Rearrangements In Leukemia Research Articles

Dexamethasone Inhibits the Growth of B-Lymphoma Cells by Downregulating DOT1L.

Dexamethasone (Dex), a synthetic glucocorticoid that acts by binding to the glucocorticoid receptor (GR), has been widely applied to treat leukemia and lymphoma; however, the precise mechanism underlying Dex action is still not well elucidated. DOT1L, a histone H3-lysine79 (H3K79) methyltransferase, has been linked to multiple cancer types, particularly mixed lineage leukemia (MLL) gene rearranged leukemia, but its contribution to lymphoma is yet to be delineated. Analysis from the TCGA database displayed that DOT1L was highly expressed in lymphoma and leukemia. We initially demonstrated that DOT1L served as a new target gene controlled by GR, and the downregulation of DOT1L was critical for the killing of B-lymphoma cells by Dex. Further study revealed that Dex had no impact on the transcriptional activity of the DOT1L promoter, rather it reduced the mRNA level of DOT1L at the posttranscriptional level. In addition, knockdown of DOT1L remarkably inhibited the B-lymphoma cell growth. Overall, our findings indicated that DOT1L may serve as a potential drug target and a promising biomarker of Dex sensitivity when it comes to treating B lymphoma.

Abstract 141: A human induced pluripotent stem cell model of KMT2A rearranged leukemia

Abstract Acute lymphoblastic leukemia in infants (iALL) is a high-risk subtype of childhood leukemia with poor survival outcomes despite intensive therapies. Rearrangement of KMT2A (KMT2A-r) occurs in 70% of cases and is associated with refractoriness to therapy, early relapse, and rapid leukemia progression. KMT2A-r generates a driver fusion oncogene, most commonly KMT2A::AFF1 in iALL, which leads to epigenetic dysregulation of target gene transcription. iALL with KMT2A::AFF1 is an unusual cancer in that other somatic mutations are uncommon, there are no known genetic risk factors, and phenotypic switch from lymphoid to myeloid, mixed, or undifferentiated phenotype is common during treatment and particularly resistant to therapies. The cell of origin is thought to be a very early hematopoietic precursor, with transcriptomic studies of iALL blasts showing similarities to hematopoietic stem and progenitor cells (HSPCs), multipotent progenitors and early lymphoid progenitors (ELPs). Unfortunately, research into this rare but devastating disease has been hindered by a lack of appropriate, representative models. Interestingly, KMT2A-r originates in HSPCs in utero and the age of onset of iALL is a strong prognostic factor, with age younger than six months associated with the highest risk of relapse. However, little is known regarding how KMT2A-r subverts early hematopoiesis or drives the severe disease phenotype. In an effort to understand the role of the developmental state of the cell of origin in iALL, we have created a highly controlled induced pluripotent stem (iPS) cell model system of KMT2A::AFF1 leukemia. Specifically, we engineered human iPS cell lines with doxycycline regulatable expression of KMT2A::AFF1 fusion and we are employing CRISPR gene editing technology to introduce clinically identified variants of interest. Utilizing directed differentiation, we have produced functional HSPCs from iPS cells. Notably, this model recapitulates hematopoietic ontogeny, with the ability to control iALL induction at specific developmental stages. Following doxycycline treatment, we demonstrate that the cells express KMT2A::AFF1 fusion transcripts. We are utilizing single cell genomics to investigate transcriptomic changes during hematopoietic differentiation of our KMT2A::AFF1 iPS cells. We will compare these results to published data sets of single cell RNA sequencing data from healthy fetal HSPCs and to our existing iALL and pediatric KMT2A-r ALL single cell sequencing data sets. Our iPS cell based iALL model system provides the opportunity to investigate a range of critical and outstanding questions of iALL disease initiation, progression, and treatment. Citation Format: Erin Guest, Meagan Vacek, Jacqelyn Nemechek, Irina Pushel, Bradley T. Thornton, Molly Leyda, Midhat S. Farooqi, John M. Perry, Jay L. Vivian. A human induced pluripotent stem cell model of KMT2A rearranged leukemia [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 141.

Cytoplasmic transcription factor sequestration drives the pathogenesis of a rearranged leukemia.

Cytoplasmic transcription factor sequestration drives the pathogenesis of a rearranged leukemia.

