Genome-Wide Analysis of the Regulatory Landscape in Different Pre-B-ALL Subtypes

Background

Acute pre-B leukemia results from a failure in cell differentiation. In normal development, cells commit to their lineage and differentiated phenotype state by the activation of transcription factors (TFs), or TF modules, in a series of decision points at which a choice is made between alternative lineage fates. Previously, we showed that the ETV6-RUNX1 gene translocation that occurs in 25% of pediatric leukemia patients silences regulatory regions containing RUNX binding sites (enhancers) at target gene loci implicated in lymphoid lineage differentiation (Teppo et al. 2016). However, the genome-wide changes in enhancer activities at binding sites of other TFs functioning in B-cell differentiation remain poorly understood. Moreover, the genome-wide identification of enhancers altered during leukemogenesis is incomplete.

Material & Methods

To measure transcripts generated both at enhancer and gene regions, global run-on sequencing (GRO-seq) technique was used to measure nascent RNAs (Heinäniemi et al. 2016) from human pre-B-ALL patient samples (N=35) and several cell lines representing different subtypes. For validation, additional samples were generated from cell line models with overexpression or silencing of leukemic TFs. To this collection of 151 nascent transcriptomes, additional 92 GRO-seq samples representing different cell lineages (Liivrand et al 2017) were used to compare the leukemic cells to primary cells and other cancers. Enhancer RNA (eRNA) levels were compared at TF binding motif centered enhancer regions. TF ChIP-seq data from leukemic cells and HSC were acquired from the NCBI Gene Expression Omnibus for validation of this approach.

Results

To gain insight into the derailed regulatory landscape in leukemic cells, we identified eRNA regions both from normal and leukemic samples and performed statistical analysis distinguishing regulatory regions with differential activity between pre-B-ALL-subtypes or compared to normal CD34+ bone marrow precursors. Next, association of the significantly altered enhancers with gene transcripts was utilized to build regulatory maps for differentially expressed gene loci. For this purpose, we developed a transcript identification and quantification pipeline suitable for detecting altered expression at different coding and non-coding RNA loci from nascent transcriptomes (Liivrand et al 2017; unpublished). To globally evaluate altered TF activities across pre-B-ALL subtypes underlying the differences observed, we present here an unbiased approach based on eRNA quantification at TF motif-centered enhancers. The analysis of eRNA levels at binding sites of TFs with established role in leukemia was used as a benchmark: we could confirm low eRNA transcription at RUNX1 binding sites in the ETV6-RUNX1 subtype, elevated eRNA levels at HOXA9 and MEIS1 binding sites in the MLL rearranged subtype, while TCF3, BCL6 and PBX1 bound sites were most active in TCF3-PBX1 samples.

Conclusions

Our results provide the first genome-wide transcriptional regulatory landscape of different pre-B-ALL subtypes. We identified novel subtype-specific active enhancers and annotated regulatory non-coding regions that can be utilized to evaluate the functional impact of genetic alterations outside gene regions.