RNPEPL1 expression comparison
The expression of RNPEPL1 in OV tumor samples was significantly higher than normal ovary samples in GSE18521, GSE40595, and GSE38666 (all P < 0.0001, Figure 2). In the Oncomine database, the meta-analysis of RNPEPL1 expression in 8 analyses showed that RNPEPL1 was overexpressed in OV tissues (P = 4.49E-04, Figure 3I). RNPEPL1 was significantly overexpressed in OV (P = 3.75E-10, Figure 3E), ovarian serous adenocarcinoma (P = 0.002, Figure 3A; P = 0.041, Figure 3H), ovarian mucinous adenocarcinoma (P = 8.06E-05, Figure 3D; P = 9.77E-05, Figure 3F), ovarian clear cell adenocarcinoma (P = 8.18E-04, Figure 3C; P = 0.003, Figure 3G) and ovarian endometrioid adenocarcinoma (P = 0.004, Figure 3B). Immunohistochemistry staining of RNPEPL1 was positive in OV samples (Figure 4) with a positive rate of 90.90%(10/11). Expression of RNPEPL1 was not detected in normal ovary tissues and normal lymph node (Figure 4).
Survival analysis
There were 375 OV patients included in the survival analysis. The main characteristics of them were summarized in Table 1. The median age of the diagnosed patients was 58 years. The results suggested that RNPEPL1 was significantly associated with the OS of OV (HR = 1.572, 95% CI =1.185-2.086; P = 0.002) in univariate Cox regression analysis. At the same time, several clinicopathological factors, including age (HR = 1.019, 95% CI = 1.006-1.032; P = 0.005), FIGO stage (HR = 1.425, 95% CI = 1.054-1.926; P =0.021) and residual disease (HR = 1.229, 95% CI = 1.068-1.414; P = 0.004) were significantly correlated with OS of OV. In the multivariate Cox regression analysis, age (HR = 1.018, 95% CI = 1.004-1.033; P = 0.011), FIGO stage (HR = 1.412, 95% CI = 1.022-1.953; P = 0.037), residual disease (HR = 1.173, 95% CI = 1.013-1.359; P = 0.033) and RNPEPL1 (HR = 1.622, 95% CI = 1.207-2.181; P = 0.001) were significantly related to OS (Table 2). Overexpression of RNPEPL1 was an independent risk factor for OS of OV.
Table 1. The characteristics of patients in the TCGA-OV cohort
Characteristic
|
Total (375)
|
Percentage (%)
|
Age
|
|
|
≤ 58
|
185
|
49.33%
|
> 58
|
190
|
50.67%
|
FIGO stage
|
|
Stage I/II
|
21
|
5.60%
|
Stage III/IV
|
349
|
93.07%
|
unknown
|
5
|
1.33%
|
Grade
|
G1
|
1
|
0.27%
|
G2
|
42
|
11.20%
|
G3
|
320
|
85.33%
|
unknown
|
12
|
3.20%
|
Residual disease
|
|
No Macroscopic disease
|
67
|
17.87%
|
1-10 mm
|
171
|
45.60%
|
11-20 mm
|
26
|
6.93%
|
>20 mm
|
70
|
18.67%
|
unknown
|
41
|
10.93%
|
Venous invasion
|
|
No
|
39
|
10.40%
|
Yes
|
62
|
16.53%
|
unknown
|
274
|
73.07%
|
Lymphatic invasion
|
No
|
48
|
12.80%
|
Yes
|
100
|
26.67%
|
unknown
|
227
|
60.53%
|
TCGA: The Cancer Genome Atlas; OV: ovarian carcinoma.
Table 2. Univariate analysis and multivariate analysis of the correlation of RNPEPL1 expression and important clinical characteristics with survival among ovarian carcinoma patients
Parameter
|
Univariate analysis
|
Multivariate analysis
|
Overall survival
|
HR
|
95%CI
|
P-value
|
HR
|
95%CI
|
P-value
|
Age
|
1.019
|
1.006-1.032
|
0.005
|
1.018
|
1.004-1.033
|
0.011
|
FIGO stage
|
1.425
|
1.054-1.926
|
0.021
|
1.412
|
1.022-1.953
|
0.037
|
Grade
|
1.391
|
0.913-2.120
|
0.125
|
|
|
|
Residual disease
|
1.229
|
1.068-1.414
|
0.004
|
1.173
|
1.013-1.359
|
0.033
|
Venous invasion
|
0.803
|
0.424-1.518
|
0.499
|
|
|
|
Lymphatic invasion
|
1.337
|
0.788-2.271
|
0.282
|
|
|
|
RNPEPL1
|
1.572
|
1.185-2.086
|
0.002
|
1.622
|
1.207-2.181
|
0.001
|
HR: hazard ratio; CI: confidence interval. Bold values indicate p-value < 0.05.
