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MYELODYSPLASTIC NEOPLASM

SLIT2 promoter hypermethylation-mediated SLIT2-IT1/miR-218 repression drives leukemogenesis and predicts adverse prognosis in myelodysplastic neoplasm

Abstract

Epigenetic modifications have been found to play crucial roles in myelodysplastic neoplasm (MDS) progression. Previously, we investigated genome-wide DNA methylation alterations during MDS evolution to acute myeloid leukemia (AML) by next-generation sequencing (NGS). Herein, we further determined the role and clinical implications of an evident methylation change in CpG islands at the SLIT2 promoter identified by NGS. First, increased SLIT2 promoter methylation was validated in 11 paired MDS/AML patients during disease evolution. Additionally, SLIT2 promoter methylation was markedly increased in MDS/AML patients compared with controls and was correlated with poor clinical phenotype and outcome. Interestingly, SLIT2 expression was particularly upregulated in AML patients and was not correlated with SLIT2 promoter methylation. However, the SLIT2-embedded genes SLIT2-IT1 and miR-218 were downregulated in AML patients, which was negatively associated with SLIT2 promoter methylation and further validated by demethylation studies. Functionally, SLIT2-IT1/miR-218 overexpression exhibited antileukemic effects by affecting cell proliferation, apoptosis and colony formation in vitro and in vivo. Mechanistically, SLIT2-IT1 may function as a competing endogenous RNA by sponging miR-3156-3p to regulate BMF expression, whereas miR-218 may directly target HOXA1 in MDS progression. In summary, our findings demonstrate that SLIT2 promoter hypermethylation is associated with disease evolution in MDS and predicts poor prognoses in both MDS and AML. Epigenetic inactivation of SLIT2-IT1/miR-218 by SLIT2 promoter hypermethylation could be a promising therapeutic target in MDS.

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Fig. 1: SLIT2 promoter methylation was significantly increased during MDS progression and correlated with poor clinical outcome.
Fig. 2: Transcriptional regulatory effects of SLIT2 promoter methylation on noncoding RNAs SLIT2-IT1/miR-218 expression in leukemogenesis.
Fig. 3: SLIT2-IT1 exerted antileukemic effects in vitro and in vivo.
Fig. 4: SLIT2-IT1 may function as a competing endogenous RNA by “sponging” miR-3156-3p to regulate BMF expression in leukemogenesis.
Fig. 5: MiR-218 elaborated antileukemic effects in vitro and in vivo by targeting HOXA1.
Fig. 6: The schematic diagram of the regulatory mechanism and role of SLIT2 promoter hypermethylation during MDS transformation.

Data availability

The datasets used and/or analyzed during the current study are available from the corresponding author on reasonable request.

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Funding

The work was supported by National Natural Science Foundation of China (81900166, 81900163, 81970118), Zhenjiang Clinical Research Center of Hematology (SS2018009), Social Development Foundation of Zhenjiang (SH2020055, SH2021052), Medical Field of Zhenjiang “Jin Shan Ying Cai” Project, Medical Education Collaborative Innovation Fund of Jiangsu University (JDY2022011), Scientific Research Foundation of Affiliated People’s Hospital of Jiangsu University for PhD (KFB202002, KFB202202).

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JQ and J-DZ conceived and designed the experiments; T-JZ and X-MW performed the experiments; Z-JX analyzed the data and provided bioinformatics analysis; YG and QY collected the clinical data; J-CM and JL provided the technical and financial supports; T-JZ wrote the manuscript; J-DZ revised the manuscript; All authors read and approved the final manuscript.

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Correspondence to Jiang Lin, Jing-dong Zhou or Jun Qian.

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The present study approved by the Ethics Committee of the Affiliated People’s Hospital of Jiangsu University. Written informed consents were obtained from all enrolled individuals prior to their participation.

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Zhang, Tj., Xu, Zj., Wen, Xm. et al. SLIT2 promoter hypermethylation-mediated SLIT2-IT1/miR-218 repression drives leukemogenesis and predicts adverse prognosis in myelodysplastic neoplasm. Leukemia (2022). https://doi.org/10.1038/s41375-022-01659-1

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