 9A). More importantly the RNA-seq data indicated that, upon FTY720 treatment, several genes overexpressed in cancer, including _MYC_ and _SET_ were downregulated (Supplementary Table


6), as well as genes associated with histone methyltransferase activity, among which several members of the _KMT2A_- fusion epigenetic complex, and _HOXA9/MEIS1_ target genes [3, 8,9,10]


(Supplementary Table 7). We performed RT-qPCR and western blot to validate the decreased expression of _MYC_ and _SET_ upon FTY720 treatment (Fig. 6C, D and Supplementary Fig. 9B-C). Upon


FTY720 treatment, _MYC_ mRNA and protein expression was down-regulated in Kasumi1 and in the _KMT2A_-R cell lines, but not in K562 (Fig. 6C, D and Supplementary Fig. 9B-C). _SET_ mRNA was


down-regulated in all leukemic cells (Fig. 6C) but, SET protein was significantly reduced only in _KMT2A_-R-cells (Fig. 6D and Supplementary Fig. 9B). RT-qPCR also confirmed a specific


decrease in the expression of the _KMT2A_ target genes _HOXA9_ and _HOXA10_, in _KMT2A_-R-cells, upon FTY720 treatment (Fig. 6C); these genes were also specifically down-regulated in


_KMT2A_-R-cells, but not in Kasumi1, when SET was knocked down (Fig. 6E, F), suggesting that SET might regulate the expression of _HOXA_ genes in _KMT2A_-R-cells. Previous reports indicated


that SET and the oncofusion protein SET::NUP214 modulate the expression of _HOXA_ gene cluster in HeLa cell line and in T-ALL primary samples [54,55,56]. To identify whether SET was enriched


on _HOXA9_ and _HOXA10_ promoters, we performed chromatin immunoprecipitation (ChIP) experiments. As expected, KMT2A localized on the promoters of both _HOXA9_ and _HOXA10_; in contrast,


SET was enriched only on _HOXA10_ promoter (Fig. 6G and Supplementary Figs. 9E and 10). Immunoprecipitation experiments revealed that SET interacted with both KMT2A and KMT2A-fusion protein


(Fig. 6H–K and Supplementary Fig. 9F–G). Collectively, our results indicate that genetic and pharmacological modulation of SET rewires the _KMT2A_-R- core gene expression signature and


reduces the expression of key genes critical for sustaining this disease. FTY720 LEADS TO INCREASED SENSITIVITY OF _KMT2A_-R LEUKEMIA TO CHEMOTHERAPY Daunorubicin is an anthracycline


included in the intensive multiagent chemotherapy to induce remission in _KMT2A_-R-AML patients [1]. We investigated whether SET targeting via FTY720 could enhance daunorubicin-induced


cytotoxicity in _KMT2A_-R-cells. To this aim, we tested 5 µM FTY720 with 10 nM daunorubicin, a concentration that had shown a very modest effect on the proliferation and survival of AML


cells, including those carrying _KMT2A-_translocations. Whereas the combination treatment FTY720 + Daunorubicin did not have any effect on eGFP-K562, the percentage of dead cells was


significantly high for all the AML cell lines (Fig. 7A). The cell death increase was modest only for eGFP-Kasumi1 cell line, but the effect was very strong in _KMT2A_-R-cell lines, namely


eGFP-THP1 and eGFP-MV411 (Fig. 7A and Supplementary Fig. 11). To assess the biological importance and therapeutic relevance of SET targeting via FTY720 in _KMT2A_-R-leukemia, we tested


FTY720 in combination with daunorubicin in two _KMT2A_-R-patient-derived-xenograft (PDX) models in vitro. Combination treatment resulted in a significant reduction of colony number compared


with vehicle and with single drug treatment of all samples (74% reduction in comparison to vehicle) (Fig. 7B, C), suggesting that FTY720 treatment enhances the response to daunorubicin.


DISCUSSION SET is an endogenous PP2A inhibitor overexpressed in several types of solid tumors and hematological malignancies [21,22,23,24,25,26]. Mechanistically, SET over-expression and the


resulting PP2A inhibition is critical for the maintenance of the leukemogenic program by BCR::ABL in CML [21, 27]. In contrast, the exact molecular mechanisms linking a SET oncoprotein


pathway with aggressive AML outcomes are not known. Here we report that SET is over-expressed in the _KMT2A_-R subtypes of AML and ALL and it positively correlates with the expression of


_MEIS_ and _HOXA_ genes. We also show that, in _KMT2A_-R-cell lines, SET is relatively more abundant in the cytoplasm than in the nucleus and is phosphorylated on Serine residues, which is


in line with the notion that the nuclear import of SET is inhibited by phosphorylation on SER9 and SER24 [26, 33, 34]. We demonstrate that SET silencing has a detrimental effect on the


proliferation of _KMT2A_-wt- leukemic cells, as also observed in CML and solid tumors [21, 57,58,59]. More importantly, we show for the first time that SET silencing completely abolishes the


ability of _KMT2A_-R-leukemic cells to form colonies in semi-solid medium, indicating that SET plays an important role in the clonogenic ability of _KMT2A_-R-cells. To provide a proof of


concept that pharmacological modulation of SET is a promising strategy for the treatment of _KMT2A_-R-leukemia, we tested in vitro FTY720 (Fingolimod), a proven inhibitor of the interaction


between SET and PP2A [28, 40,41,42,43], that had been shown to induce cell death in several solid tumors and leukemia models by various mechanisms [44, 45, 50, 51]. In agreement with


previous reports on CML [28], we show that FTY720 has a modest negative impact on the proliferation of _BCR:ABL_ + _KMT2A_-wt- leukemic cell line K562 and promotes cell death. In _KMT2A_-wt-


leukemic cell line REH, FTY720 has a greater cytostatic and cytotoxic impact, in agreement with data previously published [44]. In contrast to [45], in Kasumi1, FTY720 has a modest effect


on proliferation and it does not induce cell death. Whereas both FTY720 and SET KD have a similar impact on _KMT2A_-wt cell lines K562 and REH, FTY720 does not fully mimic the effect of SET


KD in Kasumi1, as these cells are more sensitive to SET KD than to FTY720 treatment. This might be explained by the residual level of SET. Indeed, whereas the KD induces a 90% reduction in