Functional relevance of circRNA aberrant expression in pediatric acute leukemia with KMT2A::AFF1 fusion

AbstractCircular RNAs (circRNAs) are emerging molecular players in leukemogenesis and promising therapeutic targets. In KMT2A::AFF1 (MLL::AF4)-rearranged leukemia, an aggressive disease compared with other pediatric B-cell precursor (BCP) acute lymphoblastic leukemia (ALL), data about circRNAs are limited. Here, we disclose the circRNA landscape of infant patients with KMT2A::AFF1 translocated BCP-ALL showing dysregulated, mostly ectopically expressed, circRNAs in leukemia cells. Most of these circRNAs, apart from circHIPK3 and circZNF609, previously associated with oncogenic behavior in ALL, are still uncharacterized. An in vitro loss-of-function screening identified an oncogenic role of circFKBP5, circKLHL2, circNR3C1, and circPAN3 in KMT2A::AFF1 ALL, whose silencing affected cell proliferation and apoptosis. Further study in an extended cohort disclosed a significantly correlated expression of these oncogenic circRNAs and their putative involvement in common regulatory networks. Moreover, it showed that circAFF1 upregulation occurs in a subset of cases with HOXA KMT2A::AFF1 ALL. Collectively, functional analyses and patient data reveal oncogenic circRNA upregulation as a relevant mechanism that sustains the malignant cell phenotype in KMT2A::AFF1 ALL.

Abstract A161: A differentiation based therapeutic approach for KMT2A rearranged leukemia in infants and children

Abstract Introduction: Translocations in the KMT2A gene (KMT2A-r) in leukemia is an aggressive oncodriver. Currently, few therapeutic options are available for these patients and novel therapeutic strategies are urgently needed to improve outcomes. Characteristically, leukemic cells undergo a differentiation block at an early stage of development and agents that restore terminal differentiation represent an effective therapeutic strategy. Based on the initial reports that the inhibition of the Menin-KMT2A fusion is a potent inducer of leukemic cell differentiation, we sought to study a novel treatment approach to enhance the current treatment outcomes in KMT2A-r leukemia. Methods: Pediatric leukemia cells with and without KMT2A-r were studied. Differentiation was induced by the Menin inhibitor MI-463 for 12 days, followed by assessment of differentiation on day 6 and day 12 by Giemsa-Wright staining and visualization using the Infinity analyzer software. In the next set of experiments, the differentiated and undifferentiated cells were treated with common anti-leukemic chemotherapeutic agents and the induction of apoptosis and target modulation analyses were carried out by Annexin/PI staining and immunoblotting. The differentiated cells were also treated with a panel of 220 FDA approved agents, targeting diverse oncogenic pathways to generate a sensitivity signature specific to the differentiated cells. Gene expression array studies were used to identify differentially expressed genes in the two cell populations. Results: The KMT2A-r leukemia cells showed increased dose dependent sensitivity to MI-463. The highest drug sensitivity was exhibited by the infant leukemia cell line MV4-11. At 1µM, no significant loss of cell viability was noted but the rate of proliferation was significantly decreased compared to DMSO control, providing optimal conditions for differentiation. Leukemic cells cultured with MI-463 showed characteristic morphological changes of differentiation including vacuolated cytoplasm, kidney shaped nuclei and decreased nuclei to cytoplasmic ratio. Importantly, we found that the differentiated cells showed a similar chemosensitivity pattern but the sensitivity to AraC was greatly reduced. For example, in MV4-11 cells, IC50 was 170 nM compared to 8 nM in undifferentiated cells. Directed drug screen and differential gene expression studies identified specific growth and survival pathways that can be positively targeted in differentiated cells. Discussion: Data presented demonstrate the activity of MI-463 to induce cell death as well as to initiate differentiation in KMT2A-r cells. We further characterize the sensitivity profile of current chemotherapeutic agents for multi-agent treatment regimens and identify novel agents to optimize future treatment protocols. Differential gene expression analyses were used to understand the potential mechanisms of therapeutic vulnerabilities in these cells. Our results provide the first preclinical evidence to select agents and combinations to improve the outcomes in KMT2A-r leukemia in children. Citation Format: Ritul Sharma, Aru Narendran. A differentiation based therapeutic approach for KMT2A rearranged leukemia in infants and children [abstract]. In: Proceedings of the AACR-NCI-EORTC Virtual International Conference on Molecular Targets and Cancer Therapeutics; 2023 Oct 11-15; Boston, MA. Philadelphia (PA): AACR; Mol Cancer Ther 2023;22(12 Suppl):Abstract nr A161.

Presence of leukemic clone-specific immunoglobulin heavy chain rearrangements in neonatal blood spots of children with B-cell precursor acute lymphoblastic leukemia.

