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Gene & Protein in Disease Pre-metastatic niche oral cancer: Insights

expression studies. Survival analysis of the TCGA data and non-metastatic specimens. A separate analysis was
was performed using TCGAbiolinks. Kaplan–Meier conducted, and DAVID functional analysis showed that
22
plots were constructed to explore the association between downregulated DEGs in non-metastatic tissue were
clinical outcomes and gene expression, allowing for the mainly associated with “drug metabolism,” “metabolism
visualization of survival differences. We further explored of xenobiotics by cytochrome P450,” “retinol metabolism,”
protein expression using The Human Protein Atlas. “calcium signaling pathway,” “dilated cardiomyopathy,”
“hypertrophic cardiomyopathy, ”and “steroid hormone
3. Results biosynthesis” pathways. In contrast, the “ECM-receptor
3.1. Identification of differentially expressed interaction,” “focal adhesion,” “cytokine-cytokine receptor
genes, gene ontology enrichment, and functional interaction,” “neuroactive ligand-receptor interaction,”
classification “graft-versus-host disease,” “natural killer cell-mediated
cytotoxicity,” “systemic lupus erythematosus,” and
To evaluate key factors that contribute to the development “pathways in cancer” were more active in the same group
and progression of the pre-metastatic niche in OSCC, we of specimens (Tables S1 and S2).
evaluated GEO datasets, including metastatic and non-
metastatic primary tumor samples (GSE2280), healthy oral Similarly, in metastatic samples, downregulated DEGs
tissues and OSCC samples (GSE31056), and metastatic were linked to the inactivation of “drug metabolism,”
lymph nodes from patients with OSCC and normal lymph “metabolism of xenobiotics by cytochrome P450,”
node samples (GSE70604). and “retinol metabolism” pathways. On the other
hand, upregulated DEGs in metastatic samples were
In the GSE2280 dataset (metastatic and non-metastatic associated with “ECM-receptor interaction,” “focal
primary tumor samples), downregulated DEGs indicated adhesion,” “cytokine-cytokine receptor interaction,”
the inactivation of the “intestinal immune network “neuroactive ligand-receptor interaction,” “systemic lupus
for IgA production” and “cytokine-cytokine receptor erythematosus,” “pathways in cancer,” and “cell cycle”
interaction” pathways. In contrast, upregulation of pathways. We found similar results in both perineural
the “calcium signaling pathway,” “neuroactive ligand- invasion-negative and perineural invasion-positive
receptor interaction,” “long-term potentiation,” “dilated analyses (Tables S3 and S4).
cardiomyopathy,” “gonadotropin-releasing hormone
(GnRH) signaling pathway,” and “gap junction” were 3.3. Differentially expressed genes and pre-
observed (Table 1). metastatic niche-related genes
In the GSE31056 dataset (healthy oral tissues and Using Entrez Gene and GeneCards analyses, we identified
OSCC samples), the top six downregulated pathways were 473 pre-metastatic niche-related genes. A Venn diagram
“drug metabolism,” “fatty acid metabolism,” “metabolism was created to illustrate the overlap between the DEGs
of xenobiotics by cytochrome P450,” “peroxisome identified in the meta-analysis and those related to the
proliferator-activated receptor signaling pathway,” “dilated pre-metastatic niche. The data showed that SERPINE1,
cardiomyopathy,” and “valine, leucine, and isoleucine SPP1, CALCA, and MMP13 genes were consistently
degradation.” We observed that “cell cycle,” “extracellular upregulated across all GEO and TCGA datasets.
matrix (ECM)-receptor interaction,” “DNA replication,” According to the list of 473 pre-metastatic niche-related
“focal adhesion,” “p53 signaling pathway,” and “pathways genes, the GSE70604 dataset (lymph node samples)
in cancer” were more active in OSCC samples compared showed 68 upregulated and 61 downregulated genes.
with normal tissue (Table 2). DAVID analysis showed those the upregulated genes are
Finally, in the GSE70604 dataset (metastatic lymph associated with several cancer-related pathways, while
nodes), we observed inactivated immune response the downregulated genes are mainly associated with
pathways and activated “ECM-receptor interaction,” immune response, axon guidance, and the neurotrophin
“focal adhesion,” “pathways in cancer,” “circadian rhythm,” signaling pathway (Table 4). These findings were
“steroid hormone biosynthesis,” and “adherens junction” validated using immunohistochemical analysis from The
pathways (Table 3). Human Protein Atlas (Figure 1).
We found a positive correlation between CALCA,
3.2. Overview of The Cancer Genome Atlas cancer SERPINE1, MMP13, SPP1, and MMP13 in TCGA cancer
transcriptomic analysis samples (Figure 2). Survival analysis showed that the

To validate the GEO2R results, we evaluated the TCGA overexpression of SERPINE1, SPP1, and L1CAM (axon
data, obtaining gene expression data from metastatic guidance) was associated with poor survival, while the low

Volume 3 Issue 4 (2024) 3 doi: 10.36922/gpd.2971