Characteristics of the LUAD patients from datasets
The flow chart of this study was shown in Fig. 1. A total of 316 LUAD patients from the TCGA cohort and 381 LUAD patients from the GEO (GSE116959) cohort were finally enrolled. The detailed clinical and tumor characteristics of the LUAD cohorts were summarized in Table 1. A total of 70 autophagy-dependent ferroptosis-related genes were identified by literatures review, which was shown in Fig. 2.
Table 1
Clinical and tumor characteristics of the LUAD cohorts
| TCGA cohort | GEO cohort |
No. of patients | 316 | 381 |
Age (median, range) | 64 (33–86) | 69 (38–89) |
Gender | | |
Female | 163 (51.6%) | 166 (43.6%) |
Male | 153 (48.4%) | 215 (56.4%) |
Tumor | | |
T 1–2 | 275 (87.0%) | NA |
T 3–4 | 41 (13.0%) | NA |
Node | | |
N 0–1 | 267 (84.5%) | NA |
N 2–3 | 49 (15.5%) | NA |
Metastasis | | |
M 0 | 296 (93.7%) | NA |
M 1 | 20 (6.3%) | NA |
TNM stage | | |
Ⅰ | 164 (51.9%) | 246 (64.6%) |
Ⅱ | 76 (24.1%) | 65 (17.1%) |
Ⅲ | 56 (17.7%) | 56 (14.7%) |
Ⅳ | 20 (6.3%) | 14 (3.6%) |
TP53 | | |
Wide type | NA | 287(75.3%) |
Mutant type | NA | 94(24.7%) |
Survival status | | |
OS years (median) | 2.19 | 2.24 |
LUAD, adenocarcinoma of lung, TCGA, The Cancer Genome Atlas, GEO, Gene Expression Omnibus, No: number, T: tumor, N: regional lymph node, M: metastasis, NA: not available, OS, overall survival. |
Three steps were carried out to screen the key gene. First, 7 DEGs in Fig. 3A were selected. Second, 8 genes that had prognostic values for LUAD were selected (Fig. 3B). Third, the key gene was obtained as the intersection between DEGs and prognosis-related genes using Venn diagrams (Fig. 3C). As a result, FANCD2 was identified as the key gene, which worked as a prognosis-related differentially expressed gene in LUAD.
The mRNA and protein expression levels of FANCD2 were extracted by TCGA database
The FANCD2 expression in different tumors was evaluated using TCGA RNA-sequencing data (Fig. 4). FANCD2 expression was significantly higher in various tumors compared with adjacent normal tissues, and the consistent findings were shown in LUAD (Fig. 5A). After examining the mRNA expression level of FANCD2 in LUAD, the protein expression level was further explored by immunohistochemistry. There is a higher expression level of FANCD2 in LUAD tissues than normal lung tissues (Fig. 6), which is in line with the result of HPA statabase (Fig. 5B). In summary, the present results indicated that both transcriptional and translational expression levels of FANCD2 were overexpressed in patients with LUAD which may be involved in the pathogenesis of LUAD.
Prognostic risk model and predictability evaluation
The LUAD patients were stratified into high and low risk groups by the FANCD2 expression level. Table 2 showed the association of FANCD2 expression and the clinical features. A high expression of FANCD2 achieved a significant correlation with a high TNM stage (P<0.05). In the TCGA cohort, the FANCD2 expression was defined as an independent prognostic factor after the univariate and multivariate Cox regression analyses (Figure 7A). The patients in high risk groups have a poor survival than the low risk group in TCGA cohort. Similarly, relevant data from a GEO cohort (GSE35570) was used to validate the prognostic value of FANCD2 expression in LUAD (Figure 7B). Besides the poor survival and a high TNM stage, the high expression of FANCD2 was also related to a high frequency of TP53 mutation (P<0.001, Table 2). The sensitivity and specificity of the FANCD2 model was calculated by the area under ROC (TCGA cohort: AUC = 0.736, GEO cohort: AUC = 0.677), suggesting that the FANCD2 signature was effective for predicting survival of LUAD (Figure 8). We investigated the response to chemotherapy in high- and low-risk patients with LUAD, and found that 29 chemotherapeutic drugs displayed significant differences in estimated IC50 between highand low-risk patients, and that high-risk patients with LUSC showed increased sensitivity to all 29 chemotherapies (Figure 9).
