Expression and prognostic impact of VDAC3 in colorectal adenocarcinoma

Abstract

Background: Colorectal adenocarcinoma (COAD) is a malignant tumor with high mortality and low 5-year survival rate. Voltage-dependent anion channel 3 (VDAC3) is the least understood isoform of voltage-dependent anion-selective channels in the mitochondrial outer membrane. In this thesis, we aimed to investigate the prognostic value of VDAC3 and provide new insights into colon adenocarcinoma.

Methods: We utilized The Cancer Genome Atlas (TCGA) database, Gene Expression Omnibus (GEO) database, Human Protein Atlas online database, and the University of ALabama at Birmingham CANcer data analysis Portal (UALCAN) database to analyze VDAC3 expression in COAD and assess patient survival rates. Univariate and multivariate Cox regression analyses were employed to evaluate VDAC3's prognostic significance for COAD. Gene set variation analysis (GSVA) was utilized to explore COAD-related signaling pathways associated with VDAC3. Additionally, we predicted the relationship between VDAC3 expression and anticancer drug sensitivity using the CellMiner database.

Results: In the TCGA database, VDAC3 demonstrated elevated expression levels in COAD, which was further validated by findings from the GEO database. Survival analysis conducted using Kaplan-Meier (K-M) curves highlighted that the patients with decreased VDAC3 expression exhibited significantly shorter overall survival durations. VDAC3 expression demonstrated correlation with COAD pathological stage. VDAC3 gene mutation was linked to COAD outcomes. Cox regression analysis showed that VDAC3 was an independent predictor. In addition, GSVA analysis showed that VDAC3 was closely related to mitochondria-related biological processes and involved in the occurrence and development of mitochondria-related diseases. Finally, analysis of the CellMiner database predicted that VDAC3 expression was positively correlated with chelerythrine and cladribine, but negatively correlated with Ergenyl.

Conclusions: Our study suggests that VDAC3 may be a potential biomarker for early diagnosis, prognosis, and treatment of COAD.

Keywords: Colon adenocarcinoma; biomarker; prognosis; voltage-dependent anion channel 3 (VDAC3).

Figure 1

GSVA analysis in COAD and expression analysis of VDAC3. (A) Identification of 20 pathways exhibiting significant differential expression in COAD. (B) Select the top 5 positively correlated pathways and the top 5 negatively correlated pathways with the highest differences for further analysis. (C) Pan-cancer analysis of VDAC3 expression. *, P<0.05; ***, P<0.001; ns, not statistically significant. (D) Evaluate the relative expression of VDAC3 in colorectal adenocarcinoma in comparison to non-cancerous colon tissues utilizing the TCGA database. *, P<0.05. (E) Evaluate the relative expression of VDAC3 in colorectal adenocarcinoma in comparison to non-cancerous colon tissues utilizing the GSE database. ***, P<0.001. KEGG, Kyoto Encyclopedia of Genes and Genomes; TCGA, The Cancer Genome Atlas; GSVA, gene set variation analysis; COAD, colorectal adenocarcinoma; VDAC3, voltage-dependent anion channel 3; GSE, Gene Expression Omnibus.

Figure 2

Total protein expression level of VDAC3 in COAD. (A,B) Representative immunohistochemistry images of VDAC3 in both normal and COAD tissues sourced from the Human Protein Atlas database (https://www.proteinatlas.org/). Image credit goes to the Human Protein Atlas. The following links were VDAC3 expression of normal and tumor tissue (https://www.proteinatlas.org/ENSG00000078668-VDAC3/tissue/colon#imid_6773678; https://www.proteinatlas.org/ENSG00000078668-VDAC3/pathology/colorectal+cancer#img). Scale bar, 200 μm. (C) The expression of VDAC3 protein in pan-cancer. ***, P<0.001; ns, not statistically significant. (D) VDAC3 protein expression in normal colon tissues or COAD tissues. ***, P<0.001. (E) Expression of VDAC3 protein in normal tissues and COAD tissues of different races. *, P<0.05; ***, P<0.001; ns, not statistically significant. (F) Expression of VDAC3 protein in normal tissues and COAD tissues of patients at different ages. ***, P<0.001; ns, not statistically significant. (G) Expression of VDAC3 protein in normal colon tissues and COAD tissues of patients with different pathological stages. Z-values represent standard deviations from the median across samples for the given cancer type. *, P<0.05; ***, P<0.001; ns, not statistically significant. HPA, Human Protein Atlas; NOS, not otherwise specified; RCC, renal cell carcinoma; UCEC, uterine corpus endometrial carcinoma; PAAD, pancreatic adenocarcinoma; VDAC3, voltage-dependent anion channel 3; COAD, colorectal adenocarcinoma.