SET protein levels, FTY720 does not reduce the expression of SET protein in Kasumi1. In _KMT2A_-R cells, FTY720 causes cell cycle arrest and promotes cell death. Accordingly, our


phospho-proteomic and RNA-seq analyses in KMT2A-R-models reveal decreased activity of kinases implicated in cell division and enhanced expression of genes promoting cell cycle arrest and


apoptosis. In particular, phospho-proteomic data show that FTY720 has an inhibitory effect on the signaling mediated by AURB, PLK1, ERK1 and MYC, suggesting reactivation of their upstream


negative regulator PP2A [47]. Rescue experiments with the PP2A inhibitor okadaic acid, as well as by silencing of _PPP2CA_, the gene encoding for PP2A catalytic subunit α, prove that some of


the effects of FTY720 on _KMT2A_-R-cells are dependent on PP2A activation. We are aware that some of the proteomic changes observed might not be due to PP2A activation or they might be


compensatory effects. Further studies in PPP2CA and PPP2R1A KD cells are needed to validate PP2A as mediator of each of these aforementioned signaling pathways. Significantly,


phospho-proteomic analyses indicate that FTY720 affects pathways implicated in gene transcription. RNA-seq analysis shows that FTY720 reduces the expression of SET mRNA, a result confirmed


by RT-qPCR in _KMT2A_-R as well as _KMT2A_-wt-leukemic cells. Interestingly, western blot experiments show a sustained and specific reduction of SET protein expression following FTY720


treatment only in _KMT2A_-R-leukemic cells. This latter result uncovers a novel molecular mechanism underlying FTY720 action, distinct from the current understanding of FTY720 as a


sphingosine mimetic capable of disrupting the interaction between SET and PP2A without affecting the levels of SET [41, 42, 46]. The effect of FTY720 on SET transcription could be explained


by the modulation of MYC, which is a transcriptional activator of SET [60]. Previous studies recognized MYC as a critical substrate of PP2A complex in cancer [58, 59, 61]. In pancreatic and


breast cancer cells, PP2A activation by KD of SET or by the SET antagonist OP449 decreases Ser62 and Thr58 phosphorylation of MYC and directs MYC towards ubiquitin-mediated proteasomal


degradation [58, 59]. Our data support the hypothesis of a feedforward loop between PP2A, AURB, PLK1, MYC, and SET whereby FTY720 reduces MYC transcription, by reducing the activity of AURB,


an upstream regulator of MYC [49], and it compromises MYC stability, by reducing the activity of AURB, PLK1, ERK1 and GSK3β, which modulate MYC by phosphorylation on S62 and T58 [49, 52,


53, 61]. Proteasomal degradation of MYC suppresses MYC-dependent gene transcription and therefore expression of downstream targets PLK1 [53] and SET [60] which, in turn, might feed into the


activation of PP2A, with profound effects on survival and proliferation of leukemic cells (Fig. 8). What our model does not fully explain is how SET KD or pharmacological inhibition by


FTY720 regulate the expression of _KMT2A_ signature genes. Our data indicate that SET interacts with both KMT2A wt and KMT2A fusion proteins and that it is recruited to the promoter of


_HOXA10_, suggesting that SET might recruit KMT2A to the promoter of this gene or vice versa. This is supported by a yeast two hybrid screening that reported KMT2A as a SET interactor [29]


and by experiments performed in HeLa cells showing that the interaction between SET and KMT2A has a synergistic effect on the activation of _HOXA_ gene expression [54]. More recent studies


report that the oncofusion protein SET::NUP214, which has been found in a subset of T-ALL patients with abnormal expression of _HOXA_ gene cluster, recruits both KMT2A and DOT1L to the


promotor regions of _HOXA9_ and _HOXA10_ [55, 56]. Notably, a phospho-proteomic study in HeLa cells, where _SET_ was knocked down by RNAi, identified several targets directly involved in RNA


Polymerase II (RNAPII)-mediated transcription and RNA processing, providing a possible link between SET, PP2A, and gene transcription [62]. In addition, a study identified CDK9, an


important regulator of RNAPII and critical player in KMT2A-fusion-mediated transcription [18], as a PP2A target, corroborating the crosstalk between phosphorylation and transcription [63].


Moreover, in a recent study, AAkula et al. combined the data from two phospho-proteome studies, including the one performed on HeLa where SET was downregulated by siRNA [62], to identify


phospho-proteins co-regulated by RAS and PP2A [64]. The study indicates that PP2A- and RAS-mediated phosphorylation converge on epigenetic complexes, including the DOT1L complex. The DOT1L


phosphosites Ser900 and Ser1104, identified as dephosphorylated by siSET in the study by Aaakula et al., were also found dephosphorylated by FTY720 in THP1 (Supplementary Table 2),


supporting the concept that SET mediates its anti-tumor effects though modulation of relevant epigenetic factors. Another SET-dependent DOT1L phosphosite identified by Aakula et al.,


Ser1001, was found to correlate positively with _HOXA_ gene expression in _KMT2A_-R-AML patients [65]. Therefore, the molecular mechanisms implicated in the SET-mediated regulation of KMT2A


transcriptional signature warrant further investigation. Integrating these published phospho-proteomes and validating the functional role of some of these phosphorylation sites might might


reveal further mechanistic insights into the role of SET and PP2A inhibition in leukemic transcription and chromatin accessibility and should be explored in future studies. Consistent with


its anti-proliferative effect, FTY720 treatment was shown to be synergistic with cytotoxic chemotherapeutic agent, doxorubicin, in solid tumors [66, 67]. We demonstrated that FTY720


increases the response of _KMT2A_-R-cells to daunorubicin, a standard chemotherapeutic agent used in induction and consolidation treatment for _KMT2A_-R patients. This effect might be


partially dependent on the impact of FTY720 on the DNA damage response barrier; by hyperactivating error-prone DDR pathways, such as the NHEJ via PRKDC (DNA-PK), and by simultaneously


inhibiting HR-mediated DNA repair via modulation of BRCA1 phosphorylation, FTY720 might offset the DDR HR- mediated, essential to repair faithfully the DNA damage lesions induced by


daunorubicin, and drive the leukemic cells to death. Since the anti-cancer effect of FTY720 is an off-target effect and the dose used as an anticancer drug is much higher than the dose used


