Analysis of mRNA Pentatricopeptide Repeat Domain 1 as a prospective oncogene in clear cell renal cell carcinoma that accelerates tumor cells proliferation and invasion via the Akt/GSK3β/β-catenin pathway

Abstract

Background: Although pentatricopeptide repeat domain 1 (PTCD1) has been found to modulate mitochondrial metabolic and oxidative phosphorylation, its contribution in the growth of clear cell renal cell carcinoma (ccRCC) remains unknown.

Methods: The Cancer Genome Atlas (TCGA) dataset was utilized to examine the transcriptional alterations, patient characteristics, clinical outcomes, as well as pathway activation of PTCD1. The Weighted Gene Co-expression Network Analysis (WGCNA) was performed to investigate potential genes that associated with PTCD1. The researchers estimated the relationship between PTCD1, tumor immunology, and epithelial mesenchymal transition (EMT). Researchers studied how PTCD1 affects the functional behavior of tumor cells in vitro.

Results: PTCD1 expression was greater in ccRCC samples than in normal samples, and expression increased gradually as the stage increased. In TCGA cohorts, higher PTCD1 expression was substantially associated with a poorer clinical stage, histological grading, T stage, N stage, M stage, and survival outcomes. The results of multivariate analysis showed that PTCD1 was an independent variable affecting the survival outcomes of ccRCC patients (p < 0.001). PTCD1 regulated ccRCC progression via various cancer mechanisms including PI3K-Akt signaling, focal adhesion, PD-L1 expression, and PD-1 checkpoints in cancer. WGCNA discovered a significant relationship between PTCD1 and IARS2, LRPPRC, MT-ND2, MT-CO1, MT-CO2, MT-CYB, MT-ATP6, and MT-ND4. Furthermore, PTCD1 expression levels was closely associated with immune infiltrating, immunological checkpoint, EMT, immunotherapy responsiveness, and anti-tumor medication sensitivities. Upregulation of PTCD1 in ccRCC cells resulted in considerably increased cellular invasion and migration. Mechanistically, the upregulation of PTCD1 increased the phosphorylation of AKT at Ser473 and GSK-3β at Ser9, as well as enhanced activation of Wnt/β-catenin pathway.

Conclusion: Elevated expression of PTCD1 was associated with malignant biological behaviors and poor outcomes of ccRCC patients, and PTCD1 may accelerate tumor cells proliferation and invasion via the Akt/GSK3β/β-catenin pathway. Our findings indicated that PTCD1 had the potential to become a new target for predicting prognosis and targeted therapy.

Keywords: Biomarker; Clear cell renal cell carcinoma; Immune microenvironment; Pentatricopeptide repeat domain 1; Prognosis; Weighted Gene Coexpression Network Analysis.

Fig. 1

The implementation process of this study

Fig. 2

The PTCD1 expression level and survival analysis in ccRCC. a PTCD1 expression in normal tissues and ccRCC tissues; b PTCD1 expression in ccRCC paired tissues; Box plot evaluating PTCD1 expression according to different clinical characteristics including age (c), gender (d), stage (e), grade (f), T stage (g), N stage (h) and M stage (i); The OS (j), DSS (k), PFI (l) of high-PTCD1 versus low-PTCD1 in the TCGA dataset; ROC curve demonstrated the stability of PTCD1 in evaluating 1-, 3- and 5-year OS (m); Sankey diagram of the connection between TNM stage, PTCD1 expression, and survival status (N); *p < 0.05; **p < 0.01; ***p < 0.001

Fig. 3

The stratified analysis of OS based on clinicopathological characteristics including age (a, b), gender (c, d), grade (e, f), stage (g, h), T stage (i, j) and M stage (k, l), which showed PTCD1 expression had a stable prognosis on ccRCC, respectively (all p < 0.05)

Fig. 4

a Univariate Cox regression analysis; b Multivariate Cox regression analysis; c Nomogram for predicting probability of patients with 1-, 3-, and 5-year OS; d The ROC of PTCD1 expression and clinicopathological characteristics; e Actual and predicted survivals by the calibration curves; f Decision curve analysis of nomogram and other clinical indicators

Fig. 5

Functional enrichment analysis between low-PTCD1 group and high-PTCD1 group in TCGA dataset; a Enriched biological process, cellular component, and molecular function; b Enriched Kyoto Encyclopedia of Genes and Genomes pathways; c, d The circle plot of the top 15 most relevant terms in GO analysis and KEGG analysis

Fig. 6

Identification of the module related with PTCD1 in DEGs dataset. a Clustering dendrograms of samples as well as traits; b Cluster dendrogram of co-expression network modules based on the 1-TOM matrix; c High-PTCD1 expression was closely related to the pink module; d Co-expression network of PTCD1 in the pink module; e Dot heatmap of gene correlation in co-expression network

Fig. 7

The association of PTCD1 with top eight core genes including IARS2 (a), LRPPRC (b), MT-ND2 (c), MT-CO1 (d), MT-CO2 (e), MT-CYB (f), MT-ATP6 (g) and MT-ND4 (h)

Fig. 8

Using different algorithms to calculate immune cell infiltration in 530 ccRCC cases, demonstrating that the proportion of immune cell infiltration was significantly different between the two groups

Fig. 9

The enrichment scores of eosinophils (a), macrophages (b), neutrophils (c), NK CD56 bright cell (d), T helper cells (e), Th17 cells (f), Th2 cells (g), Treg (h) between high-PTCD1 group and low-PTCD1 group; The immune checkpoint (i), EMT-related genes (j) of the high- and low-PTCD1 group for ccRCC patients in the TCGA cohorts. *p < 0.05; **p < 0.01; ***p < 0.001

Fig. 10

Analysis of anti-tumor drug sensitivity (a–h) and immunotherapy response (i, j) between high- and low-PTCD1 groups; (k) Normal tissues and Tumor tissues (l) on the protein levels of PTCD1 from HPA database

Fig. 11

Overexpression of PTCD1 promoted the proliferation, viability, migration and invasion of ccRCC cells in vitro. Expression levels of PTCD1 mRNA in HK-2 and four ccRCC cell lines were detected by qRT-PCR (a). qRT-PCR revealed that PTCD1 was markedly upregulated by pLV-PTCD1 in the 786o and ACHN cells (b). Upregulation of PTCD1 markedly promoted the proliferation (c, d) and viability (e, f) of 786o and ACHN cells; Transwell invasion assays accessing the invasive ability of 786o and ACHN cells (g, h); Wound-healing assays accessing the invasive ability of 786o and ACHN cells (i, j); Colony formation assays showed the more colonies in pLV-PTCD1 cells than LV-NC cells (k, l); Upregulation of PTCD1 increased the level of β‐catenin, and contributed the phosphorylation of AKT at Ser473, GSK-3β at Ser9 (M). *p < 0.05; **p < 0.01; ***p < 0.001