World Journal of Oncology, ISSN 1920-4531 print, 1920-454X online, Open Access
Article copyright, the authors; Journal compilation copyright, World J Oncol and Elmer Press Inc
Journal website https://www.wjon.org

Original Article

Volume 15, Number 5, October 2024, pages 809-824

SNX4 Is Correlated With Immune Infiltration and Prognosis in Clear Cell Renal Cell Carcinoma

Figures

Figure 1.
Figure 1. The expression levels of SNX4. (a) The expression levels of SNX4 in pan-cancer from TCGA database. (b, c) The expression levels of SNX4 in ccRCC and normal renal tissues from TCGA database. (d) The protein expression levels of SNX4 in ccRCC and normal renal tissues in CPTAC. *P < 0.05, **P < 0.01, ***P < 0.001. ns: no significance.
Figure 2.
Figure 2. The protein expression of SNX4 in ccRCC and normal renal tissues based on the Human Protein Atlas. (a, b) The protein levels of SNX4 in normal kidney tissues from the Human Protein Atlas database. (c, d) The protein levels of SNX4 in kidney clear cell carcinoma based on the Human Protein Atlas.
Figure 3.
Figure 3. The correlation between SNX4 expression and clinical characteristics. Lower expression levels of SNX4 were observed in patients with high histologic grade (e) and male patients (f). No significant correlation was detected between the expression levels of SNX4 and T stage (a), N stage (b), M stage (c), pathologic stage (d), age (g), or primary therapy outcome (h). *P < 0.05, **P < 0.01, ***P < 0.001. ns: no significance.
Figure 4.
Figure 4. The Kaplan-Meier survival curve of ccRCC stratified according to SNX4 expression levels indicated that ccRCC patients with low SNX4 mRNA expression had a shorter OS, DSS and PFI than those with high level of SNX4 (a-c). Besides, a subgroup analysis was performed on different gender and histologic grade, respectively (d-i). OS: overall survival; DSS: disease-specific survival; PFI: progression-free interval.
Figure 5.
Figure 5. The correlated significant genes of SNX4 were visualized in the heatmap plot (a) and volcano plot (b). (a) Heatmap of the top 50 significant differentially expressed genes between the high and low SNX4 expression groups. Blue and red dots represent downregulated and upregulated genes, respectively. (b) Volcano plot of differentially expressed genes between the high and low SNX4 expression groups.
Figure 6.
Figure 6. Prediction model nomogram and calibration curve. (a) Nomogram for predicting the probability of 1-, 3-, and 5-year OS for ccRCC patients. (b) Calibration plot of the nomogram for predicting the survival probability.
Figure 7.
Figure 7. Correlation analysis of SNX4 expression and immune cell infiltration in ccRCC (a) and relationship between SNX4 and immune checkpoints of PD-1 (b), CD274 (c), PD-L1 (d), CTLA4 (e) and FBXO3 (f) in ccRCC.
Figure 8.
Figure 8. Prediction and analysis of ceRNA network. (a) Venn diagrams of underlying miRNA were drawn to predict the mutual target miRNA. The expression levels of miR-218-5p (b), miR-221-3p (c) and miR-222-3p (e) were significantly different in ccRCC and normal renal tissue. No significant difference of the expression level of miR-34c-5p (d) was detected in ccRCC and normal tissue. We further explored the expression and prognostic influence of the four miRNAs (f-i).
Figure 9.
Figure 9. The mRNA expression levels of SNX4 in ccRCC tissues and normal tissues (a, b). WB gray scale analysis indicated the protein expression levels of SNX4 in ccRCC tissues and normal tissues (c). Western blot indicated that the protein expression levels of SNX4 were downregulated in ccRCC compared with normal renal tissue (d). *P < 0.05, ***P < 0.001.

Tables

Table 1. Univariable and Multivariable Cox Regression
 
CharacteristicsTotal (N)Univariate analysisMultivariate analysis
Hazard ratio (95% CI)P valueHazard ratio (95% CI)P value
CI: confidence interval; CR: complete response; PR: partial response; PD: progressive disease; SD: stable disease.
T stage539
  T1-T2349Reference
  T3-T41903.228 (2.382 - 4.374)< 0.0010.000 (0.000 - Inf)1.000
N stage257
  N0241Reference
  N1163.453 (1.832 - 6.508)< 0.0010.000 (0.000 - Inf)1.000
M stage506
  M0428Reference
  M1784.389 (3.212 - 5.999)< 0.0010.000 (0.000 - Inf)1.000
Pathologic stage536
  Stage I-II331Reference
  Stage III-IV2053.946 (2.872 - 5.423)< 0.00110,933,712,997.684 (0.000 - Inf)1.000
Histologic grade531
  G1 and G2249Reference
  G3 and G42822.702 (1.918 - 3.807)< 0.0013.510 (0.182 - 67.520)0.405
Gender539
  Female186Reference
  Male3530.930 (0.682 - 1.268)0.648
Age539
  ≤ 60269Reference
  > 602701.765 (1.298 - 2.398)< 0.0010.489 (0.028 - 8.506)0.624
Race532
  White467Reference
  Asian and Black or African American650.818 (0.454 - 1.474)0.505
Laterality538
  Left252Reference
  Right2860.706 (0.523 - 0.952)0.0230.000 (0.000 - Inf)0.999
Primary therapy outcome147
  CR and PR130Reference
  PD and SD175.116 (1.594 - 16.425)0.0061.694 (0.000 - Inf)1.000
SNX4539
  Low269Reference
  High2700.493 (0.362 - 0.672)< 0.0010.927 (0.049 - 17.574)0.959

 

Table 2. Association Between SNX4 and Corresponding Biomarkers of Immune Cells
 
Immune cellBiomarkerR valueP value
SNX4: sorting nexin 4.
B cellCD19-0.0770.08
CD79A-0.0730.096
CD8+ T cellCD8A0.0750.088
CD8B0.0480.28
CD4+ T cellCD40.274.4 × 10-10
M1 macrophageNOS20.383.7 × 10-19
IRF50.237.9 × 10-8
PTGS20.0830.058
M2 macrophageCD1630.170.00013
VSIG40.210.0000011
MS4A4A0.299.8 × 10-12
NeutrophilCEACAM80.10.022
ITGAM0.341.3 × 10-15
CCR70.0940.31
Dendritic cellHLA-DPB10.253.9 × 10-9
HLA-DQB10.0390.37
HLA-DRA0.311.8 × 10-13
HLA-DPA10.354.3 × 10-16
CD1C0.338.7 × 10-15
NRP10.571.1 × 10-45
ITGAX0.0570.2

 

Table 3. Prediction and Analysis of ceRNA Network
 
lncRNAmiRNAR-valueP-value
ceRNA: competing endogenous RNA; lncRNAs: long noncoding RNAs.
AC091563.1hsa-miR-221-3p-0.1560.00038
DHRS4-AS1hsa-miR-221-3p-0.1650.000167
PAXIP1-AS2hsa-miR-221-3p-0.1410.00135
DHRS4-AS1hsa-miR-222-3p-0.1260.00399
mRNA
AC091563.1SNX40.1230.00432
DHRS4-AS1SNX40.4391.13 × 10-26
PAXIP1-AS2SNX40.3571.74 × 10-17