as immune-suppressor, it has been postulated that FTY720 might be too toxic to be used in clinics. In THP1-based mouse models, we observed immunosuppression, lymphopenia and severe weight


loss (data not shown). As FTY720 exerts its immunosuppressive properties after being phosphorylated in vivo in FTY720-P, a mimetic of sphingosine-1-phosphate (S1P) critical for lymphocyte


trafficking [40], and several studies indicate that the phosphorylation of FTY720 is not essential to exert anti-leukemic effects [27, 28, 50], studies have been focused on the development


of FTY720 analogs with anti-cancer but no immunosuppressive properties. Such molecules (AAl-149 (S), (S)-FTY720-OMe, (S)-FTY720-regioisomer, and OSU- 2S, MP07-66, CM-1231) have been shown to


activate PP2A and induce apoptosis in leukemia models [46, 68, 69]. Furthermore, SH-RF-177, a FTY720 analog that is efficiently phosphorylated but that does not activate S1P receptor 1,


shows anti-leukemic activity on ALL cells [70]. Therefore, further studies are needed to evaluate the potential of these analogs in _KMT2A_-R-leukemia. In conclusion, our study demonstrates


for the first time that the expression of PP2A inhibitor SET positively correlates with _MEIS_ and _HOXA_ genes. SET is critical for the clonogenic ability of _KMT2A-_R-leukemic cells and


can be pharmacologically targeted by using FTY720, an immunosuppressive sphingosine mimetic that reactivates PP2A by suppressing SET. We provide the evidence that silencing and


pharmacological inhibition of SET in _KMT2A_-R-leukemic cells promote cell cycle arrest and apoptosis, rewire the transcriptional program, down-regulate the expression of _HOXA_ genes and


direct MYC toward proteasomal degradation. These data shed light on SET as a new therapeutic target of _KMT2A_-R leukemia. MATERIAL AND METHODS CELL LINES The cells lines used for this study


and the experimental conditions are indicated in supplementary material and methods. Some of the cell lines used in this study were stably transduced with a lentivirus vector expressing the


enhanced green fluorescent protein (eGFP) and positive clones were sorted by FACS, as described [38]. The cell lines eGFP-K562, eGFP-Kasumi1, eGFP-THP1, eGFP-MV411, eGFP-REH, eGFP-SEM,


eGFP-Hb1119, and eGFP-U937 were further tested for authenticity by STR profiling (Eurofin Genomics). PRIMARY CELLS Primary samples, described in supplementary material and methods, were


obtained from the Cancer Tissue Bank at the Barts Cancer Institute (London) under ethical approval (REC reference: 17/WM/0428). PDX SAMPLES The KMT2A-PDX, described in supplementary material


and methods and in [71, 72], were a generous gift of Prof. Owen Williams. VIRUS PRODUCTION AND CELL TRANSDUCTION Knock-down of _SET_ was conducted in vitro using the lentiviral viruses


purchased from Sigma-Merck, as described in supplementary material and methods. The viruses are based on the plasmid vector pLKO.p1 co-expressing a puromycin resistance cassette to enable


transduction selection of mammalian cells and ensure the establishment of stable clones. As a transduction negative control, we used non targeting shRNA control (shScramble), designed to


target no known gene sequence. The pLKO, 1-puro CMV-tag red fluorescent protein (RFP), with no shRNA insert and expressing the RFP, was used as a transduction positive control. CELL


PROLIFERATION AND CELL DEATH ANALYSIS Cell proliferation and cell death were monitored by GFP fluorescence and by measuring the percentage of GFP negative cells as described in ref. [38] and


in supplementary material and methods. REAGENTS FTY720 was purchased from Selleckchem (S5002). The antibodies used in this study are listed in supplementary material and methods. RT-QPCR


AND CHIP Quantitative real-time PCR (RT-qPCR) was performed using specific primers from Sigma-Merck. ChIP assay was performed as previously reported [6, 73]. The primers are listed in


supplementary material and methods. PHOSPHO-PROTEOMIC EXPERIMENTS Phospho-proteomic experiments were performed using mass spectrometry as reported in refs. [48, 74] and in supplementary


material and methods. MICROARRAY, RNA-SEQ AND BIOINFORMATIC ANALYSIS The expression profile of _SET_ in human HSC and blood cells was obtained from Bloodspot Gene expression profiles


(GSE42519) [31]. The expression profile of _SET mRNA_ in AML patients was obtained from Leucegene gene expression profiles (GSE62190, GSE66917, GSE67039) [10]. The expression of mouse _SET_


mRNA (probe1421819_a_at) was analyzed by using the micro-array data from GSE13690 [35]. This dataset was generated by Somervaille et al., by analyzing the transcriptional profiles of 34


mouse _KMT2A_-R-AML. In this study, Somervaille et al. assessed the relative LSC frequency of these AML by determining the colony-forming cell (CFC) frequencies of spleen and bone marrow


cells collected from leukemic mice. The transcriptional profiles were split in two groups: a group labeled as high-LSC frequency (comprising AML initiated by _KMT2A::MLLT3_ and


_KMT2A:MLLT1_) and one labeled as low-LSC frequency (comprising AML initiated by _KMT2A::AFF1p_, _KMT2A::AF10_ and _KMT2A::GAS7_). Meta-analyses of micro-array data from the PrognoScan


database (GSE12417) were used to determine the prognosis of AML patients expressing high or low levels of SET [32]. The data represent the analysis of 163 patients treated in the German


AMLCG 1999 trial. The survival analysis in PrognoScan is based the minimum p-value approach to find the cutpoint in continuous gene expression measurement for grouping patients. The publicly


accessible online database cBioPortal (https://www.cbioportal.org/, accessed on 29 May 2023) was used to explore the correlation of SET with the self-renewal leukemic stem cell (LSC) marker


genes published by Gentles et al. [36] and by Krivtsov et al. [37]. We checked four AML cohorts: OHSU (Cancer cell 2022, _n_ = 942), OHSU (Nature 2018, _n_ = 672), TCGA (Firehose Legacy,


