Elevated Expression of PDZD11 Is Associated With Poor Prognosis and Immune Infiltrates in Hepatocellular Carcinoma

Abstract

Epithelial cells are held together by tight and adherent junctions, which are destroyed by the activation of epithelial-to-mesenchymal transition (EMT). The PLEKHA7-PDZD11 complex has been reported to be important for epithelial cell adhesion and connecting tissues. However, there is no research regarding the expression and role of PDZD11 in liver hepatocellular carcinoma (LIHC) progression. Here, we analyzed PDZD11 mRNA expression and its clinical results in LIHC patient RNA sequencing data based on different open databases. Furthermore, we examined differences in PDZD11 expression in LIHC tissues and cell lines using western blotting and real-time qPCR. These results are the first to report that the mRNA and protein levels of PDZD11 are significantly overexpressed in LIHC. Moreover, high expression of PDZD11 was correlated with poor overall survival in patients with LIHC. Gene regulatory network analysis suggested that PDZD11 is mainly involved in copper ion homeostasis, proteasome, and oxidative phosphorylation pathways. Interestingly, we found that PDZD11 levels were positively correlated with the abundance of immune infiltrates. In particular, higher infiltration levels of CD4⁺ T cells and macrophage subsets significantly affected LIHC patient prognosis. Taken together, these results demonstrate that PDZD11 could be a potential diagnostic and prognostic biomarker in LIHC.

Keywords: PDZD11; functional network analysis; hepatocellular carcinoma; immune infiltrates; prognostic biomarker.

FIGURE 1

PDZD11 expression levels in LIHC. (A) Transcription levels of PDZD11 in different types of cancers (TIMER database). (B) PDZD11 mRNA expression levels in LIHC tissues and adjacent normal liver tissues from GEPIA 2 database. (C,D) Box plots show PDZD11 mRNA expression in liver (left plot) and hepatocellular carcinoma tissue (right plot) of the Chen Liver (C) and Wurmbach Liver (D) datasets. The fold-change of PDZD11 expression in LIHC was determined using the Oncomine database. The threshold was designed using the following specific parameters: p = 1E-4, fold change = 2, and gene rank 10%. (E) mRNA expression of PDZD11 in primary solid tumors, recurrent solid tumors, and adjacent normal liver tissues (DriverDBV3 database). (F) A representative western blot showing PDZD11 protein is expressed in LIHC tissues (T) and matched normal liver tissues (N) (n = 8). (G,H) Real-time qPCR and Western blotting analysis of PDZD11 mRNA (G) and protein expression (H) in human hepatocytes and LIHC cell lines. *p < 0.05; **p < 0.01; ***p < 0.001.

FIGURE 2

Analysis of subgroup expression of PDZD11 in LIHC (UALCAN database). (A) PDZD11 mRNA expression in LIHC tissue and adjacent normal liver tissue. (B–I) Box plot shows the PDZD11 mRNA expression of LIHC patients in the subgroups of different cancer stages (B), race (C), gender (D), age (E), weight (F), tumor grade (G), nodal metastasis status (H), and TP53 mutation status (I). The data are shown as mean ± SE. ^∗p < 0.05; ^∗∗p < 0.01; ^∗∗∗p < 0.001. The asterisk indicates a significant difference between the two sets of data.

FIGURE 3

Genetic alternations and promoter methylation levels of PDZD11 in LIHC. (A) Oncoprint in cBioPortal showed the distribution and proportion of samples with alternations in PDZD11. (B) The promoter methylation levels of PDZD11 in LIHC. (C–J) Box plots show promoter methylation level of PDZD11 in normal vs. LIHC tissues and different individual cancer stages (C), race (D), gender (E), age (F), weight (G), tumor grade (H), nodal metastasis status (I), and TP53 mutation status (J) (UALCAN database). Data are shown as mean ± SE. ^∗p < 0.05; ^∗∗p < 0.01; ^∗∗∗p < 0.001.

FIGURE 4

Visual summary of the prognostic value and biological interaction network of PDZD11 in LIHC. (A,B) Kaplan-Meier plot of the relationship of PDZD11 gene expression and survival in LIHC patients (DriverDBV3 database). The LIHC patient samples are stratified into 2 groups using the mean expression value as the cut-off point: 149 samples with highly expressed PDZD11 mRNA (red) and 216 samples with lowly expressed PDZD11 mRNA (green). Y-axis is survival probability. The left figure is the 5-year survival, and the right figure shows overall survival (OS). The X-axis is the months of survival period. Log-Rank P-value and Hazard Ration (HR) are provided on the top of plots. (C) Protein-protein interaction (PPI) network of PDZD11 (Top 10) (STRING database). (D) PPI network (Top 20) of PDZD11 from GeneMANIA database.

FIGURE 5

Differentially expressed genes that correlated with PDZD11 in LIHC (LinkedOmics database). (A) A Pearson test was used to determine the correlations between PDZD11 and differently expressed genes in LIHC. (B,C) Heat maps are showing genes (Top 50) positively or negatively correlated with PDZD11 in LIHC. Red indicates positively correlated genes and blue indicates negatively correlated genes. (D–F) The scatter plots mean that PDZD11 expression is positively correlated with the expression of FAM50A (D), NDUFA1 (E), and LAGE3 (F).

FIGURE 6

Enrichment analysis of PDZD11 co-expression genes in LIHC. (A–D) The significantly enriched GO annotations and KEGG pathways of PDZD11 co-expression genes in LIHC are analyzed using DAVID. Based on the Pearson test (Figures 5A–C), we selected the positively and negatively correlated genes with coefficient > 0.3 and < –0.3 (LinkedOmics and bioinformatics databases). (E) KEGG pathway annotations of the oxidative phosphorylation pathway. Red marked nodes are associated with the Leading Edge Genes. FDR < 0.05 was considered statistically significant.

FIGURE 7

Associations between mRNA expression of PDZD11 and immune infiltration in LIHC (TIMER2.0 database). (A) Association of PDZD11 expression with abundance of immune infiltrates (B cells, CD8⁺ T cells, CD4⁺ T cells, macrophages, neutrophils and dendritic cells). (B–D) The effect of PDZD11 expression in correlation with infiltration levels of immune cells on the prognosis of LIHC.