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. 2024 Aug 23;19(8):e0306962.
doi: 10.1371/journal.pone.0306962. eCollection 2024.

Use of extracellular vesicle microRNA profiles in patients with acute myeloid leukemia for the identification of novel biomarkers

Ka-Won Kang  1 , Jeong-An Gim  2 , Sunghoi Hong  3 , Hyun Koo Kim  4 , Yeonho Choi  5 , Ji-Ho Park  6 , Yong Park  1
Affiliations

Use of extracellular vesicle microRNA profiles in patients with acute myeloid leukemia for the identification of novel biomarkers

Ka-Won Kang et al. PLoS One. .

Abstract

Objectives: This study aimed to establish clinically significant microRNA (miRNA) sets using extracellular vesicles (EVs) from bone marrow (BM) aspirates of patients with acute myelogenous leukemia (AML), and to identify the genes that interact with these EV-derived miRNAs in AML.

Materials and methods: BM aspirates were collected from 32 patients with AML at the time of AML diagnosis. EVs were isolated using size-exclusion chromatography. A total of 965 EV-derived miRNAs were identified in all the samples.

Results: We analyzed the expression levels of these EV-derived miRNAs of the favorable (n = 10) and non-favorable (n = 22) risk groups; we identified 32 differentially expressed EV-derived miRNAs in the non-favorable risk group. The correlation of these miRNAs with risk stratification and patient survival was analyzed using the information of patients with AML from The Cancer Genome Atlas (TCGA) database. Of the miRNAs with downregulated expression in the non-favorable risk group, hsa-miR-181b and hsa-miR-143 were correlated with non-favorable risk and short overall survival. Regarding the miRNAs with upregulated expression in the non-favorable risk group, hsa-miR-188 and hsa-miR-501 were correlated with non-favorable risk and could predict poor survival. Through EV-derived miRNAs-mRNA network analysis using TCGA database, we identified 21 mRNAs that could be potential poor prognosis biomarkers.

Conclusions: Overall, our findings revealed that EV-derived miRNAs can serve as biomarkers for risk stratification and prognosis in AML. In addition, these EV-derived miRNA-based bioinformatic analyses could help efficiently identify mRNAs with biomarker potential, similar to the previous cell-based approach.

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Conflict of interest statement

The authors have declared that no competing interests exist.

Figures

Fig 1
Fig 1. Validation of extracellular Vesicles derived from BM aspirates of patients with AML.
(A) The size and concentration trend of vesicles by fractions are presented. The eluted fractions (11 and 12; 0.5 mL each) were used for vesicle isolation. Samples were diluted 10-fold. (B) The size distribution of the isolated vesicles was determined using nanoparticle tracking analysis (NTA). The average size of BM aspirate serum or plasma-derived vesicles was 115.5 ± 2.7 nm and 101.5 ± 4.4 nm, respectively; these sizes were within the size range of typical EVs. Samples were diluted 10-fold. (C) In transmission electron microscopy (TEM) images, the size of isolated vesicles was <200 nm, and they were visualized as cup-shaped vesicles under high magnification. (D) Western blotting showed that the isolated vesicles were positive for the markers of EVs (CD63 and CD81). EVs, extracellular vesicles; BM, bone marrow; AML, acute myelogenous leukemia.
Fig 2
Fig 2. Total miRNA expression landscape according to risk groups.
The expression levels of 34 differentially expressed miRNAs according to the favorable (n = 10) and non-favorable (intermediate and adverse, n = 22) risk groups based on the 2017 European LeukemiaNet recommendations are presented. The heatmap of 34 miRNAs (rows) from 32 patients (columns) shows the expression levels of each miRNA. Each column and row pair were clustered using the k-means clustering method with the package “pheatmap” in R and divided into four clusters. The column annotation bar indicates the favorable and non-favorable patients and the two-row annotation bars indicate the results from the t-test of p-value (PV) and fold change (FC) between the two genotypes (favorable and non-favorable). miRNA, microRNA.
Fig 3
Fig 3. Evaluation of selected miRNAs as biomarkers for the prediction of non-favorable risk and overall survival based on TCGA database.
Based on the results of TCGA analysis (Table 3), miRNAs of biomarker candidates for distinguishing between non-favorable risk and survival are presented. miRNA, microRNA; TCGA, The Cancer Genome Atlas.
Fig 4
Fig 4. Network analysis between EV-derived miRNA of this study and mRNA through the TCGA database analysis.
miRNA, microRNA; TCGA, The Cancer Genome Atlas.
Fig 5
Fig 5. Evaluation of candidate miRNA-associated mRNAs selected as biomarkers in this study for biomarkers or drug targets through TCGA database analysis.
miRNA, microRNA; TCGA, The Cancer Genome Atlas.
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References

    1. Bartel DP. MicroRNAs: genomics, biogenesis, mechanism, and function. Cell. 2004; 116(2): 281–97. doi: 10.1016/s0092-8674(04)00045-5 - DOI - PubMed
    1. Bartel DP. Metazoan MicroRNAs. Cell. 2018; 173(1): 20–51. doi: 10.1016/j.cell.2018.03.006 - DOI - PMC - PubMed
    1. Macfarlane L-A, Murphy PR. MicroRNA: Biogenesis, Function and Role in Cancer. Curr Genomics. 2010; 11(7): 537–61. doi: 10.2174/138920210793175895 - DOI - PMC - PubMed
    1. Garzon R, Fabbri M, Cimmino A, Calin GA, Croce CM. MicroRNA expression and function in cancer. Trends Mol Med. 2006; 12(12): 580–7. doi: 10.1016/j.molmed.2006.10.006 - DOI - PubMed
    1. Wu W, Sun M, Zou GM, Chen J. MicroRNA and cancer: Current status and prospective. Int J Cancer. 2007; 120(5): 953–60. doi: 10.1002/ijc.22454 - DOI - PubMed

Grants and funding

This research was supported by a grant from the Seoul R&BD Program through the Seoul Business Agency (SBA) funded by the Seoul Metropolitan Government (grant number: BT210040), and the National Research Foundation of Korea (NRF) grant funded by the Korean Government (MSIT) (grant number: NRF-2022R1G1A1006030). This research was also supported by a grant from Korea University (grant number: K2110281). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.