Childhood B-cell precursor acute lymphoblastic leukemia (BCP-ALL) can be traced back to birth using leukemic clone-specific immunoglobulin heavy chain (IGH) rearrangements, implying prenatal origin of this disease. We retrospectively analyzed neonatal blood spots (Guthrie cards) of 24 patients with childhood BCP-ALL aged 1-9.6 years (median 3.1 years) for the presence of clonotypic IGH rearrangements identified in diagnostic bone marrow samples. Based on the sequences of IGH rearrangements, 2 patient-specific primers were designed for each patient and used in semi-nested polymerase chain reaction for the detection of preleukemic clones at birth. Clonotypic IGH rearrangements were detected in neonatal blood spots of 54.2% of patients (13/24). In two cases with double IGH rearrangements detected at diagnosis, only one rearrangement was present at birth, while in the third case both leukemic rearrangements were detected in neonatal blood. Guthrie card-positive findings were significantly more frequent in children ≤5 years of age than in older children (p = 0.011). Regarding patients' characteristics at birth and at diagnosis, Guthrie card-positivity was not associated with sex, birth weight and mother's age, as well as with white blood cell count, percentage of bone marrow blasts, immunophenotype and the presence of ETV6/RUNX1 and TCF3/PBX1 fusion genes at diagnosis. Our study confirms that a large proportion of childhood BCP-ALL originates in utero, regardless of the molecular subtype defined by chromosomal aberrations. The observed trend toward younger age at diagnosis in Guthrie card-positive versus Guthrie card-negative patients implies that the age at diagnosis depends on the presence of preleukemic clone at birth, as well as on the timing of postnatal transforming genetic events.

Establishment of a t(11;19), KMT2A Rearranged B-ALL Cell Line for Preclinical Evaluation and Novel Therapeutics Development for Refractory Infant Leukemia.

Leukemia, diagnosed in children less than 12 months of age, is a rare condition with an aggressive disease presentation and poor response to conventional chemotherapeutic agents. In addition, the unique vulnerability of the affected population does not always permit the use of markedly intense regimens with higher doses of cytotoxic agents. However, the unique biology of these leukemic cells also provides opportunities for the identification of effective and potentially well-tolerated targeted therapeutic strategies. In this report, we describe the establishment and characterization of a cell line from the blasts of an infant diagnosed with refractory B-cell acute lymphoblastic leukemia (ALL) carrying the characteristic histone lysine methyltransferase 2A (KMT2A) gene rearrangement. This cell line consists of rapidly proliferating clones of cells with chemosensitivity patterns previously described for KMT2A rearranged leukemia cells, including relative resistance to glucocorticoids and sensitivity to cytarabine. We also show effective targetability with menin inhibitors, indicating the activity of abnormal KMT2A-related pathways and the potential utility of this cell line in comprehensive drug library screens. Overall, our findings report the establishment and in vitro validation of a cell line for research into key aspects of infant leukemia biology and targeted therapeutics development.

Ruxolitinib inhibits the proliferation and induces the apoptosis of MLL-r ALL cells through inactivating JAK/STAT signaling pathway.

The childhood patients with mixed-lineage leukemia rearrangement (MLL-r) gene have worse outcome than non-MLL, and thus often treated with high-risk chemotherapy regimens, so targeted therapy is important for this type of leukemia. This purpose of study was to explore the effects of ruxolitinib on the proliferation, apoptosis, and cell cycle of Nalm-6 cells. In this study, human acute lymphoblastic leukemia (ALL) cell line Nalm-6 was used as the research object. By constructing an MLL overexpression vector to transfect Nalm-6 cells, exogenous JAK2/STAT3 signal pathway inhibitor ruxolitinib was applied to observe the proliferation, apoptosis, and cell cycle changes of the transfected Nalm-6 cells. Western blot was performed to determine the proteins (MLL-BP, JAK, STAT) involved in the mechanism of action of MLL-r leukemia. CCK8 assay and flow cytometry (FCM) were used for testing the proliferation and apoptosis among MLL-BP transfected Nalm-6 cells. Firstly, we determine the IC50 of ruxolitinib on Nalm-6 cells. Secondly, FCM and CCK8 showed that ruxolitinib dosedependentlyinhibits proliferation of Nalm-6 cells by blocking the cell cycle at G0/G1 phase. In addition, FCM showed that ruxolitinib promoted the apoptosis of MLL-BP transfected Nalm-6 cells. Mechanistically, ruxolitinib inactivated JAK/STAT signaling pathway in MLL-BP transfected Nalm-6 cells, mediating ruxolitinib's inhibition of cell proliferation, and inducing apoptosis. Finally, ruxolitinib significantly inhibited the proliferation of MLL-r ALL cells and promoted their apoptosis. These data provide compelling evidence that ruxolitinib is a promising agent against MLL-r leukemia cell line. However, it needs going through multiple more steps to confirm before it can be an option in clinical practice.

