Investigating super-enhancer-associated chromatin interactions at the HOXA9-MEIS1 oncogene signalling axis in myeloid leukaemia

• Main Author: Wang, Benny Zheng Jie
• Other Authors: Melissa Jane Fullwood
• Format: Thesis-Doctor of Philosophy
• Language: English
• Published: Nanyang Technological University 2020
• Subjects: Science::Biological sciences::Genetics
• Online Access: https://hdl.handle.net/10356/145566
• Institution: Nanyang Technological University

Myeloid leukaemia is a form of blood cancer that is characterised by a block in haematopoietic stem cell differentiation and uncontrolled cell proliferation. HOXA9 and MEIS1 are two commonly overexpressed oncogenes that are associated with poor prognoses in myeloid leukaemia patients. However, our understanding of how 3D genome organisations including Topologically Associating Domains (TADs) and chromatin interactions regulating HOXA9 and MEIS1 expression remains limited. In this study, I suggested the presence of a type of sub-TAD or “Frequently Interacting Region” (FIRE) at the MEIS1 gene locus and the presence of chromatin loops between the super-enhancers and the MEIS1 promoter within the FIRE. The excision of the CTCF boundary at the 3’ end of the MEIS1 FIRE in K562 myeloid leukaemia cells resulted in the disruption of the FIRE as well as led to the loss of chromatin loops to the MEIS1 promoter and the subsequent downregulation of MEIS1 expression. The reorganisation of chromatin loops that are linked to the MEIS1 promoter is also seen at the distal upstream and downstream regions to the MEIS1 FIRE. Analysis of H3K27 acetylation Chromatin-Immunoprecipitation-sequencing (ChIP-seq) derived super-enhancer regions in mononuclear acute myeloid leukaemia (AML) and normal knee CD34+ haematopoietic stem cells revealed the presence of novel super-enhancers at the HOXA9 locus that are specifically present in the AML patients, thus suggesting the acquisition of novel super-enhancers in AML. Circularised chromosome conformation capture (4C) technique of myeloid leukaemia cell lines THP-1, HL-60, K562 and Hi-C sequencing of three CD34+ AML and three CD34+ normal knee samples, also showed the presence of chromatin loops between these super-enhancer regions and the HOXA9 promoter. Interestingly, these chromatin loops were present at the regions that acquired super-enhancers in both the Hi-C heatmaps of the AML and normal CD34+ clinical samples. These results suggest that the acquired super-enhancers in myeloid leukaemia could hijack the pre-existing chromatin loops with the HOXA9 promoter, thereby promoting the overexpression of HOXA9 in myeloid leukaemia. Finally, I also demonstrated that HOXA9 and MEIS1 proteins can bind to their own and each other’s promoters in the AML cell line THP-1, suggesting that they can cross-regulate each other’s transcription in myeloid leukaemia. HOXA9 proteins were also shown to be enriched at the super-enhancer near the SNX10 gene (SNX10 SE) that forms chromatin loops with the HOXA9 promoter, thus indicating that HOXA9 proteins have a role in regulating its associated super-enhancers to promote its transcription. Taken together, my work provides new insight into the mechanism of FIREs, chromatin interactions, super-enhancers and their relationship with key oncogenes regulation such as with HOXA9 and MEIS1in myeloid leukaemia.