The genetics of relapsed pediatric acute myeloid leukemia (AML) has yet to be comprehensively defined. Here, we present the spectrum of genomic alterations in 136 relapsed pediatric AMLs. We identified recurrent exon 13 tandem duplications (TD) in UBTF in 9% of relapsed AML cases. UBTF-TD AMLs commonly have normal karyotype or trisomy 8 with co-occurring WT1 mutations or FLT3-ITD but not other known oncogenic fusions. These UBTF-TD events are stable during disease progression and are present in the founding clone. Additionally, we observed that UBTF-TD AMLs account for approximately 4% of all de novo pediatric AMLs, are less common in adults, and are associated with poor outcomes and MRD positivity. Expression of UBTF-TD in primary hematopoietic cells is sufficient to enhance serial clonogenic activity and to drive a similar transcriptional program to UBTF-TD AMLs. Collectively, these clinical, genomic, and functional data establish UBTF-TD as a new recurrent mutation in AML.
Purpose: A cryptic inv(16)(p13.3q24.3) encoding the CBFA2T3-GLIS2 fusion is associated with poor outcome in infants with acute megakaryocytic leukemia. We aimed to broaden our understanding of the pathogenesis of this fusion through transcriptome profiling. Experimental Design: Available RNA from children and young adults with de novo acute myeloid leukemia (AML; N ¼ 1,049) underwent transcriptome sequencing (mRNA and miRNA). Transcriptome profiles for those with the CBFA2T3-GLIS2 fusion (N ¼ 24) and without (N ¼ 1,025) were contrasted to define fusion-specific miRNAs, genes, and pathways. Clinical annotations defined distinct fusion-associated disease characteristics and outcomes. Results: The CBFA2T3-GLIS2 fusion was restricted to infants <3 years old (P < 0.001), and the presence of this fusion was highly associated with adverse outcome (P < 0.001) across all morphologic classifications. Further, there was a striking paucity of recurrent cooperating mutations, and transduction of cord blood stem cells with this fusion was sufficient for malignant transformation. CBFA2T3-GLIS2 positive cases displayed marked upregulation of genes with cell membrane/extracellular matrix localization potential, including NCAM1 and GABRE. Additionally, miRNA profiling revealed significant overexpression of mature miR-224 and miR-452, which are intronic miRNAs transcribed from the GABRE locus. Gene-set enrichment identified dysregulated Hippo, TGFb, and hedgehog signaling, as well as NCAM1 (CD56) interaction pathways. Therapeutic targeting of fusionpositive leukemic cells with CD56-directed antibody-drug conjugate caused significant cytotoxicity in leukemic blasts. Conclusions: The CBFA2T3-GLIS2 fusion defines a highly refractory entity limited to infants that appears to be sufficient for malignant transformation. Transcriptome profiling elucidated several highly targetable genes and pathways, including the identification of CD56, providing a highly plausible target for therapeutic intervention.
Bi-allelic CEBPA mutations are associated with favorable outcomes in AML. We evaluated the clinical and biologic implications of CEBPA-bZip mutations in childhood/young adult newly diagnosed AML. CEBPA-bZip mutation status was determined in 2,958 AML patients enrolled on COG trials (NCT00003790, NCT0007174, NCT00372593, NCT01379181). Next generation sequencing (NGS) was performed in 1,863 patients, 107 with CEBPA mutations, to characterize the co-occurring mutations. CEBPA mutational status was correlated with disease characteristics and clinical outcomes. CEBPA-bZip mutations were identified in 160/2958 (5.4%) patients, with 132 (82.5%) harboring a second CEBPA mutation (CEBPA-dm) and 28 (17.5%) with a single CEBPA-bZip only. The clinical and laboratory features of the two CEBPA cohorts were very similar. CEBPA-dm and CEBPA-bZip patients experienced identical event-free survival (EFS) of 64% and similar overall survival (OS) of 81% and 89%, respectively (p=0.259); this compared favorably to EFS and OS in CEBPA wild type (CEBPA-WT) of 46% and 61%, respectively (both p<0.001). Transcriptome analysis demonstrated similar expression profiles for CEBPA-bZip and CEBPA-dm cases. Comprehensive NGS of CEBPA-mutant cases identified co-occurring CSF3R and GATA2 mutations in 13.1% and 21.5% of patients, respectively. Patients with dual CEBPA/CSF3R mutations had an EFS of 17% vs. 63% for CEBPA-mutant/CSF3R-WT (p<0.001) with a corresponding relapse rate (RR) of 83% vs. 22%, respectively (p<0.001); GATA2 co-occurrence did not impact outcome. CEBPA bZip domain mutations are associated with favorable clinical outcomes, regardless of mono or bi-allelic status. Co-occurring CSF3R and CEBPA mutations are associated with a high RR and nullifies the favorable prognostic impact of CEBPA mutations.