Telomere Transcription in MLL-Rearranged Leukemia Cell Lines: Increased Levels of TERRA Associate with Lymphoid Lineage and Are Independent of Telomere Length and Ploidy

Telomere transcription into telomeric repeat-containing RNA (TERRA) is an integral component of all aspects of chromosome end protection consisting of telomerase- or recombination-dependent telomere elongation, telomere capping, and the preservation of the (sub)telomeric heterochromatin structure. The chromatin modifier and transcriptional regulator MLL binds to telomeres and regulates TERRA transcription in telomere length homeostasis and response to telomere dysfunction. MLL fusion proteins (MLL-FPs), the product of MLL rearrangements in leukemia, also bind to telomeric chromatin. However, an effect on telomere transcription in MLL-rearranged (MLL-r) leukemia has not yet been evaluated. Here, we show increased UUAGGG repeat-containing RNA levels in MLL-r acute lymphoblastic leukemia (ALL) when compared to non-MLL-r ALL and myeloid leukemia. MLL rearrangements do not affect telomere length and UUAGGG repeat-containing RNA levels correlate with mean telomere length and reflect increased levels of TERRA. Furthermore, high levels of TERRA in MLL-r ALL occur in the presence of telomerase activity and are independent of ploidy, an underestimated source of variation on the overall transcriptome size in a cell. This MLL rearrangement-dependent and lymphoid lineage-associated increase in levels of TERRA supports a sustained telomere transcription by MLL-FPs that correlates with marked genomic stability previously reported in pediatric MLL-r ALL.

Mutant NPM1: Nuclear export and the mechanism of leukemogenesis.

Mutant NPM1: Nuclear export and the mechanism of leukemogenesis.

Design, Synthesis, and Biological Evaluations of DOT1L Peptide Mimetics Targeting the Protein-Protein Interactions between DOT1L and MLL-AF9/MLL-ENL.

On the basis of a previously identified DOT1L peptide mimetic (compound 3), a series of novel peptide mimetics were designed and synthesized. These compounds can potently bind to AF9 and ENL either in cell-free binding assays or in leukemia cells, and selectively inhibit the growth of leukemia cells containing mixed lineage leukemia (MLL) fusion proteins. The most potent compound 12 exhibited comparable anticancer cellular activities to those of EPZ5676, a clinical stage enzymatic inhibitor of DOT1L in several leukemia cell lines containing MLL fusion proteins. Mechanism studies for compound 12 indicated that it did not affect the global methylation of H3K79 catalyzed by DOT1L but could effectively suppress the methylation of H3K79 at MLL fusion proteins targeted genes and inhibit the expressions of these genes. Our studies thus demonstrated that inhibiting the protein-protein interactions between DOT1L and MLL fusion proteins is a potentially effective strategy for the treatment of MLL rearranged leukemias.

Synthesis and Biological Activity of a Cytostatic Inhibitor of MLLr Leukemia Targeting the DOT1L Protein.

Histone methyltransferase DOT1L catalyzes mono-, di- and trimethylation of histone 3 at lysine residue 79 (H3K79) and hypermethylation of H3K79 has been linked to the development of acute leukemias characterized by the MLL (mixed-lineage leukemia) rearrangements (MLLr cells). The inhibition of H3K79 methylation inhibits MLLr cells proliferation, and an inhibitor specific for DOT1L, pinometostat, was in clinical trials (Phase Ib/II). However, the compound showed poor pharmacological properties. Thus, there is a need to find new potent inhibitors of DOT1L for the treatment of rearranged leukemias. Here we present the design, synthesis, and biological evaluation of a small molecule that inhibits in the nM level the enzymatic activity of hDOT1L, H3K79 methylation in MLLr cells with comparable potency to pinometostat, associated with improved metabolic stability and a characteristic cytostatic effect.

Tip60 activates Hoxa9 and Meis1 expression through acetylation of H2A.Z, promoting MLL-AF10 and MLL-ENL acute myeloid leukemia.

Chromosome translocations involving the MLL gene are common rearrangements in leukemia. Such translocations fuse the MLL 5'-region to partner genes in frame, producing MLL-fusions that cause MLL-related leukemia. MLL-fusions activate transcription of target genes such as HoxA cluster and Meis1, but the underlying mechanisms remain to be fully elucidated. In this study, we discovered that Tip60, a MYST-type histone acetyltransferase, was required for the expression of HoxA cluster and Meis1 genes and the development of MLL-fusion leukemia. Tip60 was recruited by MLL-AF10 and MLL-ENL fusions to the Hoxa9 locus, where it acetylated H2A.Z, thereby promoting Hoxa9 gene expression. Conditional deletion of Tip60 prevented the development of MLL-AF10 and MLL-ENL leukemia, indicating that Tip60 is indispensable for the leukemogenic activity of the MLL-AF10 and MLL-ENL-fusions. Our findings provide novel insight about epigenetic regulation in the development of MLL-AF10 and MLL-ENL-fusion leukemia.

