APOA1 mRNA and protein in kidney renal clear cell carcinoma correlate with the disease outcome

Abstract

Renal cancer is one of the most common malignant tumors with high mortality, and kidney renal clear cell carcinoma (KIRC) is the most common type of renal cancer. We attempted to evaluate the clinical and prognostic significance of Apolipoprotein A1 (APOA1) mRNA and protein in KIRC patients. Clinical data along with RNA-sequencing data were downloaded from UCSC Xena. The Human Protein Atlas database was searched to reveal APOA1 protein expression profiles in KIRC and normal renal tissues. The TIMER database was applied to determine the correlations of APOA1 with immune cells and PD-1 and PD-L1 in KIRC. Ninety-one cases of KIRC patients and 93 healthy controls from our hospital were enrolled for clinical validation. Levels of APOA1 mRNA in KIRC tissues (N = 535) are not only lower than the levels in normal renal tissues (N = 117), but also in paired normal renal tissues (N = 72). High expression of APOA1 mRNA at the time of surgery was correlated with worse overall survival (OS) (HR 1.66; p = 0.037) and disease-free survival (DFS) (HR 1.65; p = 0.047), and APOA1 DNA methylation was linked to worse OS (HR 2.1; p = 0.001) rather than DFS (HR 1.12; p = 0.624) in KIRC patients. Concentrations of preoperative serum APOA1 protein were markedly decreased in KIRC patients compared to healthy controls (p < 0.01), and low levels of APOA1 protein predicted less favorable OS than those with high levels (HR = 2.84, p = 0.0407). APOA1 negatively correlated with various immune cell infiltrates and PD-L1 expression (r = - 0.283, p = 2.74e-11) according to the TIMER database. Low levels of APOA1 mRNA at the time of surgery predict favorable survival in KIRC patients. Our results provide insights to identify a novel prognostic index with great clinical utility.

Figure 1

Expression and methylation of APOA1 in KIRC tissues and the normal renal tissues. (A) The levels of APOA1 mRNA in KIRC tissues were statistically lower than that in paired normal renal tissues (p = 3.4e−5) by TNMplot (https://tnmplot.com/analysis/). (B) The levels of APOA1 mRNA in KIRC tissues were statistically lower than that in the normal renal tissues (p = 3.76e−18) by TNMplot (https://tnmplot.com/analysis/). (C) UCSC Xena webpage (http://xena.ucsc.edu/#overview) was browsed to generate the heatmap of APOA1 mRNA expression and DNA methylation in KIRC dataset. (D) Distribution of APOA1 DNA CpG site among primary tumors, normal tissues and additional-new primary tumors was obtained from UCSC Xena webpage (http://xena.ucsc.edu/#overview).

Figure 2

Survival analyses comparing low and high APOA1 mRNA/methylation in KIRC patients by Grahpad Prism version 9.0 (https://www.graphpad.com/scientific-software/prism/). KIRC patients with low levels of APOA1 mRNA (N = 269) exhibited longer overall survival (A) and disease-free survival (B) time than those with high levels of APOA1 mRNA (N = 268). KIRC patients with APOA1 hypomethylation (N = 159) exhibited longer overall survival (C) and disease-free survival (D) time than those with APOA1 hypermethylation (N = 160).

Figure 3

Representative images stained with APOA1 antibody (CAB016778; HPA046715), which were downloaded from the HPA database (https://www.proteinatlas.org/). (A–D) The normal tissues. (E–H) KIRC tissues. HPA046715 is a polyclonal antibody derived from rabbits and produced by Sigma-Aldrich, and CAB016778 is a monoclonal antibody derived from mice and produced by BioPorto Diagnostics A/S.

Figure 4

Diagnostic and prognostic significance of serum APOA1 protein in KIRC patients by Grahpad Prism version 9.0 (https://www.graphpad.com/scientific-software/prism/). (A) Levels of serum APOA1 protein in healthy individuals are much higher than that in KIRC patients (p < 0.001). (B) ROC curve of serum APOA1 protein for the identification of KIRC patients from normal controls. (C) Kaplan–Meier plot of serum APOA1 protein among 91 cases of KIRC patients. (D) Forest plot of the multivariable analysis of overall survival in KIRC patients.

Figure 5

Relationships between levels of APOA1 protein and common clinical features in 91cases of KIRC patients by Grahpad Prism version 9.0 (https://www.graphpad.com/scientific-software/prism/). (A) age (p = 0.2867); (B) gender (p = 0.1305); (C) tumor site (p = 0.1633); (D) histological grade (p = 0.0047); (E) T stage (p < 0.0001); (F) N stage (p = 0.4939); (G) M stage (p = 0.0001); (H) TNM stage (p = 0.0138).

Figure 6

Co-expressed genes with APOA1 and Go analysis of these genes in KIRC based on the LinkedOmics database (http://www.linkedomics.org/). (A) Volcano plot of the genes relevant to APOA1 expression in KIRC tissues. (B) Significant genes positively correlated with APOA1 expression. (C) Significant genes negatively correlated with APOA1 expression.