The MLLT10 gene, a known fusion partner for KMT2A, encodes AF10 protein, a transcription factor that binds unmodified histone H3 and regulates DOT1L expression. KMT2A-MLLT10 fusion portends adverse outcome, but MLLT10 function and prognostic implications in partnership with other genes has not been defined. In comprehensive transcriptome and karyotype evaluation of 2226 children and young adults (0-30 years), we defined the full spectrum of MLLT10 fusions, identified new fusion partners, and correlated MLLT10 structural variants with clinical outcome. We also evaluated transcription and methylation profiles to identify genes dysregulated in MLLT10 fusions with and without KMT2A. 2226 patients treated on Children's Oncology Group (COG) trials AAML0531 and AAML1031 were evaluated by transcriptome profiling and/or karyotyping to identify leukemia associated fusions and copy number changes associated with prognosis. Collectively, 127 patients (5.7%) had primary fusions involving MLLT10: 104 (82%) involving KMT2A (KMT2A-MLLT10), and 23 patients (18%) revealed other fusion partners (MLLT10-X). Alternate, recurrent fusion partners included PICALM (n=13), DDX3X (n=2), and TEC (n=2), while fusions with 6 other partner genes (DDX3Y, CEP164, NAP1L1, SCN2B, TREH, and XPO1) were each identified in single patients. Given the known association of KMT2A-MLLT10 fusions with adverse outcome, we sought to determine whether MLLT10-X had distinct characteristics and comparable outcomes. Initial comparison of disease characteristics in patients with and without KMT2A as fusion partner showed significant differences in age at diagnosis. Those with KMT2A-MLLT10 had a median age of 1.7 years (range 0-21.3), compared to 12.7 years (range 1.4-18.9) in those with MLLT10-X (p ≤ 0.001). There was no significant difference in gender, race, mutational status, or white blood cell count between these two cohorts. MLLT10 rearranged patients (n=127) demonstrated adverse outcomes, with 5-year event-free survival (EFS) of 18.6% vs. 49% in non-MLLT10 rearranged patients (N=1953, p<0.001, Fig 1A) and poorer 5 year overall survival (OS, 38.8% vs. 65.4%, p ≤ 0.001). Next, we investigated the outcome of MLLT10 rearranged patients with and without KMT2A as a fusion partner. Patients with KMT2A-MLLT10 fusions had an EFS from study entry of 19.5% vs. 12.7% for those with alternate fusion partners (p=0.628, Fig 1B). The two cohorts also had similar relapse risk (RR) from remission with 84.7% (KMT2A-MLLT10) to that of 74.6% for MLLT10-X (p=0.876). Next we explored the transcriptome profile of patients with MLLT10 fusions to determine the impact of fusion partners, using ribodepleted RNA-seq data from 1049 patients treated on COG AAML1031. MLLT10-fusion-positive cases (n=66) were compared to other AML cases (n=983) in a differential expression (DE) analysis (limma/voom) (Fig 1C). Of 1,910 genes significantly differentially expressed, HOXA family genes were among the top 30 upregulated genes, with HOXA11 identified as >6 logFC, or over 400x higher on average in MLLT10 rearranged patients. To determine if patients with MLLT10 fusions had distinct epigenetic profiles, we performed differential methylation analyses on samples from normal bone marrow and patients with 4 high-risk molecular features: MLLT10 rearranged, KMT2A rearranged, NUP98-NSD1 fused, and FLT3-ITD, across nearly 1 million CpG sites on the Infinium EPIC array (Illumina, CA). After fitting a multivariate model with all of the interacting