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Transcriptomic analyses unveil the mechanism of saikosaponin A in inhibiting human neuroblastoma SK‑N‑AS cells

  • Authors:
    • Ning Gao
    • Jialin Sun
    • Wei Zhao
    • Lihui Duan
    • Hongyao Cai
    • Bo Liu
    • Yupeng Cheng
  • View Affiliations / Copyright

    Affiliations: Key Laboratory of Basic and Application Research of Beiyao, Heilongjiang University of Chinese Medicine, Ministry of Education, Harbin, Heilongjiang 150040, P.R. China, Department of Medicine, Heilongjiang Minzu College, Harbin, Heilongjiang 150066, P.R. China, School of Pharmaceutical Engineering, Heilongjiang Agricultural Reclamation Vocational College, Harbin, Heilongjiang 150025, P.R. China
    Copyright: © Gao et al. This is an open access article distributed under the terms of Creative Commons Attribution License.
  • Article Number: 419
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    Published online on: July 2, 2025
       https://doi.org/10.3892/ol.2025.15165
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Abstract

Neuroblastoma (NB) is the most common pediatric malignant neoplasm. Saikosaponin A (SSa), a compound with potential therapeutic effects against this disease, inhibits the proliferation, metastasis and invasion of NB cells. However, its molecular mechanism remains elusive. The present study examined changes in gene expression in SK‑N‑AS NB cells after SSa administration using RNA sequencing. Subsequently, Gene Ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG) and Search Tool for the Retrieval of Interacting Genes/Proteins were used to analyze the differentially expressed genes between the treatment and control groups. Quantitative PCR technology confirmed the expression of the identified critical genes. The results identified multiple significant biological processes, including 717 GO terms and 55 KEGG pathways, constructing a 96‑gene protein‑protein interaction network, with FN1 as the most relevant player in anti‑NB mechanisms. The activities of SSa against NB were closely related to the regulations of the following genes: IL24, EGR1, RET, MDK, PDGFRA, HGF, VCAM1, SLIT3, CD34, FN1, COL1A1 and NCAM1. Additionally, the PI3K‑Akt signaling pathway was downregulated in the KEGG enriched results. Therefore, the results of the present study improves the critical understanding of the anti‑NB mechanism of SSa and lays a foundation for its clinical application against NB.
View Figures

Figure 1

Viability of cells treated with
various concentrations of SSa for 24 h. (A) Viability of the human
SK-N-AS NB cell line treated with SSa. (B) Viability of the human
SH-SY5Y NB cell line treated with SSa. (C) Viability of the human
MO3.13 oligodendrocytic cell line (normal cells) treated with SSa.
Data are displayed as the mean ± SD, n=6. *P<0.05, **P<0.01
vs. the 0 µM SSa group. NB, neuroblastoma; SSa, saikosaponin A.

Figure 2

Invasion and migration of SK-N-AS
cells treated with SSa for 24 h. (A) Transwell invasion assay
images (magnification, ×200) and the relative invasion rate of
SK-N-AS cells treated with SSa (0 and 5 µM). (B) Transwell
migration assay image (migration, ×200) and the relative migration
rate of SK-N-AS cells treated with SSa (0 and 5 µM). Data are
displayed as mean ± SD, n=3. *P<0.05 vs. the 0 µM SSa group.
SSa, saikosaponin A.

Figure 3

Analysis of the DEGs between the SSa
treatment and control groups. (A) Volcano plot shows the expression
level of each gene. The x-axis represents the log2
fold-change of the gene expression and the y-axis the
represents-log10 P adj value. The red spots represent
significantly upregulated DEGs and the blue spots represent
significantly downregulated DEGs in the SSa treatment group
compared with the control group. (B) Heatmap shows the gene
expression pattern of each sample. The rows correspond to genes and
the columns correspond to samples. DEGs, differentially expressed
genes; SSa, saikosaponin A.

Figure 4

Enrichment results of the Gene
Ontology terms associated with differentially expressed genes
between the saikosaponin A treatment and control group.

Figure 5

Enrichment results of the Kyoto
Encyclopedia of Genes and Genomes pathway analysis involving
differentially expressed genes between the saikosaponin A treatment
and control groups. (A) Bubble diagram of the top 20 significantly
enriched pathways. (B) Network diagram illustrating the connections
among the enriched pathways.

Figure 6

Protein-protein interaction network
of differentially expressed genes between the saikosaponin A
treatment and control groups, with the four largest clusters based
on the Markov clustering shown on the right.

Figure 7

Relative expression levels of
candidate genes validated by reverse transcription-quantitative
PCR. Data is shown as mean ± SD, n=6 for all groups. **P<0.01
vs. control group. SSa, saikosaponin A.
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Copy and paste a formatted citation
Spandidos Publications style
Gao N, Sun J, Zhao W, Duan L, Cai H, Liu B and Cheng Y: Transcriptomic analyses unveil the mechanism of saikosaponin A in inhibiting human neuroblastoma SK‑N‑AS cells. Oncol Lett 30: 419, 2025.
APA
Gao, N., Sun, J., Zhao, W., Duan, L., Cai, H., Liu, B., & Cheng, Y. (2025). Transcriptomic analyses unveil the mechanism of saikosaponin A in inhibiting human neuroblastoma SK‑N‑AS cells. Oncology Letters, 30, 419. https://doi.org/10.3892/ol.2025.15165
MLA
Gao, N., Sun, J., Zhao, W., Duan, L., Cai, H., Liu, B., Cheng, Y."Transcriptomic analyses unveil the mechanism of saikosaponin A in inhibiting human neuroblastoma SK‑N‑AS cells". Oncology Letters 30.3 (2025): 419.
Chicago
Gao, N., Sun, J., Zhao, W., Duan, L., Cai, H., Liu, B., Cheng, Y."Transcriptomic analyses unveil the mechanism of saikosaponin A in inhibiting human neuroblastoma SK‑N‑AS cells". Oncology Letters 30, no. 3 (2025): 419. https://doi.org/10.3892/ol.2025.15165
Copy and paste a formatted citation
x
Spandidos Publications style
Gao N, Sun J, Zhao W, Duan L, Cai H, Liu B and Cheng Y: Transcriptomic analyses unveil the mechanism of saikosaponin A in inhibiting human neuroblastoma SK‑N‑AS cells. Oncol Lett 30: 419, 2025.
APA
Gao, N., Sun, J., Zhao, W., Duan, L., Cai, H., Liu, B., & Cheng, Y. (2025). Transcriptomic analyses unveil the mechanism of saikosaponin A in inhibiting human neuroblastoma SK‑N‑AS cells. Oncology Letters, 30, 419. https://doi.org/10.3892/ol.2025.15165
MLA
Gao, N., Sun, J., Zhao, W., Duan, L., Cai, H., Liu, B., Cheng, Y."Transcriptomic analyses unveil the mechanism of saikosaponin A in inhibiting human neuroblastoma SK‑N‑AS cells". Oncology Letters 30.3 (2025): 419.
Chicago
Gao, N., Sun, J., Zhao, W., Duan, L., Cai, H., Liu, B., Cheng, Y."Transcriptomic analyses unveil the mechanism of saikosaponin A in inhibiting human neuroblastoma SK‑N‑AS cells". Oncology Letters 30, no. 3 (2025): 419. https://doi.org/10.3892/ol.2025.15165
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