Integration of Deep Multi-Omics Profiling Veals New Insights into the Biology of Poor-Risk Acute Myeloid Leukemia

Background: The poor-risk cytogenetic subgroup of acute myeloid leukaemia (AML) includes various chromosomal aberrations and represents a heterogeneous population of patients with a dismal 10-year overall survival. While the success of genetic landscaping studies is encouraging, it is debatable whether genomics, or indeed any single-omics platform alone, is sufficient to capture the biology of a disease that continues to evade our existing treatments so effectively. Instead, we need to develop a much better understanding of the complexity of this subgroup of AMLs: the relationship and interdependencies across biochemical pathways, how these may differ between patients and their impact on the leukemia and normal stem cell compartments. To launch this process, we have completed a multi-omics profiling programme to shed new light on the genetic and biochemical features of poor-risk AML (https://poor-risk-aml.bham.ac.uk/). Aims: Application of multi-omics and integrative approaches to decipher the complexities of cytogenetically poor-risk AML Methods: Sample inclusion criteria were based on cytogenetics and availability of sufficient diagnostic bone marrow or peripheral blood material for analysis. The 50 primary AMLs included 17 cases with complex karyotype, 13 -7/del(7), 11 KMT2A rearrangements (with the exception of t(9;11)), 4 t(6;9), 3 -5/de(5), 1 del(17) and 1 inv(3). Profiles consisted of a combination of genomics (whole genome sequencing (WGS, 60X for tumour and 30X for germ-line controls), targeted sequencing of 54 myeloid loci, and total RNA-seq (100 million reads per bulk sample), mass spectrometry proteomics and phosphoproteomics (with >6,000 proteins and > 25,000 phosphorylation sites detected and quantified), mass cytometry (CyTOF, 39 markers), drug screening (ranging from 200-500 approved or investigational compounds) and the selective generation of patient-derived xenograft (PDX) models. Results: Near complete datasets have been compiled on all 50 primary AMLs, with the exception of WGS analysis where profiling was restricted to cases where corresponding germline DNA was available. Integration of WGS and RNA-seq data identified 122 genes having notable allele-specific expression (ASE) in ≥ 5 samples supported by ≥ 3 SNPs and these included the transcription factor GATA2 and the DNA topoisomerase TOP1MT. Use of RNA fusion capture tools resolved novel inter- and intra- chromosomal gene rearrangements that were confirmed by WGS. The four t(6;9)(p23;q34)/DEK-NUP214 cases, with a mean age of diagnosis of 43.5 years and all harboring FLT3-ITD mutations, arose from the most immature hematopoietic compartment (CD34+CD117+ enrichment) and demonstrated a unique transcriptomic signature, which included upregulation of FOXO3 and GRP56. Collectively, t(6;9) primary samples also showed a selective drug sensitivity to XPO1 (selinexor and eltanexor) and JAK inhibitors (ruxolitinib, tofacitinib and momelotinib) compared to other cytogenetic risk groups. On the other hand, a comparison of in vitro drug sensitivity data with genomic data of our entire cohort of patients demonstrated that TP53 wt AMLs (n=37) were more sensitive to all four MDM2 inhibitors (AMG-232, idasanutlin, SAR405838 and NVP-CGM097) compared to TP53 mutated cases (n=13). Comparisons of transcriptomics with the in vitro sensitivity to drugs included in early/late phase AML clinical trials, identified signatures of response associated with MDM2 and Aurora B kinase (AZD1152-HQPA) inhibitors. Phosphoproteomics analysis and machine learning modeling separated KMT2A rearranged leukemias into 2 discrete groups (group A: MLLT4, MLLT10 and TET1; group B with MLLT6, ELL and SEP9 fusion partners). Functionally, group A presented with elevated HOXA10 protein expression and enhanced in vitro response to genotoxic drugs and cell cycle inhibitors when compared to group B leukemia. Conclusions: Our study demonstrates the feasibility of simultaneously generating omics data from several different platforms and highlights that a combination of genetic and proteomic profiles may help to inform the choice of therapies based on the underlying biology of a patient's AML. Disclosures Wennerberg: Novartis: Research Funding; Pfizer: Honoraria. Heckman:Celgene: Research Funding; Novartis: Research Funding; Oncopeptides: Research Funding; Orion Pharma: Research Funding; Innovative Mediicines Initiative project Harmony: Research Funding.

