Introduction: Acute Myeloid Leukemia (AML) is a heterogeneous malignancy characterized by the clonal expansion of immature myeloid precursor cells in the bone marrow and peripheral blood, leading to disrupted hematopoiesis and rapid disease progression. The incidence of AML increases with age, with a median age at diagnosis of approximately 68 years. Prognosis remains poor, particularly among older adults and those with adverse-risk genetic mutations, with 5-year overall survival rates often below 30%, even with intensive chemotherapy and hematopoietic stem cell transplantation (Ferrara et al., 2024; Ofran et al., 2023). With these clinical limitations, there remains a critical need for a better understanding of leukemogenic mechanisms and therapeutic resistance to guide novel and effective targeted treatments. In AML, long non-coding RNAs (lncRNAs) are now recognized as key players in leukemogenesis, disease progression, and therapeutic response. In particular, MALNC is a novel lncRNA recurrently overexpressed in AML subtypes harboring NPM1, IDH2 mutations, or the PML-RARA fusion gene, but its functional significance remains unclear (Esteller 2022). This study examined the role of MALNC in regulating transcriptomic response to all-trans retinoic acid (ATRA)–induced differentiation in acute promyelocytic leukemia (APL).

Methods: A publicly available RNA-seq dataset GSE299161, originally designed to investigate the independent and ATRA-interactive effects of MALNC deletion on global gene expression, was reanalyzed. The dataset included RNA-seq data from two CRISPR-Cas9 knockout conditions, namely KOA (targeting MALNC exons 1.1 and 1.2), and KOB (extended deletion of exon 1.0) as well as untreated wild-type (WT) controls. Additionally, KOB and WT NB4 APL cells were treated with 1 µM ATRA for 72 hours. Differential expression was assessed with R packages (FDR < 0.05; |log₂FC| > 0.2).

Results: No significant differentially expressed genes (DEGs) were identified between WT and KOA or between WT and KOB under untreated conditions, suggesting that deletion of MALNC exons 1.0, 1.1, and 1.2 does not independently perturb baseline gene expression in NB4 APL cells. By contrast, 72-hour ATRA exposure reprogrammed the transcriptome, generating 5,992 DEGs (2,973 up- and 3,019 downregulated genes) in WT and 5,202 ((2,670 up- and 2,732 downregulated)) in KOB cells. Among these, 2,907 transcripts (1,371 up- and 1,536 downregulated) showed significantly different log₂ fold changes between KOB and WT, demonstrating that MALNC modulates the magnitude of response to ATRA for a substantial subset of genes. A KOB-versus-WT comparison under ATRA uncovered 2,857 DEGs (1,463 up- and 1,394 downregulated); within this set, 237 genes (113 up-and 124 downregulated) were both ATRA-regulated and MALNC-dependent. This MALNC-sensitive cohort was enriched for canonical differentiation drivers (PML, ITGAM, CSF3R, ALDH1A2, SPI1, IRF1, GDF15, and TGM2, all markers of myeloid differentiation that are consistently induced during ATRA-mediated maturation of APL cells), while oncogenic or pro-survival transcripts (MYC, NPM1, BCL2, and POU2F2) were repressed, suggesting a MALNC-mediated amplification of pro-differentiation and anti-leukemic programs.

Conclusions: MALNC deletion alone does not alter gene expression under steady-state conditions, indicating that it is dispensable for basal transcription, However, MALNC significantly influences the gene expression dynamics during ATRA-induced differentiation. These findings suggest that MALNC is a key modulator of retinoid-responsive gene networks and may serve as a potential therapeutic target or biomarker for treatment stratification in AML, particularly in subtypes exhibiting sensitivity to the retinoic acid pathway. Further functional studies are warranted to elucidate the molecular mechanisms by which MALNC interacts with ATRA signaling and its implications for overcoming therapeutic resistance in leukemia.

This content is only available as a PDF.
2025
Sign in via your Institution