BANF1 is a novel prognostic biomarker linked to immune infiltration in head and neck squamous cell carcinoma

Abstract

Background: Barrier-to-autointegration factor 1 (BANF1) is an abundant and ubiquitously expressed postnatal mammalian protein that is overexpressed in numerous human cancers and can promote cancer cell proliferation. However, the role of BANF1 in prognosis remains unclear in head and neck squamous cell carcinoma (HNSCC).

Methods: BANF1 expression data were obtained from the GEO and TCGA databases. We used Cox regression and Kaplan-Meier curves to assess the prognostic potential of BANF1. The role of BANF1-related genes was investigated using Kyoto Encyclopedia of Genes and Genomes (KEGG) and Gene Ontology (GO) enrichment analyses. In addition, we explored the link between BANF1, drug sensitivity, and the tumor immune microenvironment. Finally, functional in vitro and in vivo assays were used to explore the effects of BANF1 on tumor growth and metastasis of HNSCC.

Results: BANF1 was markedly overexpressed in HNSCC and was correlated with clinicopathological characteristics. According to survival analysis, BANF1 can be inversely correlated with patient survival and can act as a prognostic risk indicator. IC50 values for chemotherapeutic treatments indicated that the group with high BANF1 expression was more responsive to most antitumor treatments. Furthermore, higher TIDE scores were observed in the low BANF1 expression group, indicating a decline in the efficacy of immune checkpoint inhibitor therapy. Functionally, the malignant biological behavior of HNSCC cell lines was inhibited when BANF1 expression was knocked down.

Conclusion: BANF1 can promote tumor progression in patients with HNSCC. BANF1 shows great promise as a potential biomarker to assess the prognosis.

Keywords: BANF1; TCGA; head and neck squamous cell carcinoma; immune infiltration; prognostic biomarker.

Figure 1

The expression of BANF1 was markedly elevated in HNSCC tissues. (A) The gene expression profiles of BANF1 in the pan-cancer dataset of the TCGA database. (B) In the TCGA database, the expression level of BANF1 was elevated in HNSCC tissue compared to the neighboring normal tissue. (C–E) The expression level of BANF1 was higher in tumor tissues in the GSE37991, GSE23558, and GSE30784 datasets. *P<0.05, **P<0.01, ***P<0.001.

Figure 2

Comparison of BANF1 expression in different subgroups of Tumor stage (A), Tumor grade (B), Nodal metastasis status (C), Gender (D), TP53 status (E), and HPV status (F). *P<0.05, **P<0.01, ***P<0.001. ns indicated no significance.

Figure 3

Investigation on the predictive importance of BANF1 in HNSCC. (A–D) Survival curves for patients with advanced HNSCC from the TCGA dataset were generated using the Kaplan-Meier plotter database. (E, F) Univariate and multivariate analyses were conducted to examine the relationship between overall survival and clinicopathologic features in individuals with HNSCC.

Figure 4

Functional enrichment analysis of BANF1 in HNSCC. (A) Volcano plot showing DEGs between high and low expressing BANF1 groups in HNSCC. (B, C) GSEA enrichment plot showing the correlation of high and low BANF1 expression with different tumor-related pathways. (D, E) GO and KEGG pathway analysis of up- and down-regulated DEGs in HNSCC.

Figure 5

Sequencing analysis of BANF1 single cells in HNSCC from the TISCH website. The main distributions of BANF1 on cell types in (A) HNSC_GSE103322, (B) HNSC_GSE139324 and (C) OSCC_GSE172577 dataset.

Figure 6

Quantification of immune-invading cells. (A) The expression of BANF1 showed a substantial negative correlation with the majority of immune cells. (B–F) The BANF1 group with lower levels had elevated TME scores and enhanced immunological activity. *P<0.05, **P<0.01, ***P<0.001. ns indicated no significance.

Figure 7

Comparison of immunotherapeutic responses between groups with high and low BANF1 expression. (A–C) There are differences in TIDE, Exclusion, and Dysfunction ratings between the groups with high and low expression. (D) Differences in BANF1 gene expression between patients with good response to treatment and those with a poor response. (E) The proportion of individuals who responded and did not respond in groups with high and low expression in TCGA cohort. (F) The TIDE biomarker determines the effectiveness of BANF1 in the immunotherapy response for HNSCC.

Figure 8

BANF1 is a predictive factor for treatment responsiveness in patients with HNSCC. (A, B) Comparative analysis of IC50 values of chemotherapeutic medication in cases of high and low expression of BANF1. (C, D) The correlation between BANF1 and HNSCC IC50 values for small and medium-molecule drugs.

Figure 9

Suppression of BANF1 hindered the growth, movement, and departure of HNSCC cells. (A) The qRT-PCR assay successfully identified the presence of BANF1 mRNA expression in HOK, HN4, HN6, SCC9, and CAL27 cells. (B) qRT-PCR measured the amounts of BANF1 mRNA in SCC9 and CAL27 cells following transfection. (C) Suppression of BANF1 expression hindered the growth and division of HNSCC cells. (D) Suppressing the expression of BANF1 hindered the ability of HNSCC cells to generate clones. (E) The impact of reduced BANF1 expression on the migratory capacity of HNSCC cells was assessed using a scratch assay. (F) The impact of reduced BANF1 expression on the migratory and invasive capabilities of HNSCC cells was assessed using a transwell assay. **P<0.01, ***P<0.001, ****P<0.0001.

Figure 10

Downregulation of BANF1 expression markedly suppressed the proliferation and expansion of SCC9 cells in a xenograft mice model. (A) Tumor formation under the skin in nude mice with varying levels of BANF1 expression. (B) Comparative analysis of tumor dimensions. (C, D) Comparative analysis of the alterations in weight and volume of subcutaneous tumors in nude mice belonging to distinct BANF1 expression cohorts. ***P<0.001, ****P<0.0001.