Analysis of Genomic Landscape in Patients with Acute Myeloid Leukemia

To investigate the gene mutation occurved in AML patients with 29 kinds of fusion genes and 51 kinds of tumor gene. Next-generation sequencing (NGS) was used to detected the 49 kinds of targeted gene. FLT3 internal tandem duplication (FLT3-ITD), CALR, NPM1 and CEBPA mutation were detected by DNA-based PCR and Sanger sequencing. Twenty-nine kinds of fusion genes were dected by multiplex nested RT-PCR. The total gene mutation rate was 91% (109/121) in all the 121 patients. On average, 2.1 mutated genes per patient were identified, among these 121 patients, coexistence of ≥ 3 mutations was frequent (34.7%). The most commonly mutated genes were NRAS (23.96%, n=29), followed by NPM1 (14.04%, n=17), CEBPA double mutations (14.04%, n=17), KRAS (11.57%, n=14)，FLT3-ITD (10.74%, n=13), CSF3R (10.74%, n=13), TET2 (9.92%, n=12) and IDH1 (9.1%, n=11). Overall, fusion genes were detected in 47 (37.3%) patients, including AML/ETO (n=12), CBFβ/MYH11 (n=11), PML/RARa (n=12), MLL rearranagement realated mutation MLL-X (n=10). TLS/ERG (n=1) and DEK/CAN (n=1) in an order of decreasing frequency. Patients with normal karyotype (NK)- AML exhibited more mutations in CEBPA, NPM1, TET2, RUNX1 and IDH1, comparing with abnormal karyotype patients. KRAS mutation in abnormal kayotype patients was significantly higher than that in normal kayotype patients (P=0.014). TP53 mutations were predominantly associated with complex cytogenetics (P=0.199). KRAS mutations were more frequent in core binding factor (CBF) acute myeloid leukemia (AML) and 11q23/MLL rearrangement leukemia, compared with NK-AML (P=0.006 and 0.003, respectively). KIT mutations predominated in CBF-AML (P=0.006). JAK2V617F mutations were detected in two patients and co-occurred with AML-ETO fusions. At least one mutation is observed in more than 90% patients. On average, more than 2 mutated genes per patient are identified. Some gene mutations are associated with gene rearrangement.

Apolipoprotein C2 - CD36 Promotes Leukemia Growth and Presents a Targetable Axis in Acute Myeloid Leukemia.

Acute myeloid leukemia (AML) is a devastating hematologic malignancy that affects the hematopoietic stem cells. The 5-year overall survival (OS) of patients with AML is less than 30%, highlighting the urgent need to identify new therapeutic targets. Here, we analyze gene expression datasets for genes that are differentially overexpressed in AML cells compared with healthy hematopoietic cells. We report that apolipoprotein C2 (APOC2) mRNA is significantly overexpressed in AML, particularly in patients with mixed-lineage leukemia rearrangements. By multivariate analysis, high APOC2 expression in leukemia blasts is significantly associated with decreased OS (HR: 2.51; 95% CI, 1.03-6.07; P = 0.04). APOC2 is a small secreted apolipoprotein that constitutes chylomicrons, very-low-density lipoproteins, and high-density lipoproteins with other apolipoproteins. APOC2 activates lipoprotein lipase and contributes to lipid metabolism. By gain and loss of function approaches in cultured AML cells, we demonstrate that APOC2 promotes leukemia growth via CD36-mediated LYN-ERK signaling activation. Knockdown or pharmacological inhibition of either APOC2 or CD36 reduces cell proliferation, induces apoptosis in vitro, and delays leukemia progression in mice. Altogether, this study establishes APOC2-CD36 axis as a potential therapeutic target in AML.

Proton pump inhibitors selectively suppress MLL rearranged leukemia cells via disrupting MLL1-WDR5 protein-protein interaction

Genetic rearrangements of the mixed lineage leukemia (MLL) leading to oncogenic MLL-fusion proteins (MLL-FPs). MLL-FPs occur in about 10% of acute leukemias and are associated with dismal prognosis and treatment outcomes which emphasized the need for new therapeutic strategies. In present study, by a cell-based screening in-house compound collection, we disclosed that Rabeprazole specially inhibited the proliferation of leukemia cells harboring MLL-FPs with little toxicity to non-MLL cells. Mechanism study showed Rabeprazole down-regulated the transcription of MLL-FPs related Hox and Meis1 genes and effectively inhibited MLL1 H3K4 methyltransferase (HMT) activity in MV4-11 cells bearing MLL-AF4 fusion protein. Displacement of MLL1 probe from WDR5 protein suggested that Rabeprazole may inhibit MLL1 HMT activity through disturbing MLL1-WDR5 protein-protein interaction. Moreover, other proton pump inhibitors (PPIs) also indicated the inhibition activity of MLL1-WDR5. Preliminary SARs showed the structural characteristics of PPIs were also essential for the activities of MLL1-WDR5 inhibition. Our results indicated the drug reposition of PPIs for MLL-rearranged leukemias and provided new insight for further optimization of targeting MLL1 methyltransferase activity, the MLL1-WDR5 interaction or WDR5.

Towards Molecularly Informed Acute Myeloid Leukemia Subtyping Reflective of Pathogenesis

