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. 2023 Nov 24;18(1):898.
doi: 10.1186/s13018-023-04362-8.

Changes in the small noncoding RNA transcriptome in osteosarcoma cells

Hui Wang #  1 , Guiquan Cai #  1 , Fengbin Yu #  2 , De Li  1 , Chenglong Wang  1 , Ding Ma  1 , Xiuguo Han  1 , Jiajia Chen  3 , Chuandong Wang  4 , Jiye He  5
Affiliations

Changes in the small noncoding RNA transcriptome in osteosarcoma cells

Hui Wang et al. J Orthop Surg Res. .

Abstract

Background: Osteosarcoma has the highest incidence among bone malignant tumors and mainly occurs in adolescents and the elderly, but the pathological mechanism is still unclear, which makes early diagnosis and treatment very difficult. Bone marrow mesenchymal stem cells (BMSCs) are considered to be one of the sources of osteosarcoma cells. Therefore, a full understanding of the gene expression differences between BMSCs and osteosarcoma cells is very important to explore the pathogenesis of osteosarcoma and facilitate the early diagnosis and treatment of osteosarcoma. Small noncoding RNAs (sncRNAs) are a class of RNAs that do not encode proteins but directly play biological functions at the RNA level. SncRNAs mainly include Piwi-interacting RNAs (piRNAs), small nucleolar RNAs (snoRNAs), small nuclear RNAs (snRNAs), repeat RNAs and microRNAs (miRNAs).

Methods: In this study, we compared the expression of sncRNAs in BMSCs and osteosarcoma cells by high-throughput sequencing and qPCR and looked for differentially expressed sncRNAs. CCK-8, clone formation and transwell assay were used to detect the effect of sncRNA in MG63 cells.

Results: We found that 66 piRNAs were significantly upregulated and 70 piRNAs were significantly downregulated in MG63 cells. As for snoRNAs, 71 snoRNAs were significantly upregulated and 117 snoRNAs were significantly downregulated in MG63 cells. As for snRNAs, 35 snRNAs were significantly upregulated and 17 snRNAs were significantly downregulated in MG63 cells. As for repeat RNAs, 6 repeat RNAs were significantly upregulated and 7 repeat RNAs were significantly downregulated in MG63 cells. As for miRNAs, 326 miRNAs were significantly upregulated and 281 miRNAs were significantly downregulated in MG63 cells. Overexpression of piRNA DQ596225, snoRNA ENST00000364830.2, snRNA ENST00000410533.1 and miRNA hsa-miR-369-5p inhibited the proliferation and migration of MG63 cells.

Conclusions: Our results provide a theoretical basis for the pathogenesis, early diagnosis and treatment of osteosarcoma.

Keywords: Osteosarcoma; Repeat RNA; miRNA; piRNA; snRNA; snoRNA.

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Conflict of interest statement

The author (s) declare no potential competing interests with respect to the research, authorship, and/or publication of this article.

Figures

Fig. 1
Fig. 1
Changes in piRNA expression in osteosarcoma cells compared to hBMSCs. Heatmap (A), MA (B), scatter plot (C) and volcano plot (D) analyses of snoRNA expression in osteosarcoma cells compared to hBMSCs. E PCA of snoRNA expression in osteosarcoma cells compared to hBMSCs. F and G qPCR analysis showing that snoRNA expression was upregulated in osteosarcoma cells compared to hBMSCs. H qPCR analysis showed that snoRNA expression was downregulated in osteosarcoma cells compared to hBMSCs. I The proliferation of MG63 cells were detected by CCK-8. J The proliferation of MG63 cells were detected by clone formation. K Statistical analysis of the number of clones. L The invasion of MG63 cells were detected by transwell. M Statistical analysis of the number of cells. **indicates p < 0.01 compared to hBMSCs, and *indicates p < 0.05 compared to hBMSCs
Fig. 2
Fig. 2
Changes in snoRNA expression in osteosarcoma cells compared to hBMSCs. Heatmap (A), MA (B), scatter plot (C) and volcano plot (D) analyses of snoRNA expression in osteosarcoma cells compared to hBMSCs. E PCA of snoRNA expression in osteosarcoma cells compared to hBMSCs. F qPCR analysis showed that snoRNA expression was upregulated in osteosarcoma cells compared to hBMSCs. G qPCR analysis showed that snoRNA expression was downregulated in osteosarcoma cells compared to hBMSCs. H The proliferation of MG63 cells were detected by CCK-8. I The proliferation of MG63 cells were detected by clone formation. J Statistical analysis of the number of clones. K The invasion of MG63 cells were detected by transwell. L Statistical analysis of the number of cells. **indicates p < 0.01 compared to hBMSCs, and *indicates p < 0.05 compared to hBMSCs
Fig. 3
Fig. 3
Changes in snRNA expression in osteosarcoma cells compared to hBMSCs. Heatmap (A), MA (B), scatter plot (C) and volcano plot (D) analyses of snRNA expression in osteosarcoma cells compared to hBMSCs. E PCA of snRNA expression in osteosarcoma cells compared to hBMSCs. F qPCR analysis showed that snRNA expression was upregulated in osteosarcoma cells compared to hBMSCs. G qPCR analysis showed that snRNA expression was downregulated in osteosarcoma cells compared to hBMSCs. H The proliferation of MG63 cells were detected by CCK-8. I The proliferation of MG63 cells were detected by clone formation. J Statistical analysis of the number of clones. K The invasion of MG63 cells were detected by transwell. L Statistical analysis of the number of cells. **indicates p < 0.01 compared to hBMSCs, and *indicates p < 0.05 compared to hBMSCs
Fig. 4
Fig. 4
Changes in repeat RNA expression in osteosarcoma cells compared to hBMSCs. Heatmap (A), MA (B), scatter plot (C) and volcano plot (D) analyses of miRNA expression in osteosarcoma cells compared to hBMSCs. E PCA of miRNA expression in osteosarcoma cells compared to hBMSCs
Fig. 5
Fig. 5
Changes in miRNA expression in osteosarcoma cells compared to hBMSCs. Heatmap (A), MA (B), scatter plot (C) and volcano plot (D) analysis of miRNA expression in osteosarcoma cells compared to hBMSCs. E PCA of miRNA expression in osteosarcoma cells compared to hBMSCs. F and G qPCR analysis of the upregulated expression of miRNAs in osteosarcoma cells compared to hBMSCs. H qPCR analysis of the expression of miRNAs downregulated in osteosarcoma cells compared to hBMSCs. I The proliferation of MG63 cells were detected by CCK-8. J The proliferation of MG63 cells were detected by clone formation. K Statistical analysis of the number of clones. L The invasion of MG63 cells were detected by transwell. M Statistical analysis of the number of cells. **indicates p < 0.01 compared to hBMSCs, and *indicates p < 0.05 compared to hBMSCs
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