Transcriptome Profiling of Pediatric Core Binding Factor AML

<div><p>The t(8;21) and Inv(16) translocations disrupt the normal function of core binding factors alpha (CBFA) and beta (CBFB), respectively. These translocations represent two of the most common genomic abnormalities in acute myeloid leukemia (AML) patients, occurring in approximately 25% pediatric and 15% of adult with this malignancy. Both translocations are associated with favorable clinical outcomes after intensive chemotherapy, and given the perceived mechanistic similarities, patients with these translocations are frequently referred to as having CBF-AML. It remains uncertain as to whether, collectively, these translocations are mechanistically the same or impact different pathways in subtle ways that have both biological and clinical significance. Therefore, we used transcriptome sequencing (RNA-seq) to investigate the similarities and differences in genes and pathways between these subtypes of pediatric AMLs. Diagnostic RNA from patients with t(8;21) (N = 17), Inv(16) (N = 14), and normal karyotype (NK, N = 33) were subjected to RNA-seq. Analyses compared the transcriptomes across these three cytogenetic subtypes, using the NK cohort as the control. A total of 1291 genes in t(8;21) and 474 genes in Inv(16) were differentially expressed relative to the NK controls, with 198 genes differentially expressed in both subtypes. The majority of these genes (175/198; binomial test <i>p</i>-value < 10⁻³⁰) are consistent in expression changes among the two subtypes suggesting the expression profiles are more similar between the CBF cohorts than in the NK cohort. Our analysis also revealed alternative splicing events (ASEs) differentially expressed across subtypes, with 337 t(8;21)-specific and 407 Inv(16)-specific ASEs detected, the majority of which were acetylated proteins (p = 1.5x10^-51 and p = 1.8x10^-54 for the two subsets). In addition to known fusions, we identified and verified 16 <i>de novo</i> fusions in 43 patients, including three fusions involving <i>NUP98</i> in six patients. Clustering of differentially expressed genes indicated that the homeobox (<i>HOX</i>) gene family, including two transcription factors (<i>MEIS1</i> and <i>NKX2-3</i>) were down-regulated in CBF compared to NK samples. This finding supports existing data that the dysregulation of <i>HOX</i> genes play a central role in biology CBF-AML hematopoiesis. These data provide comprehensive transcriptome profiling of CBF-AML and delineate genes and pathways that are differentially expressed, providing insights into the shared biology as well as differences in the two CBF subsets.</p></div

Identification of gene-fusion events in pediatric AML samples.

<p>(A) Gene-fusion events were detected using four gene fusion detection methods. (B) 69 putative fusion events shown in a circular plot. Red: intra-chromosomal fusion event; Blue: inter-chromosomal fusion event. (C) three fusion variants of NUP98. (D) Two in-frame fusions.</p

Comparison of expression profiles for those with and without <i>FLT3</i>/ITD mutation.

<p>(A) PCA for the two groups. (B) Genes with the most significant adjust <i>p</i>-value between the two groups.</p

Outpatient Bendamustine and Idarubicin for Upfront Therapy of Elderly Acute Myeloid Leukaemia/Myelodysplastic Syndrome: A Phase I/II Study Using an Innovative Statistical Design

Combinations of agents may improve outcomes among elderly acute myeloid leukaemia (AML) and high-risk myelodysplastic syndrome (MDS) patients. We performed an adaptive phase I/II trial for newly-diagnosed AML or high-risk MDS patients aged ≥50 years using a Bayesian approach to determine whether 1 of 3 doses of bendamustine (45, 60, 75 mg/m2 days 1-3), together with idarubicin (12 mg/m2 days 1-2), might provide a complete response (CR) rate ≥40% with \u3c30% grade 3-4 non-haematological toxicity. We treated 39 patients (34 AML; five MDS with \u3e10% marrow blasts; median age 73 years). None of the three bendamustine doses in combination with idarubicin met the required CR and toxicity rates; the 75 mg/m2 dose because of excess toxicity (two of three patients) and the 60 mg/m2 dose because of low efficacy (CR rate 10/33), although no grade 3-4 non-haematological toxicity was seen at this dose. Median survival was 7·2 months. All patients began treatment as outpatients but hospitalization was required in 90% (35/39). Although we did not find a dose of bendamustine combined with idarubicin that would provide a CR rate of \u3e40% with acceptable toxicity, bendamustine may have activity in AML/MDS patients, suggesting its addition to other regimens may be warranted