Genetic studies have been early introduced for the classification of acute myeloid leukemia (AML), but specific molecular lesions [e.g., t(8;21), inv(16), t(15;17)] define only a fraction of patients. In the genomic era, many mutations and cytogenetic abnormalities and their combinations have been described in AML; their diversity contributes to the heterogeneity of pathomorphologic presentations. While certain mutations are restricted to individual classical morphologic subtypes, pathognomonic lesions are difficult to find. Therefore, to date, molecular mutations or cytogenetic abnormalities have been used to assess prognosis rather than define disease sub-entities according to molecular pathogenesis, likely a future standard in AML diagnosis. Balanced translocations are prototypic founder lesions, however, founder somatic vs. subclonal mutations have not been used to define subtypes of AML. Molecular classification may better reflect the pathogenesis of AML than morphologic/clinical subtypes e.g., secondary (sAML) vs. primary AML (pAML) or AML with normal (ncAML) vs. abnormal cytogenetics (acAML). This work describes the results of a large and comprehensive analysis of genomic landscape and cytogenetics in AML. Initially, 6788 cases were analyzed, including 4867 from our institutions (Cleveland Clinic Foundation and Munich Leukemia Laboratory, n=4862) fortified by publically deposited cases (n=1926) to define gene signatures and succession of mutations distinguishing pAML vs. sAML. While data for core-binding factor AML, MLL gene rearrangement leukemia, acute promyelocytic leukemia and therapy-related AML have also been analyzed (n=1094), we focused on remaining sAML (n=876) vs. pAML (n=4808) and within these entities (ncsAML, n=367; acsAML, n=509 vs. ncpAML, n=2856 and acpAML, n=1952). Although, sAML and pAML showed usual clinical differences, a reliable diagnostic algorithm could not be constructed using supervised analytic approaches and thus we aimed at identification of molecular biomarkers with prognostic and diagnostic value. Abnormal cytogenetics were present in 57% of AML including complex: 13%, +8; 11%: -5/del(5q): 8%; and -7del7q: 8%. Deep NGS for the 25 top mutated genes was applied and correlated with clinical and cytogenetic parameters (Fig.1A-B). We then defined/compared mutational landscape in acAML and ncAML separately. AcsAML showed more complex karyotypes (58% vs. 40% in acpAML, P<.0001). Similarly, acpAML patients had increased percentages of DNMT3A (18% vs. 11%, P=.007), FLT3 (17% vs. 8%, P=.0002), NPM1 (10% vs. 4%, P=.004), KRAS (7% vs. 3%, P=.01), with less frequent hits in ASXL1 (13% vs. 21%, P=.001) and SF3B1 (3.5% vs. 7%, P=.01) as compared to acsAML. Mutations significantly enriched in ncpAML vs. ncsAML involved: DNMT3A (37% vs. 14%, P<.0001), TET2 (18% vs. 11%, P=.01), CEBPA (10% vs. 3%, P=.004). Less enriched in pAML were mutations in ASXL1, RUNX1, SF3B1, SRSF2, and U2AF1. Logistic regression analysis showed various distinctive features between sAML and pAML (Fig.1C). Using a modified PyClone pipeline, we also recapitulated clonal hierarchy of ncAML to identify founder molecular events restricted to ncpAML vs. ncsAML. Indeed, founder lesions were differently distributed: DNMT3A (23% vs. 8%, P=.0003) and TET2 (9% vs. 3%, P=.02) mutations occurred more in ncpAML, while U2AF1 (0.5% vs. 6%, P<.0001), SRSF2 (2% vs. 7%, P=.01) and STAG2 (5% vs. 13%, P=.001) in ncsAML. Secondary hits/combinations were not random; e.g, DNMT3A and NPM1 were the most common in ncpAML (vs. ncsAML: 28% vs. 7%, P<.0001 and 11% vs. 4%, P=0.02) while ASXL1 (16% vs. 3%, P<.0001), SRSF2 (14% vs. 4%, P<.0001) and RUNX1 (10% vs. 4%, P=0.02) in ncsAML. Unique clonal succession patterns were proven to affect survival; e.g., ancestral DNMT3A hits showed worse OS compared to secondary/subclonal DNMT3A lesions (median: 13.3 vs. 20.1 months, P=.04). Using combined data sets of mutations and cytogenetic abnormalities and clinical parameters, we then constructed supervised and unsupervised analyses to identify signatures of pAML vs. sAML: discordant cases between the molecular and the classic diagnostic assignment of sAML vs. pAML were investigated and a novel molecular classification irrespective of the pAML and sAML derivation has been created to include founder and secondary mutations combinations and concordance of the outcomes. Disclosures Advani: Abbvie: Research Funding; Kite Pharmaceuticals: Consultancy; Amgen: Research Funding; Pfizer: Honoraria, Research Funding; Macrogenics: Research Funding; Glycomimetics: Consultancy, Research Funding. Meggendorfer:MLL Munich Leukemia Laboratory: Employment. Nazha:Daiichi Sankyo: Consultancy; Tolero, Karyopharma: Honoraria; MEI: Other: Data monitoring Committee; Incyte: Speakers Bureau; Abbvie: Consultancy; Novartis: Speakers Bureau; Jazz Pharmacutical: Research Funding. Sekeres:Millenium: Membership on an entity's Board of Directors or advisory committees; Syros: Membership on an entity's Board of Directors or advisory committees; Celgene: Membership on an entity's Board of Directors or advisory committees. Haferlach:MLL Munich Leukemia Laboratory: Employment, Equity Ownership. Maciejewski:Alexion: Consultancy; Novartis: Consultancy.

