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1814409_1.fastq.gzftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR318/006/SRR31814406/SRR31814406_1.fastq.gzprimaryOK200GenomicsThe University of Newcastlehttps://www.ebi.ac.uk/ena/browser/view/PRJNA1202119Homo sapiensBackground Hypomethylating agents (HMA), such as azacytidine (AZA) and decitabine (DAC), are epigenetic therapies used to treat some patients with acute myeloid leukaemia (AML) and myelodysplastic syndrome (MDS). HMAs act in a replication-dependent manner to remove DNA methylation from the genome. However, AML cells targeted by HMA therapy are often quiescent within the bone marrow, where oxygen levels are low. In this study, we investigate the effects of hypoxia on HMA responses in AML cells. Results AML cell lines (MOLM-13, MV-4-11, HL-60) were treated with DAC (100nM) or AZA (500-2000nM) in normoxic (21% O2) and hypoxic (1% O2) conditions. Hypoxia significantly reduced AML cell growth and colony-forming capacity across all cell lines, with no additional effects observed upon HMA treatment. Hypoxia had no impact on the extent of DNA hypomethylation induced by DAC treatment, but limited AZA-induced loss of methylation from the genome. Transcriptional responses to HMA treatment were also altered, with HMAs failing to up-regulate antigen presentation pathways in hypoxia. In particular, cell surface expression of the MHC class II receptor, HLA-DR, was increased by DAC treatment in normoxia, but not hypoxia. Conclusion Our results suggest that HMA-induced antigen presentation may be impaired by hypoxia. This study highlights the need to consider microenvironmental factors when designing co-treatment strategies to improve HMA therapeutic efficacy. Overall design: Leukaemic cell lines (HL-60, MOLM-13 and MV-4-11) were pre-exposed to either normoxic or hypoxic conditions, followed by treatment with hypomethylating agents (HMAs) or without (untreated) as controls. Each condition has three replicates. DNA was isolated from samples after completion of the experiment and methylation levels assessed by PBAT sequencing. UPDATE: [Aug-01-2025] The MV411 Samples were removed because they were mislabeled as MV-4-11 cells.xref:PubMed:39825372ENAfalseHypoxia impairs decitabine-induced expression of HLA-DR in acute myeloid leukaemia cell lines [Bisulfite-Seq]Hypoxia impairs decitabine-induced expression of HLA-DR in acute myeloid leukaemia cell lines [Bisulfite-Seq]2025-09-242025-02-01PRJNA1202119GSE285254960639825372