Epigenetic characterisation of chronic lymphocytic leukaemia with frequently altered DNA damage response genes

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Alatawi, Sael Musallam ORCID: https://orcid.org/0000-0001-5773-5567 (2022). Epigenetic characterisation of chronic lymphocytic leukaemia with frequently altered DNA damage response genes. University of Birmingham. Ph.D.

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Abstract

Chronic lymphocytic leukaemia (CLL) is a neoplasm of mature B cells and it is considered the most common type of leukaemia in the western world. CLL is an extremely heterogeneous disease in which patients show a diverse clinical course driven among other factors by driver mutations. The most common CLL cytogenetic aberration are deletions in the 13q14 and 11q22.3 which are associated with early and later events during disease progression, respectively. Interestingly, these cytogenetic alterations affect genes encoding for DNA damage response proteins members. RNASEH2B gene resides in 13q14 region and it is a member of RNase H2 complex involved in Ribonucleotide excision repair (RER). ATM on the other hand is located to 11q22.3 regions and it is an essential kinase in the DNA double-strand break (DSB). While the consequences of ATM and RNASEH2B dysfunction on DNA repair in cancer cells are reasonably well understood, their impact on the epigenetic landscape remains to be elucidated.

The frequent alterations in these DDR genes suggests that CLL cells use cellular addictions in form of alternative pathways and mechanisms to maintain their survival. Thus, identifying different levels of these cellular addictions is the first step towards the design of personalized, targeted therapy.

Here, I generated chromatin accessibility, histone modifications and variants, and gene expression profiles using genome-wide methodologies on CLL cell lines that harbour defects in RNASEH2B and ATM. CLL cells harboring defects in ATM showed a unique pattern of chromatin accessibility, which was correlated with changes in gene expression. Global histone modification changes were observed and the epigenetic regulator KDM5B, a histone demethylase, were found to be upregulated in ATM-defective cells demonstrating a potential vulnerability that can be targeted therapeutically. On the other hand, RNASEH2B- defective CLL cells showed a unique transcriptional program associated with increased DNA-RNA hybrid levels. The results suggest that RUNX Transcription Factors (TF) were required to maintain the proliferation of RNASEH2B defective cells and this was confirmed by CRISPR KO screen. Together, these results provide novel insights into the mechanisms underlying CLL cells survival and pave the way for therapeutic agents targeting tumours cells harbouring mutations in ATM and RNASEH2B genes.

Type of Work:

Thesis (Doctorates > Ph.D.)

Award Type:

Doctorates > Ph.D.

Supervisor(s):