_n_ = 200) and TCGA (NEJM 2013, _n_ = 200). The co-expression of SET with the genes of interest was tested by the Spearman’s correlation coefficient (Rs), that summarize the strength and


direction (positive or negative) of a relationship between two variables. A significant correlation of co-expression with SET was considered according to the absolute value of the Spearman’s


correlation coefficient as weak (0.20–0.39), moderate (0.40–0.59), strong (0.60–0.79) or very strong (0.80–1) when the _p_ value was lower than 0.05 (_p_ < 0.05). The graphs were made


using GraphPad Prism 9 software. The RNA-seq in FTY720- vs vehicle-treated THP1 cells was performed by Novogene. Downstream analysis was performed using a combination of programs including


STAR, HTseq, Cufflink and Novogene wrapped scripts. Differential expression analysis between two conditions/groups (three biological replicates per condition) was performed using the DESeq2


R package (2_1.6.3), as described in supplementary material and methods. STATISTICAL ANALYSIS Data are expressed as mean ± standard deviation (SD) from at least three independent


experiments, unless stated otherwise. Statistical significance was determined using GraphPad Prism 7 with the tests reported in the figure legends. Additional methods are available in the


supplementary materials and methods. DATA AVAILABILITY The FTY720-RNASeq datasets generated during the current study are available in the GEO repository (GSE218708). The three plot shown in


Fig. 1 has been drawn based on data obtained from Bloodspot Gene expression profiles (GSE42519). The heatmap shown in Fig. 1 has been generated by analyzing data available from Leucegene


(GSE62190, GSE66917, GSE67039). The expression of SET mRNA in murine KMT2A-LSC has been obtained by meta-analyses of micro-array data from GSE13690. Kaplan–Meier analysis of AML patients


with high and low expression levels of SET is based on micro-array data from the PrognoScan database (GSE12417). The mass spectrometry proteomics data have been deposited to the


ProteomeXchange Consortium via the PRIDE partner repository with the dataset identifier PXD038288 and 10.6019/PXD038288. REFERENCES * Winters AC, Bernt KM. MLL-rearranged leukemias-an update


on science and clinical approaches. Front Pediatr. 2017;5:4. Article  PubMed  PubMed Central  Google Scholar  * Meyor C, Larghero P, Lopes BA, Burmeister T, Gröger D, Sutton R, et al. The


_KMT2A_ recombinome of acute leukemias in 2023. Leukemia. 2023;37:988–1005. Article  Google Scholar  * Chan AKNKN, Chen C-WW. Rewiring the epigenetic networks in MLL-rearranged leukemias:


epigenetic dysregulation and pharmacological interventions. Front Cell Dev Biol. 2019;7:81. Article  PubMed  PubMed Central  Google Scholar  * Bernt KM, Zhu N, Sinha AU, Vempati S, cell F-J.


MLL-rearranged leukemia is dependent on aberrant H3K79 methylation by DOT1L. Cancer Cell. 2011;20:66–78. Article  CAS  PubMed  PubMed Central  Google Scholar  * Dawson MA, Prinjha RK,


Dittmann A, Nature GG. Inhibition of BET recruitment to chromatin as an effective treatment for MLL-fusion leukaemia. Inhibition of BET recruitment to chromatin as an effective treatment for


MLL-fusion leukaemia. Nature. 2011;478:529–33. Article  CAS  PubMed  PubMed Central  Google Scholar  * Fioretti T, Cevenini A, Zanobio M, Raia M, Sarnataro D, Salvatore F, et al. Crosstalk


between 14-3-3theta and AF4 enhances MLL-AF4 activity and promotes leukemia cell proliferation. Cell Oncol. 2019;42:829–45. Article  CAS  Google Scholar  * MacPherson L, Anokye J, Yeung MM,


Lam EYN, Chan YC, Weng CF, et al. HBO1 is required for the maintenance of leukaemia stem cells. Nature. 2020;577:266–70. Article  CAS  PubMed  Google Scholar  * Zeisig BB, Milne T,


García-Cuéllar M-PP, Schreiner S, Martin M-EE, Fuchs U, et al. Hoxa9 and Meis1 are key targets for MLL-ENL-mediated cellular immortalization. Mol Cell Biol. 2004;24:617–28. Article  CAS 


PubMed  PubMed Central  Google Scholar  * Faber J, Krivtsov AV, Stubbs MC, Wright R, Davis TN, van den Heuvel-Eibrink M, et al. HOXA9 is required for survival in human MLL-rearranged acute


leukemias. Blood. 2009;113:2375–85. Article  CAS  PubMed  PubMed Central  Google Scholar  * Lavallee VP, Baccelli I, Krosl J, Wilhelm B, Barabe F, Gendron P, et al. The transcriptomic


landscape and directed chemical interrogation of MLL-rearranged acute myeloid leukemias. Nat Genet. 2015;47:1030–7. Article  CAS  PubMed  Google Scholar  * Esposito MT, Zhao L, Fung TK, Rane


JK, Wilson A, Martin N, et al. Synthetic lethal targeting of oncogenic transcription factors in acute leukemia by PARP inhibitors. Nat Med. 2015;21:1481–90. Article  CAS  PubMed  Google


Scholar  * Miyamoto R, Kanai A, Okuda H, Komata Y, Takahashi S, Matsui H, et al. HOXA9 promotes MYC-mediated leukemogenesis by maintaining gene expression for multiple anti-apoptotic


pathways. eLife. 2021;10:e64148. Article  CAS  PubMed  PubMed Central  Google Scholar  * Wong NM, So CWE. Novel therapeutic strategies for MLL-rearranged leukemias. Biochim Biophys Acta Gene


Regul Mech. 2020;1863:194584. Article  CAS  PubMed  Google Scholar  * Tsakaneli A, Williams O. Drug repurposing for targeting acute leukemia with KMT2A (MLL)-gene rearrangements. Front


Pharmacol. 2021;12:741413. Article  CAS  PubMed  PubMed Central  Google Scholar  * Cantilena S, Gasparoli L, Pal D, Heidenreich O, Klusmann JH, Martens JHA, et al. Direct targeted therapy


for MLL-fusion-driven high-risk acute leukaemias. Clin Transl Med. 2022;12:e933. Article  CAS  PubMed  PubMed Central  Google Scholar  * Li D, Yu X, Kottur J, Gong W, Zhang Z, Storey AJ, et


al. Discovery of a dual WDR5 and Ikaros PROTAC degrader as an anti-cancer therapeutic. Oncogene. 2022;41:3328–40. Article  CAS  PubMed  PubMed Central  Google Scholar  * Kampen KR, Ter Elst


A, Mahmud H, Scherpen FJ, Diks SH, Peppelenbosch MP, et al. Insights in dynamic kinome reprogramming as a consequence of MEK inhibition in MLL-rearranged AML. Leukemia. 2014;28:589–99.


