Endogenous tumor suppressor microRNA-193b: Therapeutic and prognostic value in acute myeloid leukemia

Purpose Dysregulated microRNAs are implicated in the pathogenesis and aggressiveness of acute myeloid leukemia (AML). We describe the effect of the hematopoietic stem-cell self-renewal regulating miR-193b on progression and prognosis of AML. Methods We profiled miR-193b-5p/3p expression in cytogenetically and clinically characterized de novo pediatric AML (n = 161) via quantitative real-time polymerase chain reaction and validated our findings in an independent cohort of 187 adult patients. We investigated the tumor suppressive function of miR-193b in human AML blasts, patient-derived xenografts, and miR-193b knockout mice in vitro and in vivo. Results miR-193b exerted important, endogenous, tumor-suppressive functions on the hematopoietic system. miR-193b-3p was downregulated in several cytogenetically defined subgroups of pediatric and adult AML, and low expression served as an independent indicator for poor prognosis in pediatric AML (risk ratio 6 standard error, 20.56 6 0.23; P = .016). miR-193b-3p expression improved the prognostic value of the European LeukemiaNet risk-group stratification or a 17-gene leukemic stemness score. In knockout mice, loss of miR-193b cooperated with Hoxa9/Meis1 during leukemogenesis, whereas restoring miR-193b expression impaired leukemic engraftment. Similarly, expression of miR-193b in AML blasts from patients diminished leukemic growth in vitro and in mouse xenografts. Mechanistically, miR-193b induced apoptosis and a G1/S-phase block in various human AML subgroups by targeting multiple factors of the KIT-RAS-RAF-MEK-ERK (MAPK) signaling cascade and the downstream cell cycle regulator CCND1. Conclusion The tumor-suppressive function is independent of patient age or genetics; therefore, restoring miR-193b would assure high antileukemic efficacy by blocking the entire MAPK signaling cascade while preventing the emergence of resistance mechanisms

Combining LSD1 and JAK-STAT inhibition targets Down syndrome-associated myeloid leukemia at its core

Individuals with Down syndrome (DS) are predisposed to developing acute megakaryoblastic leukemia (ML-DS) within their first years of life [1]. Although, ML-DS is associated with a favorable prognosis, children with DS often experience severe toxicities from chemotherapy [2]. This highlights the unmet need for targeted therapies with improved risk profiles in this entity. Consequently, the aim of this study was to investigate a novel therapeutic approach specifically tailored to intervene with hallmarks of ML-DS leukemogenesis. The evolution of ML-DS occurs in a step-wise process originating from pre-malignant transient abnormal myelopoiesis (TAM) [3]. The molecular mechanisms underlying the progression from TAM to ML-DS are not fully understood. However, it was previously shown that epigenetic changes play a pivotal role in ML-DS leukemogenesis. The lysine demethylase LSD1 was identified as a crucial player in this process, as LSD1-driven gene signatures become activated in ML-DS [4]. Accordingly, RNA-sequencing analysis of pediatric acute myeloid leukemia (AML) subtypes revealed that LSD1 was highly expressed in acute megakaryoblastic leukemia (AMKL), and especially in TAM and ML-DS patients (Supplementary Fig. 1). LSD1 is essential for hematopoiesis, particularly during granulocytic and erythroid differentiation [5], and was shown to contribute to differentiation blockade in different AML subtypes [6,7,8]. Consequently, various irreversible LSD1 inhibitors have been developed, with some currently undergoing clinical trials for AML [9]. Therefore, we sought to investigate the rational use of LSD1 inhibitors in pediatric AMKL. The non-DS-AMKL cell line M-07e and the ML-DS cell line CMK were highly sensitive to irreversible LSD1 inhibition (IC50M-07e = 9.1 nM; IC50CMK = 38.8 nM; Supplementary Fig. 2A). Testing serial dilutions of the irreversible LSD1 inhibitor in non-DS-AMKL and ML-DS patient samples expanded via xenotransplantation (see Supplementary Table 1 for patient characteristics), both entities were equally sensitive to LSD1 inhibition (non-DS-AMKL: IC50#1 = 15.0 nM, IC50#2 = 2.0 nM; ML-DS: IC50#1 = 31.2 nM, IC50#2 = 17.1 nM, IC50#3 = 3.8 nM). All dose-response curves plateaued at a certain LSD1 inhibitor concentration (Supplementary Fig. 2B). The non-linear relationship between cytotoxicity and dosage points toward proliferation arrest and differentiation in response to LSD1 inhibition. In line with this, we observed myeloid differentiation upon visual inspection (Supplementary Fig. 3A) and upregulation of the myeloid markers CD86 and CD11b after 3 days of LSD1 inhibitor treatment (Supplementary Fig. 3B). These results revealed a potent proliferation block and induction of differentiation in non-DS-AMKL and ML-DS samples, however, the therapeutic efficacy of LSD1 inhibition may be limited by its non-linear dose-response relationship. Consequently, we aimed to design a rational drug combination to increase its anti-leukemic effects. Another hallmark of ML-DS development is the acquisition of activating mutations in Janus kinases (JAK) and cytokine receptors [4], promising potent anti-leukemic effects of the combination of LSD1 inhibition and the JAK1/JAK2 inhibitor ruxolitinib, as it was previously proposed for JAK2V617F mutated myeloproliferative neoplasms, secondary AML and a CSF3Rmut/CEBPαmut AML model [10,11,12]. Accordingly, pre-treatment with 350 nM LSD1 inhibitor for 3 days followed by exposure to serial dilutions of ruxolitinib led to synergistic growth inhibition in non-DS-AMKL and ML-DS cell lines (Supplementary Fig. 4), as well as in all ML-DS patient samples (Fig. 1A). The combination of LSD1 inhibition and ruxolitinib proved to be very effective in non-DS-AMKL blasts, however, with only additive cytotoxic effects in one of the two patient samples (Fig. 1A). Drug synergy in the ML-DS samples was confirmed when calculating the Bliss synergy scores (Fig. 1B). Interestingly, samples ML-DS #1 (JAK1mut) and #2 (wild-type for JAK1, JAK2, and JAK3, Supplementary Fig. 5) showed particularly high synergy scores (ML-DS #1 synergy score = 10.4; ML-DS #2 synergy score = 15.6; Fig. 1B). Contrary, the JAK3mut patient sample ML-DS #3 (Supplementary Fig. 5) only displayed mild drug synergy between LSD1 inhibition and ruxolitinib (synergy score = 2.0; Fig. 1B). Consequently, as ruxolitinib is a JAK1/JAK2 inhibitor, synergistic anti-leukemic effects seem to depend on JAK mutational status, which must be considered in future pre-clinical and clinical testing of this drug combination for ML-DS patients