molecular features, the 250 most discriminative regions were extracted and plotted (ComplexHeatmap) (Fig 1D). Strikingly, patients with MLLT10-X fusions cluster discretely with ultra-high-risk NUP98-NSD1 fusion patients, showing a broadly hypermethylated profile, while KMT2A-MLLT10 patients cluster within the larger KMT2A category and show far fewer hypermethylated regions. We identified patients with MLLT10 fusion partners not previously described, and compared them to other AML patients, as well as patients with known MLLT10 partners KMT2A and PICALM. All MLLT10-aberrant cases had poor EFS and OS, high RR, overexpressed HOXA genes, and distinct DNA methylation profiles, while patients with MLLT10-X fusions tend to be older children. Regardless of fusion partner, patients with MLLT10 fusions exhibit very high risk, and should be prioritized for alternative therapeutic intervention. Disclosures Farrar: Novartis: Research Funding. Deshpande:A2A Pharmaceuticals: Consultancy; Salgomed Therapeutics: Consultancy.
In an effort to identify acute myeloid leukemia (AML)-restricted targets for therapeutic development in AML, we analyzed the transcriptomes of 2051 children and young adults with AML and compared the expression profile with normal marrow specimens. This analysis identified a large cohort of AML-restricted genes with high expression in AML, but low to no expression in normal hematopoiesis. Mesothelin (MSLN), a known therapeutic target in solid tumors, was shown to be highly overexpressed in 36% of the AML cohort (range, 5-1077.6 transcripts per million [TPM]) and virtually absent in normal marrow (range, 0.1-10.7 TPM). We verified MSLN transcript expression by quantitative reverse transcription polymerase chain reaction, confirmed cell surface protein expression on leukemic blasts by multidimensional flow cytometry, and demonstrated that MSLN expression was associated with promoter hypomethylation. MSLN was highly expressed in patients with KMT2A rearrangements (P < .001), core-binding factor fusions [inv(16)/t(16;16), P < .001; t(8;21), P < .001], and extramedullary disease (P = .001). We also demonstrated the presence of soluble MSLN in diagnostic serum specimens using an MSLN-directed enzyme-linked immunosorbent assay. In vitro and in vivo preclinical efficacy of the MSLN-directed antibody-drug conjugates (ADCs) anetumab ravtansine and anti-MSLN–DGN462 were evaluated in MSLN+ leukemia cell lines in vitro and in vivo, as well as in patient-derived xenografts. Treatment with ADCs resulted in potent target-dependent cytotoxicity in MSLN+ AML. In this study, we demonstrate that MSLN is expressed in a significant proportion of patients with AML and holds significant promise as a diagnostic and therapeutic target in AML, and that MSLN-directed therapeutic strategies, including ADCs, warrant further clinical investigation.
scite is a Brooklyn-based organization that helps researchers better discover and understand research articles through Smart Citations–citations that display the context of the citation and describe whether the article provides supporting or contrasting evidence. scite is used by students and researchers from around the world and is funded in part by the National Science Foundation and the National Institute on Drug Abuse of the National Institutes of Health.
hi@scite.ai
10624 S. Eastern Ave., Ste. A-614
Henderson, NV 89052, USA
Copyright © 2024 scite LLC. All rights reserved.
Made with 💙 for researchers
Part of the Research Solutions Family.