Development of a gene signature associated with iron metabolism in lung adenocarcinoma

Figures & data

Table 1. Clinical characteristics of the lung cancer patients used in this study

Features	TCGA (n, %)	GSE42127 (n, %)
Platform	Illumina HiSeq	Illumina HumanWG-6 v3 Array
≤ 60 years	156 (32.1%)	22 (16.8%)
> 60 years	330 (67.9%)	109 (83.2%)
NA	0 (0.0%)	0 (0.0%)
Male	225 (46.3%)	67(51.1%)
Female	261 (53.7%)	64 (48.9%)
NA	0 (0.0%)	0 (0.0%)
StageI	258 (53.1%)	87(66.4%)
StageII	116 (23.9%)	22(16.8%)
StageIII	79 (16.3%)	20(15.3%)
StageIV	25 (5.1%)	1 (0.75%)
NA	8 (1.6%)	1 (0.75%)
T1	163 (33.5%)	123 (93.9%)
T2	259 (53.3%)	7 (5.35%)
T3	43 (8.9%)	0 (0.0%)
T4	18 (3.7%)	0 (0.0%)
TX	3 (0.6%)	1(0.75%)
NA	0(0.0%)	0(0.0%)
N0	312 (64.2%)	一
N1	93 (19.1%)	一
N2	68 (14.0%)	一
N3	2(0.4%)	一
N4	0(0.0%)	一
NX	10 (2.1%)	一
NA	1(0.2%)	一
M0	322 (66.3%)	一
M1	24 (4.9%)	一
MX	136 (28.0%)	一
NA	4 (0.8%)	一
Alive	328 (67.5%)	90 (68.7%)
Dead	158 (32.5%)	41 (31.3%)

Table 2. Univariate Cox analysis results of TCGA cohort-46 candidate genes

Gene	HR	95% CI(low)	95% CI(high)	P value
AURKA	1.025	1.008	1.042	0.003
FBP1	0.993	0.988	0.998	0.004
MKI67	1.045	1.021	1.069	<0.001
CYP4B1	0.994	0.989	0.998	0.005
HAVCR1	1.133	1.071	1.199	<0.001
FEN1	1.028	1.011	1.046	0.001
CYP27A1	0.984	0.973	0.996	0.007
MCM4	1.019	1.006	1.033	0.003
RRM2	1.026	1.012	1.04	<0.001
ITGB4	1.006	1.002	1.01	0.004
VIPR1	0.839	0.753	0.936	0.002
ENO1	1.002	1.001	1.002	<0.001
INHA	1.008	1.003	1.014	0.004
HSPD1	1.006	1.003	1.009	<0.001
ADRB2	0.785	0.673	0.914	0.002
PFKP	1.009	1.004	1.013	<0.001
TK1	1.009	1.003	1.014	0.002
CCNB1	1.019	1.009	1.029	<0.001
TXNRD1	1.002	1.001	1.004	0.001
PLOD2	1.013	1.007	1.02	<0.001
MAD2L1	1.05	1.012	1.09	0.009
SPN	0.896	0.831	0.966	0.004
BIRC5	1.023	1.008	1.038	0.003
KRT19	1.001	1	1.001	0.004
GAPDH	1.001	1	1.001	<0.001
KPNA2	1.012	1.006	1.017	<0.001
ANGPTL4	1.009	1.004	1.013	<0.001
CCNA2	1.034	1.016	1.052	<0.001
PRSS3	1.024	1.009	1.04	0.002
KRT8	1.001	1.001	1.002	<0.001
LDHA	1.005	1.003	1.006	<0.001
HMMR	1.075	1.041	1.11	<0.001
ABCC2	1.019	1.007	1.031	0.001
CDKN3	1.039	1.013	1.066	0.003
SLC2A1	1.01	1.007	1.012	<0.001
FOXM1	1.035	1.017	1.053	<0.001
SCN4B	0.763	0.63	0.923	0.005
NT5E	1.009	1.002	1.016	0.008
DLC1	0.96	0.932	0.99	0.009
IGFBP3	1.003	1.001	1.004	0.002
CYP24A1	1.003	1.002	1.005	<0.001
LOXL2	1.02	1.014	1.027	<0.001
TIMP1	1.001	1	1.002	0.001
ALDOA	1.002	1.001	1.003	0.002
PTPRH	1.036	1.012	1.061	0.003
TPX2	1.011	1.004	1.019	0.001

Figure 1. (a)(b) Heat map and volcano map of 257 different gene expression levels. (c) Coefficient distribution of 12 prognostic genes. (d) The dashed lines represent the minimum value and the optimal λ of the optimal volume of the variable respectively. (e) PPI network downloaded from STRING database shows the interaction among 46 candidate genes. Correlation coefficients are expressed in different colors

Figure 2. (a) Distribution of median of risk scores and OS status and risk score in TCGA cohort. (b) Survival analysis of TCGA high-risk group and low-risk group (P < 0.001). (c) Nomogram analysis results of TCGA cohort. (d)(e)(f) AUC of time-dependent ROC curves in TCGA cohort for 1 year, 3 years and 5 years. (g)(h)(i) Calibration curve for 1 year, 3 years and 5 years in TCGA cohort

Figure 3. (a) Distribution of median of risk scores and OS status and risk score in GEO cohort. (b) Survival analysis of GEO high-risk group and low-risk group (P = 0.001). (c) Nomogram analysis results of GEO cohort. (d)(e)(f) AUC of time-dependent ROC curves in GEO cohort for 1 year, 3 years and 5 years. (g)(h)(i) Calibration curve for 1 year, 3 years and 5 years in GEO cohort

Table 3. Univariate and multivariate Cox analysis of the 12-gene prognostic signature and clinical risk factors

Variables	Univariate analysis			Multivariate analysis
Training set
id	HR	HR (95% CI)	p-value	HR	HR (95% CI)	p-value
Age	0.997	0.978–1.015	0.718	1.014	0.994 − 1.035	0.16
Gender	1	0.694–1.441	1	0.85	0.585 − 1.235	0.394
Stage	1.648	1.396–1.946	<0.001	1.921	1.154 − 3.198	0.012
T	1.6	1.285–1.994	<0.001	1.009	0.785 − 1.296	0.946
M	1.748	0.959–3.187	0.068	0.368	0.095 − 1.423	0.147
N	1.787	1.455–2.195	<0.001	0.943	0.603 − 1.476	0.798
Risk Score	3.982	2.867–5.530	<0.001	3.313	2.273 − 4.827	<0.001
Test set
id	HR	HR (95% CI)	p-value	HR	HR (95% CI)	p-value
Age	1.01	0.977 − 1.044	0.561	0.985	0.950 − 1.021	0.407
Gender	1.905	0.994 − 3.650	0.052	1.23	0.616 − 2.454	0.557
Stage	1.652	1.144 − 2.387	0.007	1.568	1.052 − 2.337	0.027
RiskScore	82.97	10.025 − 686.710	<0.001	84.063	7.882 − 896.502	<0.001

HR: Hazard ratio; CI:confidence interval; T: Tumor; M: Metastasis; N: Node.

Figure 4. (a) Immune grouping results and tumor microenvironment heat map. Distribution of tumor purity, ESTIMATE score, immune score, and stromal score in high vs low immunity groups. (b) GO enrichment analysis results (P < 0.05). (c)(d)(e)(f) Results of immune cell scores and immune-related functions in TCGA and GEO groups

(*** P < 0.001, ** P < 0.01, * P < 0.05, ns = not significant).