The role of RUNX1 in MLL-AF4 leukaemia

During the past decades advances in our understanding of the biology of paediatric acute lymphoblastic leukaemias and optimization of therapeutic protocols have led to survival rates up to 85%. However, childhood leukaemias caused by translocation of MLL (Mixed Lineage Leukaemia) gene and its fusion with different partner genes are characterized by poor survival rates. Leukaemias caused by MLL-AF4 fusion protein are the most frequent among the MLL rearranged leukaemias and are characterized by small number of cooperating mutations and a very short latency, which underlines the role of MLL as a driver in the process of leukaemogenesis.

The goal of this project will be to elucidate the role of specific transcription factors, previously identified in the lab, to MLL leukaemogenesis. The transcription factors involved in leukaemogenesis fall into two classes: (i) transcription factors that are downstream targets of the MLL-AF4 fusion protein; these are upregulated in MLL rearranged leukaemias and contribute directly to leukaemogenesis; and (ii) transcription factors that are normally expressed in lymphoid cells, but their normal function is abrogated in leukaemia cells due to the altered chromatin landscape and epigenetic signatures caused by the fusion protein.

The binding patterns of the identified transcription factors will be investigated by high-throughput methods including ChIP-sequencing in the SEM leukaemia cell line, which harbours the MLL-AF4 mutation. In this way I will investigate whether this is affected after treatment with small molecule inhibitors that abrogate leukaemic growth. In addition, the role of the identified transcription factors will be examined by performing knockdown experiments in the SEM cell line, in order to determine the effects on leukaemic growth. Furthermore, I will employ newly developed techniques, including CITE-Seq and REAP-Seq, that combine high-throughput single cell RNA-sequencing with cell surface protein detection. This will enable us to examine the expression of different transcription factors in primary MLL-AF4 cells, compared to normal B cells and B cell progenitors, and will provide valuable insight into the origin of MLL leukaemias and the molecular biology of the disease.