Article  CAS  PubMed  Google Scholar  * Baker A, Gregory GP, Verbrugge I, Kats L, Hilton JJ, Vidacs E, et al. The CDK9 inhibitor dinaciclib exerts potent apoptotic and antitumor effects in


preclinical models of MLL-rearranged acute myeloid leukemia. Cancer Res. 2016;76:1158–69. Article  CAS  PubMed  Google Scholar  * Cruickshank MN, Ford J, Cheung LC, Heng J, Singh S, Wells J,


et al. Systematic chemical and molecular profiling of MLL-rearranged infant acute lymphoblastic leukemia reveals efficacy of romidepsin. Leukemia. 2017;31:40–50. Article  CAS  PubMed 


Google Scholar  * von Lindern M, Breems D, van Baal S, Adriaansen H, Grosveld G. Characterization of the translocation breakpoint sequences of two DEK-CAN fusion genes present in t(6;9)


acute myeloid leukemia and a SET-CAN fusion gene found in a case of acute undifferentiated leukemia. Genes Chromosomes Cancer. 1992;5:227–34. Article  Google Scholar  * Neviani P, Santhanam


R, Trotta R, Notari M, Blaser BW, Liu S, et al. The tumor suppressor PP2A is functionally inactivated in blast crisis CML through the inhibitory activity of the BCR/ABL-regulated SET


protein. Cancer Cell. 2005;8:355–68. Article  CAS  PubMed  Google Scholar  * Cristobal I, Garcia-Orti L, Cirauqui C, Alonso MM, Calasanz MJ, Odero MD. PP2A impaired activity is a common


event in acute myeloid leukemia and its activation by forskolin has a potent anti-leukemic effect. Leukemia. 2011;25:606–14. Article  CAS  PubMed  Google Scholar  * Christensen DJ, Chen Y,


Oddo J, Matta KM, Neil J, Davis ED, et al. SET oncoprotein overexpression in B-cell chronic lymphocytic leukemia and non-Hodgkin lymphoma: a predictor of aggressive disease and a new


treatment target. Blood. 2011;118:4150–8. Article  CAS  PubMed  PubMed Central  Google Scholar  * Cristobal I, Garcia-Orti L, Cirauqui C, Cortes-Lavaud X, Garcia-Sanchez MA, Calasanz MJ, et


al. Overexpression of SET is a recurrent event associated with poor outcome and contributes to protein phosphatase 2A inhibition in acute myeloid leukemia. Haematologica. 2012;97:543–50.


Article  CAS  PubMed  PubMed Central  Google Scholar  * Sirma Ekmekci S, G Ekmekci C, Kandilci A, Gulec C, Akbiyik M, Emrence Z, et al. SET oncogene is upregulated in pediatric acute


lymphoblastic leukemia. Tumori. 2012;98:252–6. Article  PubMed  Google Scholar  * Di Mambro A, Esposito MT. Thirty years of SET/TAF1Beta/I2PP2A: from the identification of the biological


functions to its implications in cancer and Alzheimer’s disease. Biosci Rep. 2022;42:BSR20221280. Article  PubMed  PubMed Central  Google Scholar  * Neviani P, Harb JG, Oaks JJ, Santhanam R,


Walker CJ, Ellis JJ, et al. PP2A-activating drugs selectively eradicate TKI-resistant chronic myeloid leukemic stem cells. J Clin Investig. 2013;123:4144–57. Article  CAS  PubMed  PubMed


Central  Google Scholar  * Neviani P, Santhanam R, Oaks JJ, Eiring AM, Notari M, Blaser BW, et al. FTY720, a new alternative for treating blast crisis chronic myelogenous leukemia and


Philadelphia chromosome-positive acute lymphocytic leukemia. J Clin Investig. 2007;117:2408–21. Article  CAS  PubMed  PubMed Central  Google Scholar  * Adler HT, Nallaseth FS, Walter G,


Tkachuk DC. HRX leukemic fusion proteins form a heterocomplex with the leukemia-associated protein SET and protein phosphatase 2A. J Biol Chem. 1997;272:28407–14. Article  CAS  PubMed 


Google Scholar  * Esposito MT. The impact of PI3-kinase/RAS pathway cooperating mutations in the evolution of KMT2A-rearranged leukemia. Hemasphere. 2019;3:e195. Article  PubMed  PubMed


Central  Google Scholar  * Rapin N, Porse BT. Oncogenic fusion proteins expressed in immature hematopoietic cells fail to recapitulate the transcriptional changes observed in human AML.


Oncogenesis. 2014;3:e106. Article  CAS  PubMed  PubMed Central  Google Scholar  * Metzeler KH, Hummel M, Bloomfield CD, Spiekermann K, Braess J, Sauerland MC, et al. An 86-probe-set


gene-expression signature predicts survival in cytogenetically normal acute myeloid leukemia. Blood. 2008;112:4193–201. Article  CAS  PubMed  PubMed Central  Google Scholar  * Yu G, Yan T,


Feng Y, Liu X, Xia Y, Luo H, et al. Ser9 phosphorylation causes cytoplasmic detention of I2PP2A/SET in Alzheimer disease. Neurobiol Aging. 2013;34:1748–58. Article  CAS  PubMed  Google


Scholar  * Arriazu E, Vicente C, Pippa R, Peris I, Martínez-Balsalobre E, García-Ramírez P, et al. A new regulatory mechanism of protein phosphatase 2A activity via SET in acute myeloid


leukemia. Blood Cancer J. 2020;10:3. Article  PubMed  PubMed Central  Google Scholar  * Somervaille TC, Matheny CJ, Spencer GJ, Iwasaki M, Rinn JL, Witten DM, et al. Hierarchical maintenance


of MLL myeloid leukemia stem cells employs a transcriptional program shared with embryonic rather than adult stem cells. Cell Stem Cell. 2009;4:129–40. Article  CAS  PubMed  PubMed Central


  Google Scholar  * Gentles AJ, Plevritis SK, Majeti R, Alizadeh AA. Association of a leukemic stem cell gene expression signature with clinical outcomes in acute myeloid leukemia. JAMA.