PF161 THIOREDOXIN SYSTEM INHIBITORS ARE EFFECTIVE AGAINST B CELL ACUTE LYMPHOBLASTIC LEUKEMIA IN VITRO AND IN VIVO

Background:B‐cell acute lymphoblastic leukemia (B‐ALL) is a heterogeneous hematological disorder characterized by accumulation of B cell precursors. Although undeniable improvement has been made in the therapy ofB‐ALL (>90% of pediatric patients experience remission), there are still specific subtypes associated with poor outcome. Among such subtypes are B‐ALL with mixed lineage leukemia rearrangements (MLLr ALL) or BCR‐ABL1 fusion protein (BCR‐ABL1+ ALL). Importantly, MLLr ALL does not respond to novel immunotherapies, thus novel treatment options are urgently needed. More and more data highlight disturbed redox homeostasis as a novel target in cancer treatment. Cancer cells upregulate different antioxidant machineries to overcome excessive production of reactive oxygen species (ROS) in result of increased metabolism and uncontrolled proliferation. One of such ROS‐defending systems is the thioredoxin (TXN) system, which is composed of three independent enzymes: thioredoxin reductase (TXNRD), thioredoxin (TXN), and peroxiredoxin (PRDX).Aims:To investigate the efficacy of TXN‐family enzymes inhibitors – auranofin (AUR) and adenanthin (ADE) in B‐ALL in vitro and in vivo.Methods:Primary material was isolated from pediatric and adult B‐ALL patients at diagnosis. Primograft B‐ALL samples representing BRC‐ABL1+ and MLLr ALL were generated in NOD scid gamma (NSG) mice by tail vein injections of primary B‐ALL cells. The engraftment of leukemic cells was assessed by whole blood staining and flow cytometry. Primary bone marrow derived mesenchymal stem cells (BM‐MSC) were isolated from non‐leukemic donors who underwent hip replacement surgery. Cytostatic/cytotoxic effects of TXN‐family enzymes inhibitors, AUR and ADE were assessed in mono‐ and co‐culture with BM‐MSC by MTT viability assay or by trypan blue exclusion method. The efficacy of AUR in vivo was evaluated in MLLr ALL patient derived xenograft model in NSG mice. For mechanistic studies we used SEM cell line representing MLLr ALL.Results:We have previously found increased mRNA and protein levels of particular enzymes of TXN system in B‐ALL cell lines and primary cells, thus we evaluated efficacy of two thioredoxin system inhibitors, AUR and ADE in B‐ALL primary cells. We found that both inhibitors decreased the viability of various B‐ALL cells grown not only in monoculture, but also in a co‐culture with bone marrow derived mesenchymal stem cells (BM‐MSC) of confirmed characteristics (Fig. 1A), which were shown to protect leukemic cells from drugs toxic effects. Next, we compared the effects of both inhibitors against normal peripheral blood mononuclear cells (PBMC) and found that ADE is significantly more toxic than AUR, thus we chose the latter for further studies. Accordingly, we observed that in patient derived xenograft model of MLLr ALL, AUR delayed the progression and prolonged the survival of NSG mice (Fig. 1B). Elucidating the mechanism standing behind AUR toxic effects, we found increased oxidative stress, as we observed elevated ROS levels which were abrogated by ROS scavengers, pyruvate and catalase. In addition, we observed that AUR induced oxidative stress biomarker, heme oxygenase 1 and moderate DNA oxidative damage in primograft B‐ALL cells (Fig. 1C).Summary/Conclusion:Above results show that targeting TXN system with their inhibitors can be considered as novel approach in the treatment of B‐ALL. Considering that AUR is an FDA approved drug, it could be repurposed and tested in combination with other targeted drugs in B‐ALL.image

The developmental stage of the hematopoietic niche regulates lineage in MLL-rearranged leukemia.

Leukemia phenotypes vary with age of onset. Delineating mechanisms of age specificity in leukemia could improve disease models and uncover new therapeutic approaches. Here, we used heterochronic transplantation of leukemia driven by MLL/KMT2A translocations to investigate the contribution of the age of the hematopoietic microenvironment to age-specific leukemia phenotypes. When driven by MLL-AF9, leukemia cells in the adult microenvironment sustained a myeloid phenotype, whereas the neonatal microenvironment supported genesis of mixed early B cell/myeloid leukemia. In MLL-ENL leukemia, the neonatal microenvironment potentiated B-lymphoid differentiation compared with the adult. Ccl5 elaborated from adult marrow stroma inhibited B-lymphoid differentiation of leukemia cells, illuminating a mechanism of age-specific lineage commitment. Our study illustrates the contribution of the developmental stage of the hematopoietic microenvironment in defining the age specificity of leukemia.