Importance of gene expression signatures in pancreatic cancer prognosis and the establishment of a prediction model

Figures & data

Figure 1 DEGs in five GEO datasets.

Notes: The figure shows 389 downregulated (A) and 556 upregulated (B) genes in PC samples. (C) GO biological process analysis for the DEGs. (D) KEGG pathway enrichment analysis for the DEGs. Set size refers to the number of genes differentially expressed between tumor and non-tumor samples in different GEO datasets.

Abbreviations: DEGs, differentially expressed genes; GO, Gene ontology; KEGG, Kyoto Encyclopedia of Genes and Genomes; PC, pancreatic cancer.

Figure 2 Relationship between SRGs and clinicopathological information.

Notes: (A) The Venn diagram shows four SRGs in four datasets. (B) Relationship between SRGs and tissues types. (C, D) Relationship between SRGs and histological grade. (E) Relationship between SRGs and PT. (F) Relationship between SRGs and tumor subtype. Other, including neuroendocrine carcinoma, colloid carcinomas, acinar cell carcinoma, and adenocarcinoma not otherwise specified.

Abbreviations: M, metastatic samples; N, normal samples; PDAC, pancreatic ductal adenocarcinoma; PT, the extent of the tumor; SRGs, survival-related genes; T, tumor samples.

Figure 3 Survival analysis of SRGs in four datasets.

Notes: Survival curves of LYRM1 (A_1–4), KNTC1 (B_1–4), IGF2BP2 (C_1–4), and CDC6 (D_1–4) in GSE28735, GSE62452, GSE71729, and TCGA datasets.

Abbreviations: SRGs, survival-related genes; TCGA, The Genome Cancer Atlas.

Figure 4 Performance of risk score in predicting prognosis in four datasets.

Notes: Survival curves, AUC, and calibration plots for risk score in TCGA (A_1–3), GSE71729 (B_1–3), GSE62452 (C_1–3), and GSE28735 (D_1–3).

Abbreviations: AUC, area under the curve; TCGA, The Genome Cancer Atlas.

Table 1 Cox regression analysis of risk factors associated with overall survival in the TCGA dataset

	Unadjusted		Adjusted 1a		Adjusted 2b
Variables	HR (95% CI)	P-value	HR (95% CI)	P-value	HR (95% CI)	P-value
Risk score	1.667 (1.261-2.205)	<0.001	1.539 (1.098-2.157)	0.012	1.524 (1.082-2.146)	0.016
Age	1.035 (1.007-1.063)	0.013	1.041 (1.008-1.076)	0.015	1.043 (1.012-1.075)	0.006
Sex
Female
Male	1.045 (0.608-1.797)	0.874	0.694 (0.355-1.358)	0.286
Malignancy history
No
Yes	0.993 (0.421-2.341)	0.988	2.046 (0.737-5.686)	0.170
Diabetes history
No
Yes	1.019 (0.534-1.945)	0.954	0.776 (0.373-1.616)	0.498
Pancreatitis history
No
Yes	1.006 (0.429-2.361)	0.988	1.469 (0.533-4.054)	0.458
Tumor size	1.225 (1.030-1.458)	0.022	1.394 (1.120-1.735)	0.003	1.284 (1.051-1.569)	0.014
Tumor site
Body
Head	4.064 (0.982-16.830)	0.053	1.439 (0.268-7.730)	0.672
Tail	2.301 (0.420-12.620)	0.337	0.852 (0.128-5.680)	0.869
Tumor subtype
Othersc
PDAC	6.849 (2.103-22.300)	0.001	5.760 (1.436-23.109)	0.014	4.412 (1.226-15.886)	0.023
Grade
G1
G2	2.207 (0.832-5.857)	0.111	0.651 (0.189-2.240)	0.496	0.773 (0.254-2.351)	0.650
G3 and G4	3.427 (1.263-9.294)	0.016	1.140 (0.304-4.272)	0.846	1.040 (0.317-3.414)	0.949
Residual tumor
R0
R1	1.724 (0.994-2.992)	0.053	1.889 (0.973-3.670)	0.060
AJCC Stage
I
IIA	1.964 (0.546-7.069)	0.302	0.996 (0.194-5.119)	0.996	1.180 (0.310-4.485)	0.808
IIB	5.185 (1.820-14.771)	0.002	1.125 (0.255-4.962)	0.877	1.756 (0.579-5.326)	0.320
III and IV	11.391 (1.977-65.628)	0.006	5.353 (0.502-57.097)	0.165	8.755 (1.292-59.344)	0.026
Radiation treatment
No
Yes	0.387 (0.182-0.822)	0.014	0.378 (0.160-0.896)	0.027	0.411 (0.175-0.964)	0.041
Targeted therapy
No
Yes	0.506 (0.295-0.869)	0.014	0.317 (0.157-0.640)	0.001	0.403 (0.214-0.759)	0.005

Notes:

a Adjusted covariates include all the indicators above;

b Adjusted covariates include the prognostic factors from an unadjusted COX analysis;

c Including neuroendocrine carcinoma, colloid carcinomas, acinar cell carcinoma and adenocarcinoma not otherwise specified. Bold number indicates statistical significance.

Abbreviations: AJCC, the current American Joint Committee on Cancer stage; PDAC, pancreatic ductal adenocarcinoma; TCGA, The Genome Cancer Atlas.

Figure 5 Performance of the nomogram in predicting prognosis in the TCGA dataset.

Notes: (A) Nomogram for predicting 1-, 2-, and 3-year OS in PC patients. (B) Calibration plot for 1-, 2-, and 3-year OS of the nomogram. (C) Comparison of the predictive power of the nomogram model, AJCC stage, and risk score, as assessed using C-index. (D, E) Comparison of the predictive power of the nomogram model, AJCC stage, and risk score by AUC at 1 and 2 years. (F) Kaplan–Meier analysis of risk groups stratified using total point of the proposed nomogram. Other, including neuroendocrine carcinoma, colloid carcinomas, acinar cell carcinoma, and adenocarcinoma not otherwise specified; vertical bars, 95% CI.

Abbreviations: AJCC, the American Joint Committee on Cancer; AUC, area under the curve; C-index, concordance index; OS, overall survival; PC, pancreatic cancer; PDAC, pancreatic ductal adenocarcinoma; TCGA, The Genome Cancer Atlas.