2010;304:2706–15. Article  CAS  PubMed  PubMed Central  Google Scholar  * Krivtsov AV, Twomey D, Feng Z, Stubbs MC, Wang Y, Faber J, et al. Transformation from committed progenitor to


leukaemia stem cell initiated by MLL-AF9. Nature. 2006;442:818–22. Article  CAS  PubMed  Google Scholar  * Arroyo-Berdugo Y, Sendino M, Greaves D, Nojszewska N, Idilli O, So CW, et al. High


throughput fluorescence-based in vitro experimental platform for the identification of effective therapies to overcome tumour microenvironment-mediated drug resistance in AML. Cancers.


2023;15:1988. Article  CAS  PubMed  PubMed Central  Google Scholar  * Ghasemi M, Turnbull T, Sebastian S, Kempson I. The MTT assay: utility, limitations, pitfalls, and interpretation in bulk


and single-cell analysis. Int J Mol Sci. 2021;22:12827. Article  CAS  PubMed  PubMed Central  Google Scholar  * White C, Alshaker H, Cooper C, Winkler M, Pchejetski D. The emerging role of


FTY720 (Fingolimod) in cancer treatment. Oncotarget. 2016;7:23106–27. Article  PubMed  PubMed Central  Google Scholar  * Switzer CH, Cheng RY, Vitek TM, Christensen DJ, Wink DA, Vitek MP.


Targeting SET/I(2)PP2A oncoprotein functions as a multi-pathway strategy for cancer therapy. Oncogene. 2011;30:2504–13. Article  CAS  PubMed  PubMed Central  Google Scholar  * Pippa R,


Dominguez A, Christensen DJ, Moreno-Miralles I, Blanco-Prieto MJ, Vitek MP, et al. Effect of FTY720 on the SET-PP2A complex in acute myeloid leukemia; SET binding drugs have antagonistic


activity. Leukemia. 2014;28:1915–8. Article  CAS  PubMed  Google Scholar  * Palma RM, Parnham SR, Li Y, Oaks JJ, Peterson YK, Szulc ZM, et al. The NMR‐based characterization of the


FTY720‐SET complex reveals an alternative mechanism for the attenuation of the inhibitory SET‐PP2A interaction. FASEB J. 2019;33:7647–66. Article  PubMed  PubMed Central  Google Scholar  *


Wallington-Beddoe CT, Hewson J, Bradstock KF, Bendall LJ. FTY720 produces caspase-independent cell death of acute lymphoblastic leukemia cells. Autophagy. 2011;7:707–15. Article  CAS  PubMed


  Google Scholar  * Chen L, Luo L-F, Lu J, Li L, Liu Y-F, Wang J, et al. FTY720 induces apoptosis of M2 subtype acute myeloid leukemia cells by targeting sphingolipid metabolism and


increasing endogenous ceramide levels. PLoS ONE. 2014;9:e103033. Article  PubMed  PubMed Central  Google Scholar  * Ciccone M, Calin GA, Perrotti D. From the biology of PP2A to the PADs for


therapy of hematologic malignancies. Front Oncol. 2015;5:21. Article  PubMed  PubMed Central  Google Scholar  * Perrotti D, Neviani P. Protein phosphatase 2A: a target for anticancer


therapy. Lancet Oncol. 2013;14:e229–38. Article  CAS  PubMed  PubMed Central  Google Scholar  * Hijazi M, Smith R, Rajeeve V, Bessant C, Cutillas PR. Reconstructing kinase network topologies


from phosphoproteomics data reveals cancer-associated rewiring. Nat Biotechnol. 2020;38:493–502. Article  CAS  PubMed  Google Scholar  * Jiang J, Wang J, Yue M, Cai X, Wang T, Wu C, et al.


Direct phosphorylation and stabilization of MYC by aurora B kinase promote T-cell leukemogenesis. Cancer Cell. 2020;37:200–15.e5. Article  CAS  PubMed  PubMed Central  Google Scholar  *


Roberts KG, Smith AM, McDougall F, Carpenter H, Horan M, Neviani P, et al. Essential requirement for PP2A inhibition by the oncogenic receptor c-KIT suggests PP2A reactivation as a strategy


to treat c-KIT+ cancers. Cancer Res. 2010;70:5438–47. Article  CAS  PubMed  PubMed Central  Google Scholar  * Young MM, Bui V, Chen C, Wang H-G. FTY720 induces non-canonical


phosphatidylserine externalization and cell death in acute myeloid leukemia. Cell Death Dis. 2019;10:847. Article  PubMed  PubMed Central  Google Scholar  * Xiao D, Yue M, Su H, Ren P, Jiang


J, Li F, et al. Polo-like kinase-1 regulates Myc stabilization and activates a feedforward circuit promoting tumor cell survival. Mol Cell. 2016;64:493–506. Article  CAS  PubMed  Google


Scholar  * Ren Y, Bi C, Zhao X, Lwin T, Wang C, Yuan J, et al. PLK1 stabilizes a MYC-dependent kinase network in aggressive B cell lymphomas. J Clin Investig. 2018;128:5517–30. Article 


PubMed  PubMed Central  Google Scholar  * Shimoyama T, Kato K, Miyaji-Yamaguchi M, Nagata K. Synergistic action of MLL, a TRX protein with template activating factor-I, a histone chaperone.