The stem cell-specific long noncoding RNA HOXA10-AS in the pathogenesis of KMT2A-rearranged leukemia.

HOX genes are highly conserved, and their precisely controlled expression is crucial for normal hematopoiesis. Accordingly, deregulation of HOX genes can cause leukemia. However, despite of intensive research on the coding HOX genes, the role of the numerous long noncoding RNAs (lncRNAs) within the HOX clusters during hematopoiesis and their contribution to leukemogenesis are incompletely understood. Here, we show that the lncRNA HOXA10-AS, located antisense to HOXA10 and mir-196b in the HOXA cluster, is highly expressed in hematopoietic stem cells (HSCs) as well as in KMT2A-rearranged and NPM1 mutated acute myeloid leukemias (AMLs). Using short hairpin RNA- and locked nucleic acid-conjugated chimeric antisense oligonucleotide (LNA-GapmeR)-mediated HOXA10-AS-knockdown and CRISPR/Cas9-mediated excision in vitro, we demonstrate that HOXA10-AS acts as an oncogene in KMT2A-rearranged AML. Moreover, HOXA10-AS knockdown severely impairs the leukemic growth of KMT2A-rearranged patient-derived xenografts in vivo, while high HOXA10-AS expression can serve as a marker of poor prognosis in AML patients. Lentiviral expression of HOXA10-AS blocks normal monocytic differentiation of human CD34+ hematopoietic stem and progenitor cells. Mechanistically, we show that HOXA10-AS localizes in the cytoplasm and acts in trans to induce NF-κB target genes. In total, our data imply that the normally HSC-specific HOXA10-AS is an oncogenic lncRNA in KMT2A-r AML. Thus, it may also represent a potential therapeutic target in KMT2A-rearranged AML

Myeloid leukemia vulnerabilities embedded in long noncoding RNA locus MYNRL15

Summary: The noncoding genome presents a largely untapped source of new biological insights, including thousands of long noncoding RNA (lncRNA) loci. While lncRNA dysregulation has been reported in myeloid malignancies, their functional relevance remains to be systematically interrogated. We performed CRISPRi screens of lncRNA signatures from normal and malignant hematopoietic cells and identified MYNRL15 as a myeloid leukemia dependency. Functional dissection suggests an RNA-independent mechanism mediated by two regulatory elements embedded in the locus. Genetic perturbation of these elements triggered a long-range chromatin interaction and downregulation of leukemia dependency genes near the gained interaction sites, as well as overall suppression of cancer dependency pathways. Thus, this study describes a new noncoding myeloid leukemia vulnerability and mechanistic concept for myeloid leukemia. Importantly, MYNRL15 perturbation caused strong and selective impairment of leukemia cells of various genetic backgrounds over normal hematopoietic stem and progenitor cells in vitro, and depletion of patient-derived xenografts in vivo