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Differential gene expression analysis reveals signaling pathways of proliferation, angiogenesis and metastasis is associated with interferon suppression in advanced hypopharyngeal cancer cells

  • Authors:
    • Chia-Wei Kao
    • Yen-Ping Yeh
    • Ting-Wen Chen
    • Min-Ying Lin
    • Jyh-Der Leu
    • Yi-Jang Lee
  • View Affiliations / Copyright

    Affiliations: Department of Biomedical Imaging and Radiological Sciences, National Yang Ming Chiao Tung University, Taipei 112, Taiwan, R.O.C., Industrial Development Graduate Program of College of Engineering Bioscience, National Yang Ming Chiao Tung University, Hsinchu 30068, Taiwan, R.O.C., Institute of Bioinformatics and Systems Biology, National Yang Ming Chiao Tung University, Hsinchu 30068, Taiwan, R.O.C., Division of Radiation Oncology, Taipei City Hospital Renai Branch, Taipei 106, Taiwan, R.O.C.
    Copyright: © Kao et al. This is an open access article distributed under the terms of Creative Commons Attribution License.
  • Article Number: 56
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    Published online on: November 27, 2025
       https://doi.org/10.3892/ol.2025.15409
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Abstract

Hypopharyngeal cancer (HPC) is a highly aggressive cancer with a poor prognosis due to frequent metastasis and resistance to therapy. However, genes associated with the malignancy of advanced HPC remain to be elucidated. To investigate molecular changes associated with HPC progression, RNA sequencing was performed to compare transcriptomic profiles between parental FaDu HPC cells and advanced FaDu cells (FaDuex) derived from late‑stage xenograft tumors. The present analysis revealed 86 markedly upregulated genes and 166 markedly downregulated genes in FaDuex cells compared with FaDu cells. Gene set enrichment analysis revealed enrichment of pathways associated with epithelial‑mesenchymal transition and cell proliferation among upregulated genes, whereas downregulated genes were associated with metastasis inhibition, angiogenesis suppression and immune response regulation. Notably, several interferon (IFN)‑stimulated genes were suppressed in advanced cells, indicating impaired IFN signaling and reduced antitumor immune responses. The most notable changes in the expression levels of genes associated with these tumor characteristics were then validated using quantitative PCR. These findings suggest that genes associated with tumor malignancy and immunosuppressive pathways potentially contribute to HPC progression and highlight potential molecular targets for diagnostic and therapeutic intervention in the future.
View Figures

Figure 1

Comparison of DEGs between FaDuex and
FaDu cells. (A) Heatmap of 252 DEGs between FaDuex and FaDu cells,
with log2 fold-change ≥1.5 or ≤-1.5 and adjusted
P<0.05; (B) the volcano plot displays upregulated and
downregulated genes, with the x-axis representing the
log2 fold-change and the y-axis representing the
-log10 adjusted P-value with log2 fold-change
≥1.5 or ≤-1.5 and -log10(adjusted P-value)
>-log10(0.05). DEGs, differentially expressed genes.
TPM, transcripts per million; FaDuex, advanced FaDu.

Figure 2

Gene set enrichment analysis between
FaDuex and FaDu cells, using the human molecular signatures
database. The image displays (A) top 10 significantly suppressed
signaling pathways in FaDuex cells, identified using the hallmark
gene set. (B) top signaling pathways activated and suppressed in
FaDuex cells using the C2 gene set. The number of genes involved is
represented by the size of each dot and the color indicates the
adjusted P-value. FaDuex, advanced FaDu.

Figure 3

Heatmaps of Z-score normalized TPM
values and bar plots of log2 fold-change of DEGs. The
DEGs were associated with (A) metastasis, (B) angiogenesis, (C)
proliferation and survival and (D) epithelial-mesenchymal
transition-related genes. The color gradient indicates the Z-score
of TPM. Bars were colored black for adjusted P≥0.05 and
log2 fold-changes between −1.5 and 1.5. For bar plots
with adjusted P<0.05, log2 fold-changes <-1.5 are
marked in green, while those >1.5 are marked in red, indicating
significant fold-changes. TPM, transcripts per million; DEGs,
differentially expressed genes; FaDuex, advanced FaDu.

