Defining and exploiting the developmental origin of MLL-AF4-driven infant Acute Lymphoblastic Leukaemia

Abstract

Infant MLL-AF4-driven pro-B Acute Lymphoblastic Leukaemia (ALL) is the most common leukaemia in infants. This devastating disease, which arises in utero, renders the infant patients with an aggressive disease and with a 5-year survival rate of less than 50%. It has long been speculated that along with the fusion protein, the foetal origin of the disease is one of the main contributing factors to its aggressive nature. The first aim of this work was to identify if and how this was the case. Towards this end, multiple RNA sequencing experiments were performed comparing foetal and neonatal/adult populations in both humans and mice. This allowed for the identification of the transcriptional differences between foetal and neonatal/adult cells. The results showed that the foetal derived cells were characterised by a proliferative and oncogenic nature whereas neonatal/adult cells had a mature and immune celllike profile. From this it can be concluded that the foetal nature of the leukaemia-initiating cell could support the aggressive nature of the infant disease. To address the question of whether the foetal characteristics were maintained in the transcriptome of the blasts, the transcriptional profile of the foetal cells was compared to that of blasts derived from infant patients. Interestingly, there was a large commonality between the two. To further investigate whether the common genes were critical for the disease, 21 were selected and functional assays performed using the SEM cell line. With this approach, several genes were identified deletion of which had a tremendous impact on the survival of the SEM cells. The genes that were shown to be critical for the SEM cells included PLK1, BUB1B, HSPD1, ELOVL1, CCNB1, NUTF2 and TPX2. Of particular interest was PLK1 because there is an inhibitor (Volasertib) available that is currently in phase III clinical trials. Inhibition of PLK1 using Volasertib in the SEM cells resulted in cell cycle arrest, which led to apoptosis. Another gene of interest was ELOVL1, because its knockout effect appears to be unique to the infant disease. Knockout of ELOVL1 in SEM resulted in apoptosis and investigation into the lipidome of the knockout cells identified a dramatic decrease in lipids that contain very long fatty acid chains. Additionally, using overexpression assays, DACH1 was shown to decrease the proliferation potential of the SEM cells. From this data it can be concluded that the foetal origin of the disease could be used as a means to identify novel therapeutic targets. A further aim of this work was to investigate and understand the early disease stages. For this, an additional RNA sequencing experiment was performed. This experiment used an Mll-AF4 expressing mouse model to characterise the transcriptional profile of a pre-leukemic population. Of particular interest was Skida1 which was shown to be upregulated in the Mll-AF4 expressing cells. Intriguingly, SKIDA1 was also upregulated in the blasts of infants with MLLAF4 driven ALL compared to blasts derived from paediatric patients with the same disease and healthy controls. Interestingly, Skida1 belongs to the same family of proteins as DACH1. Intriguingly, while SKIDA1 was upregulated in the infant patients, DACH1 was not expressed at all. These findings suggest that this family of proteins could play an important role for the infant disease. This has been a proof of concept study where it was shown that by defining the transcriptome of the cell of origin of the disease and by identifying early molecular aberration caused by MLL-AF4 it was possible to identify novel disease targets.