Dysregulated genes in HIGK-treated F. nucleatum and their possible association with HNSCC

Abstract

The present study aims to identify the differentially expressed genes in HIGK treated with Fusobacterium nucleatum (Fn) and their possible role in establishing head and neck squamous cell carcinoma. The study design follows a computational approach wherein multiple databases and tools are used to derive the possible association between Fn exposure and the development of HNSCC. The GEOmnibus dataset GSE6927 provided data on the differentially expressed genes in the HIGK treated with Fn. The GEO2R analysis revealed 22 differentially expressed genes in HIGK cells treated with Fn. The expression profile of these genes was then analyzed in the HNSCC (TCGA, Firehose Legacy) dataset employing the UALCAN database. The present study revealed 5 genes viz., GSDMD, NUP214, ZNF426, FUT2, and SERPINB2 exhibiting similar expression patterns in Fn-treated HIGK and HNSCC datasets. The GSDMD and NUP214 were found to be upregulated, and the genes ZNF426, FUT2, and SERPINB2 were downregulated. Among the five genes, the ZNF426 demonstrated a significant association with the survival of HNSCC patients. The low expression of ZNF426 presented a poor prognosis compared to the high expression. The study's results identified ZNF426 as a candidate gene involved in Fusobacterium nucleatum infection and HNSCC. Validating this result is necessary to gain insights into the role of the ZNF426 gene in developing HNSCC. Furthermore, probing the epigenetic factors targeting ZNF426 can be a potential therapeutic lead.

Keywords: Microbes; Cancer; Genotoxicity; Gene expression; Prognosis.

Figure 1

Volcano plot demonstrating differentially expressed genes (DEGs) that are upregulated (red) and downregulated (blue) in Fusobacterium nucleatum-treated human immortalized gingival keratinocytes (HIGK). A p-value less than 0.05 is considered significant.

Figure 2

Protein network interactions of the differentially expressed genes (DEGs) as compared using Fn infected-HIGK vs Sham-HIGK cells.

Figure 3

Gene ontology analysis using Panther (http://www.pantherdb.org/) revealed the molecular pathways associated with the differentially expressed genes.

Figure 4

(a) Bar chart demonstrating the expression profile of Fn-infected HIGK vs. Sham-HIGK (b) Box Whisker plot demonstrating the gene expression profile of the ZNF426 gene in HNSCC datasets. The gene expression between the normal and the HNSCC primary tumor group demonstrated significant downregulation in transcript levels (p=1.896×10^-03), (c) Kaplan Meier plot demonstrating survival probability of patients presenting with high and low levels of ZNF426 in HNSCC datasets.

Figure 5

(a) Box Whisker plot demonstrating the gene expression profile of the hsa-miR-181d in HNSCC datasets. The gene expression between the normal and the HNSCC primary tumor group demonstrated significant upregulation in transcript levels (p = 6.46 × 10^-11), (b) Kaplan Meier plot demonstrating survival probability of patients presenting with high and low levels of ZNF426 in HNSCC datasets. The patients exhibiting high expression of hsa-miR-181d were found to have a poor prognosis (p=0.085) compared to the low expression group.

Figure 6

Gene enrichment analysis of potential gene targets of (a) hsa-miR-181d-5p and (b) hsa-miR-181d-3p