FEBS Lett. 2005;579:757–62. Article  CAS  PubMed  Google Scholar  * Vlierberghe P, van Grotel M, Tchinda J, Lee C, Beverloo HB, van der Spek PJ, et al. The recurrent SET-NUP214 fusion as a


new HOXA activation mechanism in pediatric T-cell acute lymphoblastic leukemia. Blood. 2008;111:4668–80. Article  PubMed  PubMed Central  Google Scholar  * Cigdem S, Saito S, Nishikata D,


Nagata K, Okuwaki M. SET-NUP214 and MLL cooperatively regulate the promoter activity of the HoxA10 gene. Genes Cells Devot Mol Cell Mech. 2021;26:830–7. Article  CAS  Google Scholar  *


Sobral LM, Sousa LO, Coletta RD, Cabral H, Greene LJ, Tajara EH, et al. Stable SET knockdown in head and neck squamous cell carcinoma promotes cell invasion and the mesenchymal-like


phenotype in vitro, as well as necrosis, cisplatin sensitivity and lymph node metastasis in xenograft tumor models. Mol Cancer. 2014;13:32. Article  PubMed  PubMed Central  Google Scholar  *


Farrell AS, Allen-Petersen B, Daniel CJ, Wang X, Wang Z, Rodriguez S, et al. Targeting inhibitors of the tumor suppressor PP2A for the treatment of pancreatic cancer. Mol Cancer Res.


2014;12:924–39. Article  CAS  PubMed  PubMed Central  Google Scholar  * Janghorban M, Farrell AS, Allen-Petersen BL, Pelz C, Daniel CJ, Oddo J, et al. Targeting c-MYC by antagonizing PP2A


inhibitors in breast cancer. Proc Natl Acad Sci USA. 2014;111:9157–62. Article  CAS  PubMed  PubMed Central  Google Scholar  * Pippa R, Dominguez A, Malumbres R, Endo A, Arriazu E,


Marcotegui N, et al. MYC-dependent recruitment of RUNX1 and GATA2 on the SET oncogene promoter enhances PP2A inactivation in acute myeloid leukemia. Oncotarget. 2017;8:53989–4003. Article 


PubMed  Google Scholar  * Yeh E, Cunningham M, Arnold H, Chasse D, Monteith T, Ivaldi G, et al. A signalling pathway controlling c-Myc degradation that impacts oncogenic transformation of


human cells. Nat Cell Biol. 2004;6:308–18. Article  CAS  PubMed  Google Scholar  * Kauko O, Imanishi SY, Kulesskiy E, Yetukuri L, Laajala TD, Sharma M, et al. Phosphoproteome and


drug-response effects mediated by the three protein phosphatase 2A inhibitor proteins CIP2A, SET, and PME-1. J Biol Chem. 2020;295:4194–211. Article  CAS  PubMed  PubMed Central  Google


Scholar  * Vervoort SJ, Welsh SA, Devlin JR, Barbieri E, Knight DA, Offley S, et al. The PP2A-Integrator-CDK9 axis fine-tunes transcription and can be targeted therapeutically in cancer.


Cell. 2021;184:3143–62.e32. Article  CAS  PubMed  PubMed Central  Google Scholar  * Aakula A, Sharma M, Tabaro F, Natkin R, Kamila J, Honkanen H, et al. RAS and PP2A activities converge on


epigenetic gene regulation. Life Sci Alliance. 2023;6:e202301928. Article  CAS  PubMed  PubMed Central  Google Scholar  * Casado P, Rio-Machin A, Miettinen JJ, Bewicke-Copley F,


Rouault-Pierre K, Krizsan S, et al. Integrative phosphoproteomics defines two biologically distinct groups of KMT2A rearranged acute myeloid leukaemia with different drug response


phenotypes. Signal Transduct Target Ther. 2023;8:80. Article  CAS  PubMed  PubMed Central  Google Scholar  * Rincón R, Cristóbal I, Zazo S, Arpí O, Menéndez S, Manso R, et al. PP2A


inhibition determines poor outcome and doxorubicin resistance in early breast cancer and its activation shows promising therapeutic effects. Oncotarget. 2015;6:4299–314. Article  PubMed 


PubMed Central  Google Scholar  * Cristóbal I, Manso R, Rincón R, Caramés C, Senin C, Borrero A, et al. PP2A inhibition is a common event in colorectal cancer and its restoration using


FTY720 shows promising therapeutic potential. Mol Cancer Ther. 2014;13:938–47. Article  PubMed  Google Scholar  * Zonta F, Pagano M, Trentin L, Tibaldi E, Frezzato F, Trimarco V, et al. Lyn


sustains oncogenic signaling in chronic lymphocytic leukemia by strengthening SET-mediated inhibition of PP2A. Blood. 2015;125:3747–55. Article  CAS  PubMed  Google Scholar  * Vicente C,


Arriazu E, Martínez-Balsalobre E, Peris I, Martínez-Balsalobre N, García-Ramírez P. et al. A novel FTY720 analogue targets SET-PP2A interaction and inhibits growth of acute myeloid leukemia


cells without inducing cardiac toxicity. Cancer Letters. 2020;468:1–13. Article  CAS  PubMed  Google Scholar  * McCracken AN, McMonigle RJ, Tessier J, Fransson R, Perryman, Chen B, et al.


Phosphorylation of a constrained azacyclic FTY720 analog enhances anti-leukemic activity without inducing S1P receptor activation. Leukemia. 2017;31:669–77. Article  CAS  PubMed  Google


Scholar  * Walf-Vorderwulbecke V, Pearce K, Brooks T, Hubank M, van den Heuvel-Eibrink MM, Zwaan CM, et al. Targeting acute myeloid leukemia by drug-induced c-MYB degradation. Leukemia.


2018;32:882–9. Article  CAS  PubMed  Google Scholar  * Clesham K, Walf-Vorderwulbecke V, Gasparoli L, Virely C, Cantilena S, Tsakaneli A, et al. Identification of a c-MYB-directed


therapeutic for acute myeloid leukemia. Leukemia. 2022;36:1541–9. Article  CAS  PubMed  PubMed Central  Google Scholar  * Fioretti T, Cevenini A, Zanobio M, Raia M, Sarnataro D, Cattaneo F,


et al. Nuclear FGFR2 Interacts with the MLL-AF4 oncogenic chimera and positively regulates HOXA9 gene expression in t(4;11) leukemia cells. Int J Mol Sci. 2021;22:4623. Article  CAS  PubMed


  PubMed Central  Google Scholar  * Casado P, Rodriguez-Prados JC, Cosulich SC, Guichard S, Vanhaesebroeck B, Joel S, et al. Kinase-substrate enrichment analysis provides insights into the


heterogeneity of signaling pathway activation in leukemia cells. Sci Signal. 2013;6:rs6. Article  PubMed  Google Scholar  Download references ACKNOWLEDGEMENTS We would like to thank


