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Identification of three novel DNMT3A mutations with compromising methylation capacity in human acute myeloid leukaemia

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Abstract

Background

Acute myeloid leukaemia (AML) is a complex and heterogeneous hematopoietic stem and progenitor cell malignancy characterised by the accumulation of immature blast cells in the bone marrow, blood, and other organs linked to environmental, genetic, and epigenetic factors. Somatic mutations in the gene DNA (cytosine-5)-methyltransferase 3A (DNMT3A; NM_022552.4) are common in AML patients.

Methods

In this study, we used Sanger sequencing to detect the mutations in the DNMT3A gene in 61 Iraqi AML patients, Hence, the protein function and stability within alterations were identified and analyzed using a variety of computational tools with the goal of determining how these changes affect total protein stability, and then the capacity of methylation was analyzed by methylation specific PCR MSP status at CpG islands.

Results

Three novel mutations in exon 23 of DNMT3A were identified in 14 patients (22.9%; V877I, N879delA, and L888Q). The V877I and L888Q substitutions are caused by heterozygous C2629G > A and C2663T > A mutations, respectively, while frameshift mutation C2635delA caused protein truncation with stop codon N879T*. Methylation was detected in the DNMT3A promoter region in 9 patients carrying DNMT3A mutations (64.28%) by MSP, and we found significant correlations between DNMT3A mutations and promoter methylation (p = 8.52 × 105). In addition, we found a significant overrepresentation of DNMT3A methylation status in patients ≥ 50 years old (p = 0.025).

Conclusion

Our findings highlight the importance of studying the effects of DNMT3A methylation alteration in Iraqi populations beyond R882 substitutions in the leukemogenic pathway so that patient treatment can be tailored to prevent therapeutic resistance and relapse.

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Data availability

The datasets generated during the current study were deposited into the NCBI GenBank Banklt database and can be accessed with the accession numbers BSeq#1 ON881280, BSeq#2 ON881281 and BSeq#3 ON881282 (https://www.ncbi.nlm.nih.gov/Genbank/ON881280/ON881280/ON881280).

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Authors and Affiliations

  1. Department of Chemistry, College of Science, University of Garmian, Kalar, KRG, Iraq

    Ayad M. Ali

  2. Department of Biology, College of Science, University of Sulaimani, Sulaimania, KRG, Iraq

    Gaza F. Salih

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  1. Ayad M. Ali
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  2. Gaza F. Salih
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Contributions

AMA and GFA conceived of the idea and planned the experiments. AMA has performed the lab work, data analysis and wrote and prepares the manuscript, GFA contributed as a supervisor. Both authors discussed the results and contributed to the final manuscript.

Corresponding authors

Correspondence to Ayad M. Ali or Gaza F. Salih.

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Competing interest

The authors declare no competing interests.

Ethical approval

The study protocol was approved by the Ethical Committee of the Sulaimania General Directorate of Health, Ministry of Health, Kurdistan Regional Government (KRG), Iraq (No. 9811; approved on 23/08/2021). Prior to participation in this study, the Declaration of Helsinki, which covers the ethical criteria for medical research involving human subjects, was also reviewed with each participant and the guardians of patients under the age of 18, who provided verbal and written consent. All investigations were carried out in accordance with relevant guidelines and regulations by university of Sulaimani, college of science (No. 1917/259 on 01/08/2021).

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Ali, A.M., Salih, G.F. Identification of three novel DNMT3A mutations with compromising methylation capacity in human acute myeloid leukaemia. Mol Biol Rep 49, 11685–11693 (2022). https://doi.org/10.1007/s11033-022-07977-y

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