Targeting METTL3 disrupts oncogenic transcriptional programs and activates immune and apoptotic pathways in Acute Myeloid Leukemia

Abstract Introduction: Acute Myeloid Leukemia (AML) is an aggressive hematologic malignancy characterized by the clonal expansion of undifferentiated myeloid precursors in the bone marrow and peripheral blood. This uncontrolled proliferation is primarily driven by a range of genetic mutations that disrupt normal hematopoiesis and impair the function of healthy leukocytes, erythrocytes, and platelets. Among emerging regulatory mechanisms, N6-methyladenosine (m6A) RNA modification plays a critical role in post-transcriptional gene regulation and cancer progression. The m6A methyltransferase complex (MAC), which catalyzes the methylation of adenosine residues in mRNA, is primarily composed of METTL3 and METTL14. METTL3 serves as the catalytic subunit responsible for methyltransferase activity, while METTL14 provides structural support and enhances substrate recognition and binding. Together, this heterodimeric complex efficiently installs m6A marks on mRNA, thereby influencing RNA stability, translation, and splicing. Dysregulation of m6A modification has been implicated in the pathogenesis of multiple cancers, including AML. This study investigated the regulatory role of METTL3 in AML by reanalyzing publicly available RNA-seq datasets from AML MOLM13 cells treated with ZW27941, a potent small-molecule degrader of METTL3. Methods: Human AML MOLM13 cells were treated with either DMSO (control) or ZW27941 for 24 hours. Following treatment, total RNA was extracted, and RNA-seq was performed. Transcriptome data (GSE273361) were reanalyzed to identify differentially expressed genes (DEGs) using R packages (false discovery rate 0.05 and |log₂ fold-change| 0.2). Gene ontology (GO) enrichment analysis was conducted to identify biological processes significantly altered upon METTL3 degradation. Results: ZW27941 treatment induced substantial transcriptomic changes, with 534 genes upregulated and 641 genes downregulated. The suppressed genes included key drivers of AML progression (e.g., TREM1, S100A8/A9, TLR4, CD84, CXCR3, ITPK1, PECAM1, and ADGRE1), indicating pathways related to innate immune signaling, cytokine-mediated activation, and inflammatory cell adhesion. Downregulation of genes involved in lipid metabolism (e.g., PPARGC1A, ELOVL6, CYP27A1/B1/W1, ABCA1/2/9, and SLC-family transporters) suggests a disruption in fatty acid synthesis and cholesterol homeostasis, pathways known to support leukemic cell survival and drug resistance. Additionally, the downregulation of transcription factors and developmental regulators (e.g., RUNX1, TNR, SOX18, NR2F2, and FOXM1) indicates interference with lineage identity, cell proliferation, and AML subtype specification. Conversely, genes and pathways involved in apoptosis, DNA damage repair, cell cycle arrest, and immune activation (e.g., IL-2, IL-6, TNFα, NF-κB, and JAK-STAT3 signaling), were significantly upregulated in response to METTL3 degradation. Conclusion: Our study demonstrates that METTL3 plays a pivotal role in sustaining AML cell survival by regulating genes associated with inflammation, lipid metabolism, proliferation, and immune evasion. Pharmacological degradation of METTL3 by ZW27941 not only suppresses oncogenic transcriptional programs but also activates apoptotic and immune responses. These findings demonstrate METTL3 as a promising therapeutic target in AML and support further exploration of m6A modulators in anti-leukemic strategies.