Genome and Transcriptome Profiling of Monosomy 7 AML Defines Novel Risk and Therapeutic Cohorts

Monosomy 7 (mono7) alterations in acute myeloid leukemia (AML) are associated with poor outcome and disease progression. Through advancements in multi-omic approaches, more specific treatment strategies may be available for high-risk cohorts. Here we describe pediatric cases of AML with mono7, co-occurring fusions, associated outcome, and potential therapeutic treatments.

Of the 2200 patients treated in 3 consecutive Children’s Oncology Group protocols (AAML03P1, AAML0531, and AAML1031), 45 patients (2%) had karyotypic evidence of mono7 with full complement of clinical data for analysis. RNA sequencing was available for 37 and whole genome sequencing (WGS) for 8 cases. Fusions were identified using TransAbyss, STARfusion, and Cicero algorithms, while structural variants were analyzed by CREST in the WGS samples. Differential expression comparing mono7 AML (N=28) vs. other AML (N=1064) was performed and epigenetic profiling was evaluated using Illumina’s EPIC array (N=1025, N=79 normal bone marrow controls).

Of the 45 patients with mono7, 22 had additional karyotypic alterations including copy number variants in 7 and translocations in 15 (6 had confirmatory evidence by RNA seq). RNA seq also identified 9 additional cryptic fusions. In total, the cohort contains 5 cases (11.1%) with KMT2A fusions, 3 (6.7%) with CBF fusions, 7 (15.7%) with 3q26 alterations, and 7 (15%) with copy number alterations (Fig. 1A). In 14 patients (31%), mono7 was the sole karyotypic alteration. In 28 patients with ribo-depleted RNA seq data, cryptic fusions involving the ALK gene were identified in 4 patients (14.3%) with ALK fused to either SPTBN1 (n=3) or RANBP2 (n=1) genes. Cryptic ALK fusions were not detected in the 1064 cases of other AML (p=1.5x10^-37), suggesting a unique association between ALK fusions and mono7 and potential genomic cooperation.

A differential expression analysis compared patients with mono7 (N=28) to all other AML (N=1064). This analysis identified 1547 dysregulated genes. Of these, MECOM (MDS1/EVI1 COMplex) was identified as the top upregulated gene (logFC 7.24; p=4.4x10^-74) with a median expression 5.45 TPM (range 0-89.2 TPM) in patients with mono7 vs. 0.013 TPM in other AML patients. Evaluation of outcome based on MECOM expression demonstrated that patients with high MECOM expression (greater than median) had a 3-yearOS of 22%±20% compared to that of 68%±20% with low MECOM expression, (p=0.026, Fig. 1B)

All patients with 3q26 variants had elevated MECOM expression (n=7). In addition, 11 patients without 3q26 alterations/MECOM fusions had MECOM overexpression.

Given lack of underlying genomic etiology, we sought to determine whether epigenetic factors might mediate MECOM expression. A panel of 6 CpGs was sufficient to distinguish hematopoietic stem cells (HSCs) from granulocyte-monocyte progenitors (GMPs). HSC-like hypermethylation of these CpGs was strongly associated with high MECOM expression. Further, there was high correlation between total MECOM expression and the methylation status of a CpG island proximal to the short EVI1 transcript variant of MECOM (Spearman’s rho = -0.51, p < 0.001, Fig. 1C), suggesting a regulatory underpinning for permissive expression of EVI1.

The stem-like epigenetic signature and concordant high MECOM expression of poor-prognosis mono7 AML are consistent with a “stemness” signature and portend poor survival (Fig. 1D). Stemness mRNA signatures have been implicated in high-risk pediatric AML (Smith JL, ASH 2017) and the epigenetic signatures of these genes further corroborate cell of origin as an independently prognostic factor even within high-risk AML.

Focused interrogation of the MECOM locus thru integration of the RNA Seq and WGS identified allele specific MECOM expression, adding additional potential mechanism of modulation to MECOM expression. Structural variant analysis confirmed no other CNVs on chromosome 3, indicating cis dysregulation of MECOM.

Here, by interrogation of the genome, phenome, transcriptome, and epigenome of mono7 AML a substantial phenotypic and prognostic heterogeneity exists defining a cohort of patients, regulated by genomic and epigenomic alterations. Further, discovery of cryptic ALK fusions in mono7 present a target for ALK inhibitors (FDA approved for non-small cell lung cancer) in this high-risk population.