Overexpression of RNPEPL1 in OV tumor tissues was significantly correlated with poor OS (P = 0.0016, Figure 5A) in OV patients. Besides, a subgroup analysis suggested that the overexpression of RNPEPL1 in OV tumor tissue was correlated with reduced 5 year (P = 0.0179, Figure 5B) and 10 years survival (P = 0.0068, Figure 5C).
In different clinicopathological groups, overexpression of RNPEPL1 was correlated with poor survival in patients with age ≤ 58 years (P = 0.0450, Figure 6A), while no significant difference was found in patients with age > 58 years (P = 0.191, Figure 6B). Moreover, overexpression of RNPEPL1 significantly correlated with poorer OS in patients with late stage (P = 0.0009, Figure 6D) , high grade (P = 0.0032, Figure 6E) and ≥1mm residue disease (P = 0.0038, Figure 6H), but not determined as risk factors for OV patients with early stage (P = 0.3819, Figure 6C), low grade (P = 0.4486, Figure 6F) and no macroscopic disease(P = 0.1839, Figure 6G).
The correlations between RNPEPL1 expression and clinicopathological characteristics
The analysis of clinical data and gene expression data downloaded from TCGA-OV showed that the expression of RNPEPL1 in younger patients (≤ 58 years old) was significantly higher than older patients (> 58 years old) (P < 0.0001, Figure 7A). RNPEPL1 was highly expressed in early stage (P < 0.0001, Figure 7B) and low grade (P < 0.0001, Figure9C) patients. RNPEPL1 increased with venous invasion (P < 0.0001, Figure 7D) and lymphatic invasion(P < 0.0001, Figure 7E). RNPEPL1 was significantly distributed differently in different groups of residue disease and highly expressed in patients with 1mm-10mm and 10mm-20mm residue disease classification (P < 0.0001, Figure 7F).
GO and KEGG analyses by GSEA
The results of KEGG analysis showed that genes were mainly enriched RNA degradation, RNA polymerase, spliceosome, oxidative phosphorylation and ribosome when the expression level of RNPEPL1 is high, genes were mainly enriched in T cell receptor signaling pathway, B cell receptor signaling pathway, apoptosis, natural killer cell mediated cytotoxicity and cell adhesion molecules cams when the expression level of RNPEPL1 is low (Figure 8). The results of GO analysis suggested that genes were mainly enriched in spliceosomal snrnp assembly, U2 type spliceosomal complex, nuclear transcribed mRNA catabolic process, viral gene expression, and polysome when the expression level of RNPEPL1 is high, genes were mainly enriched in specific granule, positive regulation of NF kappab transcription factor activity, macrophage activation, actin cytoskeleton reorganization, negative regulation of toll like receptor signaling pathway when the expression level of RNPEPL1 is low (Figure 9).
Correlation between immune cells and RNPEPL1 expression
The analysis of TIMER database showed that RNPEPL1 expression levels correlated with B cells (r = 0.099, P = 3.08e-02), CD8+ T cells (r = 0.035, P =4.39e-01), CD4+ T cells (r = −0.002, P =9.37e-01), macrophage (r = -0.083, P =6.90e-02), neutrophils (r = -0.044, P =3.32e-01) and dendritic cells (r = -0.047, P =3.09e-01) (Figure 10A). The prognostic value of the six types of immune cells for OV was shown in Figure 10B, low level of dendritic cells (P = 0.039) can predict poor survival of OV (Figure 10B).
Immune-related genes enrichment analysis
There are 2483 immune-related genes (IRGs) extracted from the ImmPort website. A total of 249 IRGs are significantly related with the expression of RNPEPL1 in TCGA dataset (Table 3). The most significantly correlated IRGs gene ontology terms and the corresponding genes were exhibited using a cross-link analysis. The expression of RNPEPL1 was significantly correlated with the immune signaling pathway of antigen processing and presentation, antimicrobials, TCR signaling pathway, BCR signaling pathway and natural killer cell cytotoxicity (Figure 11).
