Gene Expression Profiles and Methylation Analysis in Down Syndrome Related Acute Lymphoblastic Leukemia

Background

Children with Down syndrome (DS), which caused by an extra copy of chromosome 21, are predisposed to develop acute lymphoblastic leukemia (ALL). On the other hand, in non-DS children, acquisition of chromosome 21 gain is observed in 95% of hyperdiploid (HD) ALL, which is the most common cytogenetic abnormality pattern in childhood ALL. These may suggest that gain of chromosome 21 relates molecular pathogenesis of ALL. Genetic aberrations of RUNX1 locus on chromosome 21 including iAMP21 or t(12; 21)(p13; q22)/ETV6-RUNX1 were often found in pediatric ALL. While recent studies implicated that HMGN1 or DYRK1A on chromosome 21 were associated with molecular pathogenesis of DS-ALL, it remains to be elucidated what predispose DS children to develop ALL. Compared with ALL of non-DS children, DS-ALL have uncommon genetic alterations such as mutations in JAK2 and RAS, mutations or overexpression of CRLF2. These suggest that DS-ALL may have unique biological features compared with ALL of non-DS children. Difference of biological basis between them may correlate to worse prognosis of DS-ALL. Although microarray transcript profiling provided some characteristic gene expression in DS-ALL, no study showed comprehensive transcriptome analysis in DS-ALL.

Purpose

This study was conducted to elucidate comprehensive transcriptomic landscape in DS-ALL and to reveal biological features through clustering by gene expression profiling.

Methods

Our cohort includes 72 pediatric B-cell precursor ALL samples (48 DS-ALL, 13 HD-ALL, and 11 euploid (EP) ALL). All HD-ALL samples gained chromosome 21. Three cases of DS-ALL and one case of EP-ALL had ETV6-RUNX1 rearrangement. We applied genome-wide analysis using whole-transcriptome sequencing (WTS) to 55 samples, Illumina 450k methylation array to 12 samples, and Illumina EPIC methylation array to 26 samples. For gene expression profiling, we conducted consensus clustering algorithms. Data from methylation arrays were normalized by beta-mixture quantile normalization and merged by common probes.

Results

Our consensus clustering analysis of gene expression stratified samples into three groups such as DS-ALL (cluster 1), DS-ALL and HD-ALL (cluster 2), and EP-ALL (cluster 3). Eight cases with DS-ALL having RAS mutations were classified into cluster 1. DYRK1A, HMGN1, ETS2 on chromosome 21 were highly expressed in cluster 1 and cluster 2 compared with cluster 3. Expression of RUNX1 was lower in cluster 1 and cluster 2 although it was not significant. In addition, FLT3, ELK1, and ETV6 were more highly expressed in cluster 1 and cluster 2 compared with cluster 3. Comparing cluster 1 with cluster 2, NRAS, MAP2K1, JUN, FOS, WT1, EPOR, and PDGFRB were highly expressed in cluster 1. Methylation analysis indicated that methylation pattern of DS-ALL was distinct from that of HD-ALL. Using methylation analysis, we detected differentially methylated regions (DMRs) between DS-ALL and HD-ALL. In DMRs of promoter-associated regions, RUNX1, IGF2BP1, and ETV6 were included. These genes were significantly hypermethylated in DS-ALL. Next, we elucidated methylation profiling of DS-ALL compared with HD-ALL and found hypermethylated genes in DS-ALL. Although these genes may participate pathogenesis of DS-ALL, we could not find any association of gene expression pattern.

Conclusion

We identified specific gene expression profiling of DS-ALL and significantly upregulated genes in DS-ALL compared with HD-ALL and EP-ALL. Overexpression of these genes was characteristic gene profiling common to ALL with gaining extra chromosome 21. While ETS2, FLT3, ELK1, NRAS, MAP2K, JUN, FOS, and WT1 were highly expressed in AML, overexpression of these genes may also be related to pathogenesis of DS-ALL. In addition, DS-ALL highly expressed PDGFRB and EPOR, to which these genes are targetable by TKIs and may improve prognosis of DS-ALL. Intriguingly, RUNX1 was hypermethylated in DS-ALL compared with HD-ALL and EP-ALL, indicating that underexpression of RUNX1 was a unique gene profiling of DS-ALL and was due to hypermethylation of RUNX1. In DS patient, hyprmethylation of RUNX1 in their normal blood cells has been reported. This aberrant hypermethylation may be related to pathogenesis of DS-ALL. In this study, we unveiled gene expression profiling and methylation pattern of DS-ALL. However, to elucidate the whole picture of molecular pathogenesis of DS-ALL, we may need further analysis.