EP_074. Genome-wide DNA methylation profiling reveals epigenetic alterations in acute myeloid leukaemia cell lines

Yuslina Mat Yusoff^1*, Norfarhana Mazlan¹, Mohd Khairul Nizam Mohd Khalid², Zahidah Abu Seman¹, Muhammad Redha Abdullah Zawawi³, Saiful Effendi Syafruddin³, Mohamad Aimanuddin Mohtar³, Noor Atiqah Fakharuzi¹, Shaik Ahmad Kamal Shaik M Fakiruddin¹, Azian Naila Md Nor¹, Ermi Neiza Mohd Sahid¹ and Adiratna Mat Ripen¹.

1. Haematology Unit, Cancer Research Centre, Institute for Medical Research, National Institute of Health, Section U13 Setia Alam, 40170 Shah Alam, Selangor

2. Inborn Error of Metabolism and Genetic Unit, Nutrition, Metabolism and Cardiovascular Research Centre, Institute for Medical Research, National Institute of Health, Section U13 Setia Alam, 40170 Shah Alam, Selangor

3. UKM Medical Molecular Biology Institute, Jalan Yaacob Latif, Bandar Tun Razak, 56000 Cheras, Kuala Lumpur

*Corresponding author: Dr Yuslina Binti Mat Yusoff. This email address is being protected from spambots. You need JavaScript enabled to view it.

ABSTRACT

INTRODUCTION: Acute myeloid leukaemia (AML) is a haematological malignancy characterised by clonal expansion of immature myeloid precursors. While genetic mutations have been extensively studied in AML, emerging evidence highlights the pivotal role of epigenetic modifications, particularly DNA methylation, in leukaemogenesis.

OBJECTIVE(S): This study aims to elucidate epigenetic alterations that may drive the onset and progression of acute myeloid leukaemia (AML).

MATERIALS & METHODS: This study utilised Whole Genome Bisulfite Sequencing (WGBS) to analyse DNA methylation profiles. The methylomes of two AML cell lines (THP-1 and CG-SH) were compared against a publicly available healthy hematopoietic control (HC) sample (GEO accession: GSM916052). Alignment of bisulfite-treated reads to the GRCh38 reference genome was performed using Bismark Version 0.24.0, and differentially methylated regions (DMRs) were identified using DSS Version 2.12.0.

RESULTS: Comparative DNA methylation analysis between AML cell lines and healthy controls (HC) reveals extensive epigenetic reprogramming associated with leukaemogenesis. Both THP-1 and CG-SH exhibit widespread hypermethylation across differentially methylated regions (DMRs), averaging around 1,000 base pairs. This aberrant methylation affects genes involved in transcriptional regulation, leading to the silencing of those essential for normal haematopoietic differentiation. Notably, differential methylation was observed in AML-related genes such as FLT3 and MLLT3, which are involved in proliferation and differentiation. These changes are mainly enriched in gene regulatory regions, including CpG islands, promoters, transcription start sites (TSS), as well as exonic and intronic regions. CG-SH shows a more uniform hypermethylation profile, while THP-1 displays greater variability, likely reflecting cytogenetic or subtype differences. These findings underscore the role of DNA methylation in disrupting gene expression and promoting the accumulation of undifferentiated myeloid cells in leukaemia.

CONCLUSION: These findings underscore the distinct methylation dynamics in AML and highlight the potential of methylation profiling in understanding leukaemogenesis and guiding therapeutic strategies.

KEYWORDS: Epigenetic, DNA Methylation, Leukaemia, WGBS