Table 3. RNPEPL1-related immune genes
Description
|
Gene ID
|
Antigen_processing_and_presentation
|
CD4/CIITA/CD74/RELB/HLA-E/PSMC6/CD1C/HLA-DPA1/HLA-DPB1/HLA-DQA1/SEM1/PSMC1/ECPAS/CTSB/HLA-DQB1/CD1E/FCER1G/HLA-DMA/PSMD10/TAPBP/NFYB/HLA-DRB1/PDIA3/CD1A/HLA-DRA/HLA-DOA/ICAM1/THBS1/CTSS/CD8A/PSMD6/HLA-DMB/PSMD13/PSMD14/B2M/HLA-B/HLA-DQA2/RFX5
|
Antimicrobials
|
GRK2/AHNAK/TLR7/IRF5/CYBB/FURIN/PML/CD14/MAVS/IL1B/HCK/CCR5/PRDX2/TGFB1/UNC93B1/PTK2B/OLR1/TLR2/CSK/FGR/CD86/CXCL16/IKBKE/ZYX/SLC11A1/NFKB1/FABP5/CACYBP/HMGB1/MAPK8/TLR4/JAK1/BCL3/ARRB1/GRN/NLRX1/TMSB15A/TMSB10/VDR/IFNAR1/IL7R/BIRC5/MAP2K1/TRAF3/RELA/CCL3L1/PLAU/SLC29A3/LRP1/RNASE2/IRF1/STAT3/CCL4L2/CCL4/MAP2K2/IFNAR2/RBP1/TPT1/SP1/RBP7/SYTL1/MSR1/CCL3/CCR1/HMOX1/ELAVL1/IL18/MAPK3/CLDN4/SLC22A17/DHX58/GBP2/LMBR1/SOD1/BPHL/GNAI1/TNFRSF10B/APOBEC3C/NEO1/ADAR/NDRG1
|
BCR signaling pathway
|
INPP5D/CHP1/VAV2/PIK3CD/VAV1/PTPN6/FCGR2B/CARD11/RAC2/LYN/NFATC2/NFKBIE/NFATC1/PIK3R3/IKBKB/RAC3/PPP3R1/IGHA1/IGHG2
|
Chemokine_receptors
|
PLXNB2/PTAFR/CX3CR1/PLXNA1/PLXND1/PLAUR/PLXNA3/C5AR1/PLXNB1/FPR1/CXCR3/ACKR1/TYMP/SEMA4D/SEMA4B/SEMA3B/C3/SBDS
|
Chemokines
|
TYMP/SEMA4D/SEMA4B/SEMA3B/C3/SBDS
|
Cytokine_receptors
|
CSF1R/IL10RA/IL17RA/CSF2RA/NPR1/C3AR1/SDC3/TNFRSF14/CSF2RB/PPARD/PPARA/TNFRSF1B/RARG/OGFR/RXRA/IL2RB/IL1R1/ESRRA/IL4R/SDC2/SORT1/IL15RA/IL13RA1/IL17RC/ENG/NR3C1/IL17RB/OSMR/NRP1/TGFBR2/APLNR/IL10RB/NRP2/ANGPTL2/IL2RG/IL11RA/IGF2R/NR1D1/LTBR/NR1H2/IL6R/LGR5/PTGER2/SDC4/EGFR
|
Cytokines
|
CSF1/TNFSF12/CMTM4/TNFSF13/TXLNA/LTBP3/NRTN/BMP1/EBI3/OSM/LRSAM1/PDGFB/VEGFB/NGF/ESM1/HDGF/IL1RN/MDK/LTBP2/NTF3/FAM3C/BTC/RABEP2/LIF/CMTM3/ADA2/CLCF1/CD320/SPP1/APLN/NMB
|
NaturalKiller_cell_cytotoxicity
|
ITGB2/ITGAL/LCP2/SH3BP2/FCGR3A/SHC1/PRF1/TYROBP/GRB2/FYN/PRKCA
|
TCR signaling pathway
|
PTPRC/CBLC/CD3E/CDK4/PRKCQ/TRAC
|
BCR: B cell receptor; TCR: T cell receptor.