LeukaemiaUK, the University of Roehampton, the British Society of Hematology and the Institute of Biomedical Science for funding this study, the patients for donating their samples for


research purposes, Prof Kamil Kranc for providing constructive feedback on the manuscript, Prof. Fulvio D’Acquisto and Prof. Jolanta Opacka-Juffry for their mentoring. Figure 8 was created


in BioRender.com. FUNDING This project has been supported by Leukemia UK (John Goldman fellowship), the British Society of Hematology, the Institute of Biomedical Science and the University


of Roehampton. AUTHOR INFORMATION Author notes * Maria Teresa Esposito Present address: School of Biosciences, University of Surrey, Guildford, UK * These authors contributed equally:


Antonella Di Mambro, Yoana Arroyo-Berdugo. * These authors jointly supervised this work: Bela Patel, Maria Teresa Esposito. AUTHORS AND AFFILIATIONS * School of Life and Health Sciences,


University of Roehampton, London, UK Antonella Di Mambro, Yoana Arroyo-Berdugo, Yolanda Calle & Maria Teresa Esposito * CEINGE Biotecnologie Avanzate, Via Gaetano Salvatore, Napoli,


Italy Tiziana Fioretti, Armando Cevenini & Gabriella Esposito * Chester Centre for Leukaemia Research, Chester Medical School, University of Chester, Chester, UK Michael Randles & 


Claire M. Lucas * Centre Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain Luca Cozzuto & Julia Ponomarenko * Barts Cancer Institute, Queen


Mary University of London, London, UK Vinothini Rajeeve, Michael J. Austin, Pedro Cutillas, John Gribben & Bela Patel * Department of Molecular Medicine and Medical Biotechnologies,


University of Naples Federico II, Via Pansini 5, 80131, Naples, Italy Armando Cevenini & Gabriella Esposito * University Pompeu Fabra (UPF), Barcelona, Spain Julia Ponomarenko * Great


Ormond Street Institute of Child Health London, UCL, London, UK Owen Williams Authors * Antonella Di Mambro View author publications You can also search for this author inPubMed Google


Scholar * Yoana Arroyo-Berdugo View author publications You can also search for this author inPubMed Google Scholar * Tiziana Fioretti View author publications You can also search for this


author inPubMed Google Scholar * Michael Randles View author publications You can also search for this author inPubMed Google Scholar * Luca Cozzuto View author publications You can also


search for this author inPubMed Google Scholar * Vinothini Rajeeve View author publications You can also search for this author inPubMed Google Scholar * Armando Cevenini View author


publications You can also search for this author inPubMed Google Scholar * Michael J. Austin View author publications You can also search for this author inPubMed Google Scholar * Gabriella


Esposito View author publications You can also search for this author inPubMed Google Scholar * Julia Ponomarenko View author publications You can also search for this author inPubMed Google


Scholar * Claire M. Lucas View author publications You can also search for this author inPubMed Google Scholar * Pedro Cutillas View author publications You can also search for this author


inPubMed Google Scholar * John Gribben View author publications You can also search for this author inPubMed Google Scholar * Owen Williams View author publications You can also search for


this author inPubMed Google Scholar * Yolanda Calle View author publications You can also search for this author inPubMed Google Scholar * Bela Patel View author publications You can also


search for this author inPubMed Google Scholar * Maria Teresa Esposito View author publications You can also search for this author inPubMed Google Scholar CONTRIBUTIONS MTE, BP, and YC


conceived the experimental design; ADM, YAB, TF, and MTE performed the experiments and analyzed data; MA performed the in vivo experiment; MR, VR, and PC performed phospho-proteomic


experiments and data analysis; LC performed RNAseq data analysis and visualization with input from JP; AC and GE supervised and interpreted the ChiP and IP data; OW, BP, and JG gathered


patients’ material and provided clinical data; CL contributed intellectually to the interpretation of the data; BP contributed critical intellectual input in design and interpretation of


data; MTE conceptualized, supervised the study, provided the funding and wrote and edited the manuscript; all the authors critically reviewed and edited the manuscript. CORRESPONDING AUTHOR


Correspondence to Maria Teresa Esposito. ETHICS DECLARATIONS COMPETING INTERESTS The authors declare no competing interests. ADDITIONAL INFORMATION PUBLISHER’S NOTE Springer Nature remains


neutral with regard to jurisdictional claims in published maps and institutional affiliations. SUPPLEMENTARY INFORMATION SUPPLEMENTARY DATA AND MATERIAL AND METHODS SUPPLEMENTARY TABLE 1


SUPPLEMENTARY TABLE 3 SUPPLEMENTARY TABLE 4 SUPPLEMENTARY TABLE 5 SUPPLEMENTARY FIGURE 1 SUPPLEMENTARY FIGURE 2 SUPPLEMENTARY FIGURE 3 SUPPLEMENTARY FIGURE 4 SUPPLEMENTARY FIGURE 5


SUPPLEMENTARY FIGURE 6 SUPPLEMENTARY FIGURE 7 SUPPLEMENTARY FIGURE 8 SUPPLEMENTARY FIGURE 9 SUPPLEMENTARY FIGURE 10 SUPPLEMENTARY FIGURE 11 RIGHTS AND PERMISSIONS OPEN ACCESS This article is


licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give


appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in


this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative


Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a


copy of this license, visit http://creativecommons.org/licenses/by/4.0/. Reprints and permissions ABOUT THIS ARTICLE CITE THIS ARTICLE Di Mambro, A., Arroyo-Berdugo, Y., Fioretti, T. _et


al._ SET-PP2A complex as a new therapeutic target in KMT2A (MLL) rearranged AML. _Oncogene_ 42, 3670–3683 (2023). https://doi.org/10.1038/s41388-023-02840-1 Download citation * Received: 21


February 2023 * Revised: 07 September 2023 * Accepted: 13 September 2023 * Published: 27 October 2023 * Issue Date: 08 December 2023 * DOI: https://doi.org/10.1038/s41388-023-02840-1 SHARE


THIS ARTICLE Anyone you share the following link with will be able to read this content: Get shareable link Sorry, a shareable link is not currently available for this article. Copy to


clipboard Provided by the Springer Nature SharedIt content-sharing initiative