Figure 3

Relationship between VDAC3 and clinicopathological features of COAD. (A) Prospect of clinicopathological features associated with VDAC3 in colon adenocarcinoma from TCGA database. Relationship between VDAC3 expression and clinicopathological parameters. (B) N, (C) T, (D) phase, (E) M, (F) gender, (G) age. *, P<0.05; **, P<0.01; ns, not statistically significant. (H) Kaplan-Meier analysis of VDAC3 expression in the TCGA database, and the significance of prognostic value was tested by log-rank test. *, P<0.05. VDAC3, voltage-dependent anion channel 3; FPKM, fragments per kilobase million; TCGA, The Cancer Genome Atlas; COAD, colorectal adenocarcinoma.

Figure 4

Univariate and multivariate Cox analysis of VDAC3 in COAD. (A) Univariate Cox analysis was used to analyze the relationship between VDAC3 expression and clinicopathological variables in COAD in TCGA database. (B) Multivariate Cox analysis in TCGA database was used to analyze the relationship between VDAC3 expression and clinicopathological variables in COAD. CI, confidence interval; VDAC3, voltage-dependent anion channel 3; COAD, colorectal adenocarcinoma; TCGA, The Cancer Genome Atlas.

Figure 5

VDAC3 is closely related to the biological activities and functions of mitochondria. (A-D) BP, CC, and MF are mostly related to VDAC3 in the TCGA database. KEGG analysis of VDAC3 in the TCGA database. (E) In the COAD data, enrichment scores for VDAC3 expression and mitochondrial related biological activities were obtained for each patient. Samples were arranged in ascending order of VDAC3 expression. The bar and line graphs on the right show the R and P values from the correlation analysis. (F) PPI network associated with VDAC3. (G) Pearson correlation between VDAC3 and related genes. BP, biological processes; TCGA, The Cancer Genome Atlas; CC, cellular components; KEGG, Kyoto Encyclopedia of Genes and Genomes; MF, molecular function; GO, Gene Ontology; ATP, adenosine triphosphate; VDAC3, voltage-dependent anion channel 3; COAD, colorectal adenocarcinoma; PPI, protein-protein interaction.

Figure 6

Analyses the mutational profile of VDAC3 and its prognosis in COAD using the cBioPortal database. (A) Change frequency of VDAC3 mutation types in pan-cancer in TCGA database. (B) Mutation sites of VDAC3 in COAD in TCGA database. (C) Kaplan-Meier survival analysis of VDAC3 mutations on OS. *, P<0.05. (D) Kaplan-Meier survival analysis of VDAC3 mutations on DSS. **, P<0.01. (E) Kaplan-Meier survival analysis of VDAC3 mutations on PFS. *, P<0.05. (F) Kaplan-Meier survival analysis of VDAC3 mutations on DFS. ns, not statistically significant. CNA, copy number alteration; VDAC3, voltage-dependent anion channel 3; COAD, colorectal adenocarcinoma; TCGA, The Cancer Genome Atlas; OS, overall survival; DSS, disease-specific survival; PFS, progression-free survival; DFS, disease-free survival.

Figure 7

The relationship between VDAC3 and HRD, MSI, MATH, TMB, Ploidy, LOH. *, P<0.05; **, P<0.01; ***, P<0.001. (A) Association of VDAC3 with HRD. (B) Association of VDAC3 with MSI. (C) Association of VDAC3 and MATH. (D) Association of VDAC3 with TMB. (E) Association of VDAC3 with Ploidy. (F) Association of VDAC3 with LOH. HRD, homologous recombination deficiency; MSI, microsatellite instability; MATH, mutant-allele tumor heterogeneity; TMB, tumor mutational burden; LOH, loss of heterozygosity; VDAC3, voltage-dependent anion channel 3.

Figure 8

Relationship between VDAC3 expression and tumor drug sensitivity. (A,B) Relationship between VDAC3 expression and sensitivity to chelerythrine drugs. *, P<0.05; ***, P<0.001. (C,D) Relationship between VDAC3 expression and sensitivity to Ergenyl drugs. *, P<0.05. (E,F) Relationship between VDAC3 expression and sensitivity to cladribine drugs. *, P<0.05. VDAC3, voltage-dependent anion channel 3.