Low level of PDZ domain containing 1 (PDZK1) predicts poor clinical outcome in patients with clear cell renal cell carcinoma

Abstract

Clear cell renal cell carcinoma (ccRCC) is the most lethal neoplasm of the urologic system. Clinical therapeutic effect varies greatly between individual ccRCC patients, so there is an urgent need to develop prognostic molecular biomarkers to help clinicians identify patients in need of early aggressive management. In this study, samples from primary ccRCC tumor and their corresponding nontumor adjacent tissues (n=18) were analyzed by quantitative proteomic assay. Proteins downregulated in tumors were studied by GO and KEGG pathways enrichment analyses. Six proteins were found both downregulated and annotated with cell proliferation in ccRCC patients. Of these proteins, PDZK1 and FABP1 were also involved in the lipid metabolism pathway. The downregulation of PDZK1 was further validated in TCGA_KIRC dataset (n=532) and independent set (n=202). PDZK1 could discriminate recurrence, metastasis and prognosis between ccRCC patients. Low level of PDZK1 in both mRNA and protein was associated with reduced overall survival (OS) and disease-free survival (DFS) in two independent sets. In univariate and multivariate analyses, PDZK1 was defined as an independent prognostic factor for both OS and DFS. These findings indicated that low level of PDZK1 could predict poor clinical outcome in patients with ccRCC.

Keywords: CAP70; CLAMP; NHERF3; PDZ; Prognostic markers; Proteomics; Renal cancer.

Fig. S1

The correlation between the mRNA levels of FABP1, PDZK1 and T, M stage, recurrence, tumor maximum diameter and weight. (a) FABP1 mRNA level was obtained from TCGA_KIRC dataset and the trend of expression level with the increase of T stage was analyzed by ANOVA. The differences of FABP1 mRNA level between ccRCC patients without and with distant metastasis, recurrence were analyzed by independent sample t-test. (b) PDZK1 mRNA level was obtained from TCGA_KIRC dataset and the trend of expression level with the increase of T stage was analyzed by ANOVA. The correlations of PDZK1 mRNA level with tumor volume, maximum diameter and weight were analyzed by Pearson correlation analysis. PDZK1 protein level was obtained from IHC of 112 cases. The correlations of PDZK1 protein level with tumor maximum diameter was analyzed by Pearson correlation analysis.

Fig. S2

The prognostic significance of PDZK1 expression levels for stage I ccRCC patients. (a) KM curve for OS of patients in stage I with high and low PDZK1 mRNA level by median value. (b) KM curve for OS of patients in stage I with high and low PDZK1 protein level by median value. (c) That PDZK1 protein level stratified stage I ccRCC patients with good and poor prognosis for OS was analyzed by ROC curve.

Fig. 1

PDZK1 and FABP1, which are involved in both cell proliferation and lipid metabolism pathways, are downregulated in ccRCC tissues. The proteins of paired ccRCC and its adjacent normal tissues from 18 ccRCC patients were extracted respectively. Protein lysates from the same TNM stage (stage I, n = 8; stage II, n = 7; stage III, n = 1; stage IV, n = 2) were combined as a group, respectively (Tumor Tissue Stage I, II, III, IV; Adjacent Normal Tissue Stage I, II, III, IV) in equal amounts and analyzed by iTRAQ quantitative proteomics. The downregulated proteins were performed with the GO and KEGG pathway analysis. Results revealed that 174 proteins were both downregulated and participated in 52 KEGG pathways, mainly lipid metabolism pathways. Six proteins were both downregulated and annotated with cell proliferation. Two proteins annotated with cell proliferation (FABP1 and PDZK1) participated in lipid metabolism pathways.

Fig. 2

The levels of both PDZK1 and FABP1 mRNA are downregulated in ccRCC tissues and correlated with lipid metabolism in ccRCC. (a,b) The mRNA levels of both FABP1 and PDZK1 in ccRCC by RNA sequencing were obtained from the TCGA_KIRC dataset. Seventy-two normal tissues and 532 ccRCC tissues were sequenced. Outlier values (> mean ± 3 SD) were removed. (c,d) The correlation between lipid metabolism process gene set and mRNA level of FABP1 or PDZK1 was analyzed by GSEA assay. FDR < 0.001 was considered as statistically significant.

Fig. 3

Low level of PDZK1 mRNA predicts poor prognosis of ccRCC patients. (a) The mRNA level of PDZK1 between ccRCC patients with and without recurrence, metastasis was compared by independent sample t-test. (b, c) Patients were divided into high and low groups by median value of PDZK1 mRNA level. Kaplan-Meier (KM) curves for OS and DFS of patients were performed. (d, e) The mRNA level of PDZK1 between ccRCC patients with good and poor prognosis for OS and DFS was compared by independent sample t-test.

Fig. 4

Low level of PDZK1 protein predicts poor clinical outcome in patients with ccRCC. (a) The protein level of PDZK1 in paired biopsies of tumor (Ca) and normal (Adj) tissues from 38 ccRCC patients were analyzed by WB analysis. Representative blots of PDZK1 protein level in normal and ccRCC tissues were shown. β-actin was used as a loading control. (b) IHC was performed with anti-PDZK1 antibody in 19 normal tissues and 112 tumor tissues. Outlier values (> Mean ± 3 SD) were removed. Representative IHC images (20 × magnification, all panels) were shown. (c) The protein level of PDZK1 in 90 paired ccRCC samples was detected with IHC. (d) Patients were divided into high and low groups by median value of PDZK1 protein level. KM survival curve for OS was performed. (e) ROC curve for PDZK1 protein level in classifying ccRCC patients with good and poor prognosis for OS. The area under the receiver operating characteristic curve (AUC) was 0.877 (95% CI, 0.772–0.945).

Fig. 5

External comparison of biomarkers-OS and DFS. mRNA levels of five previously reported prognostic markers (BIRC5, LDHA, FSCN2, IMP3 and CA9) were extracted from TCGA_KIRC dataset. mRNA levels between patients with good and poor prognosis were compared by independent sample t-test. (a) for OS and (b) for DFS.

Fig. 6

External comparison of biomarkers-recurrence. mRNA levels of five previously reported prognostic markers (BIRC5, LDHA, FSCN2, IMP3 and CA9) were extracted from TCGA_KIRC dataset. mRNA levels between patients with and without recurrence were compared by independent sample t-test.