Decitabine enhances tumor immunogenicity via transposable element reactivation but concurrently induces oncogene expression in Acute Myeloid Leukemia Free

Background: Decitabine (DCB), a DNA methyltransferase inhibitor used in the treatment of acute myeloid leukemia (AML), induces global hypomethylation and transcriptional derepression. This epigenetic reprogramming reactivates silenced genomic regions, including transposable elements (TEs)—repetitive DNA sequences that can stimulate antiviral immune responses when expressed. TE reactivation may enhance tumor immunogenicity through the induction of innate immune pathways, but global hypomethylation may also activate oncogenes. This study was designed to investigate the dual effects of DCB on tumor immunogenicity and oncogene expression in AML cell models.

Methods: Human AML cell lines KG-1 and THP-1 were treated with increasing concentrations of DCB (0 µM, 0.5 µM, 1.5 µM, 2.5 µM) for 72 and 96 hours, either alone or in co-culture with CD3+ T cells at a 1:1 ratio. RNA sequencing (RNA-seq) was used to quantify TE expression, interferon signaling, cancer/testis antigen (CTA) activation, and oncogene upregulation. Bisulfite PCR and Sanger sequencing assessed the CpG methylation status at selected TE loci. IFN-γ production by CD3+ cells was measured by flow cytometry.

Results: DCB treatment led to dose- and time-dependent transcriptional activation of numerous TEs, particularly in KG-1 cells. Reactivated TEs spanned LINE, SINE, LTR, and DNA transposon subfamilies, with a mean fold-increase of ~12-fold and maxima exceeding 200-fold. THP-1 cells showed limited TE induction. Bisulfite sequencing confirmed CpG demethylation at the top 12 upregulated TEs in DCB-treated cells. RNA-seq analysis demonstrated upregulation of RIG-I/MDA5-MAVS and cGAS-STING antiviral signaling pathways, including increased expression of IRF3, IRF7, CCL5, CXCL9, and CXCL10. Accumulation of cytosolic dsRNA/dsDNA was observed in KG-1 cells. Co-cultured CD3+ T cells showed a DCB dose-dependent increase in IFN-γ secretion, indicating enhanced AML immunogenicity.

In parallel, DCB induced the expression of ~30 cancer/testis antigens, including MAGEA1, MAGEB1/2, and DAZL, all of which are known immunotherapeutic targets. However, DCB also upregulated several oncogenes (MMP9, CD248, S100A8, MET, and ID2), previously implicated in AML progression, treatment resistance, and immune evasion. In addition, DCB treatment was associated with downregulation of core histone genes (H4C12, H2AC4, H3C11), suggesting chromatin remodeling as a mechanism underlying these transcriptional changes.

Conclusions: Decitabine enhances tumor immunogenicity in AML through reactivation of endogenous TEs and activation of cytosolic nucleic acid sensing pathways, resulting in increased IFN signaling and antigen expression. However, these beneficial immunostimulatory effects are accompanied by concurrent upregulation of oncogenes. These findings highlight a critical duality of DCB therapy in AML, underscoring the need for rational combination strategies to harness its immunogenic potential while minimizing oncogenic risk.