Figure 4

Heatmaps of Z-score-normalized TPM
values and bar plots of log2 fold-changes for
differentially expressed genes associated with the
interferon-responsive signaling pathway. (A) Analysis of
interferon-stimulated genes using the C2 gene set and (B) the
hallmark gene set. The color gradient indicates the Z-score of TPM.
Bars are colored black for adjusted P-values ≥0.05 and
log2 fold-changes between −1.5 and 1.5. For bar plots
with adjusted P-values <0.05, log2 fold-changes
<-1.5 are marked in green, while those >1.5 are marked in
red, indicating significant fold-changes. TPM, transcripts per
million; FaDuex, advanced FaDu.

Figure 5

Quantitative PCR analysis of genes
expressed in FaDu cells and FaDuex cells. (A) KRT13; (B)
IF16; (C) STC1; (D) IFI44L and (E)
MUC16. Data are presented as mean ± SD from four independent
experiments. **P<0.01 and ****P<0.0001. KRT13, keratin 13;
IFI44L, interferon-induced protein 44-like; IFI6, interferon
α-inducible protein 6; STC1, stanniocalcin-1; MUC16, mucin-16;
FaDuex, advanced FaDu.
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Copy and paste a formatted citation
Spandidos Publications style
Kao C, Yeh Y, Chen T, Lin M, Leu J and Lee Y: Differential gene expression analysis reveals signaling pathways of proliferation, angiogenesis and metastasis is associated with interferon suppression in advanced hypopharyngeal cancer cells. Oncol Lett 31: 56, 2026.
APA
Kao, C., Yeh, Y., Chen, T., Lin, M., Leu, J., & Lee, Y. (2026). Differential gene expression analysis reveals signaling pathways of proliferation, angiogenesis and metastasis is associated with interferon suppression in advanced hypopharyngeal cancer cells. Oncology Letters, 31, 56. https://doi.org/10.3892/ol.2025.15409
MLA
Kao, C., Yeh, Y., Chen, T., Lin, M., Leu, J., Lee, Y."Differential gene expression analysis reveals signaling pathways of proliferation, angiogenesis and metastasis is associated with interferon suppression in advanced hypopharyngeal cancer cells". Oncology Letters 31.2 (2026): 56.
Chicago
Kao, C., Yeh, Y., Chen, T., Lin, M., Leu, J., Lee, Y."Differential gene expression analysis reveals signaling pathways of proliferation, angiogenesis and metastasis is associated with interferon suppression in advanced hypopharyngeal cancer cells". Oncology Letters 31, no. 2 (2026): 56. https://doi.org/10.3892/ol.2025.15409
Copy and paste a formatted citation
x
Spandidos Publications style
Kao C, Yeh Y, Chen T, Lin M, Leu J and Lee Y: Differential gene expression analysis reveals signaling pathways of proliferation, angiogenesis and metastasis is associated with interferon suppression in advanced hypopharyngeal cancer cells. Oncol Lett 31: 56, 2026.
APA
Kao, C., Yeh, Y., Chen, T., Lin, M., Leu, J., & Lee, Y. (2026). Differential gene expression analysis reveals signaling pathways of proliferation, angiogenesis and metastasis is associated with interferon suppression in advanced hypopharyngeal cancer cells. Oncology Letters, 31, 56. https://doi.org/10.3892/ol.2025.15409
MLA
Kao, C., Yeh, Y., Chen, T., Lin, M., Leu, J., Lee, Y."Differential gene expression analysis reveals signaling pathways of proliferation, angiogenesis and metastasis is associated with interferon suppression in advanced hypopharyngeal cancer cells". Oncology Letters 31.2 (2026): 56.
Chicago
Kao, C., Yeh, Y., Chen, T., Lin, M., Leu, J., Lee, Y."Differential gene expression analysis reveals signaling pathways of proliferation, angiogenesis and metastasis is associated with interferon suppression in advanced hypopharyngeal cancer cells". Oncology Letters 31, no. 2 (2026): 56. https://doi.org/10.3892/ol.2025.15409
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