Functional annotation of DEGs in different risk groups
GO and KEGG pathway enrichment analyses were used to evaluate the possible functions and pathways of the screened DEGs. As shown in Figure 10 A, the top five GO terms were response to reactive oxygen species, regulation of peptidase activity, neutrophil degranulation, neutrophil activation involved in immune response, and neutrophil activation. The top five pathways were phagosome, antigen processing and presentation, human T-cell leukemia virus, Th17 cell differentiation, and salmonella infection by KEGG enrichment (Figure 10 B).
The results of GO analysis showed that these DEGs might be involved in response to reactive oxygen species and immune processes. The data were consistent with our results that FANCD2 is correlated with ferroptosis and immune responses. Pathway enrichment analysis revealed that DEGs may be enriched in pathways related to phagosome and antigen processing and presentation, indicating that these genes function in autophagy and immune system.
Association between FANCD2 and immune-related scores
The potential immune mechanisms of LUAD were further explored through the scoring of tumor immune component (TumorPurity, ESTIMATEScore, ImmuneScore, StromalScore), and immune infiltrating cells, which all counted according to immunity-enriched groups (Figure 11). Each patient in the LUAD cohort was scored by above indicators. The immune cell infiltration levels changed along with the FANCD2 gene copy numbers (Figure 12). The LUAD patients with a high expression level of FANCD2 had a low ESTIMATEScore (Figure 12A), ImmuneScore (Figure 12B) and StromalScore (Figure 12C), but high TumorPurity (Figure 12D)was found in the high expression of FANCD2. Neutrophil cell infiltration levels seemed to positively associate with altered FANCD2 gene copy numbers in LUAD (cor = 0.15, P<0.001, Figure 13), which is consistent with the GO results of neutrophil degranulation, neutrophil activation involved in immune response, and neutrophil activation in Figure 10A.
Landscape of mutation profiles in LUAD cohort
Mutation information of LUAD cohort was displayed in oncoplot, where various colors with annotations represented the different mutation types (Figure 14). Then, the top 5 mutated genes in LUAD with ranked percentages were exhibited, including P53 (47%), TTN (41%), MUC16 (40%), RYR2 (34%) and CSMD3 (34%). These mutations were further classified according to different mutation categories. Findings indicated that missense mutation accounted for the most fraction (Figure 15A), and single nucleotide polymorphism (SNP) occurred more frequently than insertion or deletion (Figure 15B), and C>A was the most common single nucleotide variants (SNV) in LUAD (Figure 15C). The LUAD patients with a high expression level of FANCD2 showed a higher TMB (P<0.001, Figure 15D), which suggested that FANCD2 could work as a TMB marker and play a role in prediction of response to immunotherapy.
Table 2. Baseline characteristics of the patients in different risk groups
Characteristics
|
TCGA-LUAD cohort
|
GEO-LUAD cohort
|
|
High risk
|
Low risk
|
P value
|
High risk
|
Low risk
|
P
value
|
Gender(%)
|
|
|
0.09
|
|
|
0.25
|
Female
|
71(46.4%)
|
88(57.1%)
|
|
112(58.9%)
|
103(53.9%)
|
|
Male
|
82(53.6%)
|
66(42.9%)
|
|
78 (41.1%)
|
88(46.1%)
|
|
Age (%)
|
|
|
0.17
|
|
|
0.99
|
< 65y
|
74(48.4%)
|
60(39.0%)
|
|
52 (27.4%)
|
52(27.2%)
|
|
≥65y
|
79(51.6%)
|
94(61.0%)
|
|
138(72.6%)
|
139(72.8)
|
|
TNM stage
|
|
|
0.03
|
|
|
0.01
|
Ⅰ-Ⅱ
|
112(73.2%)
|
120(77.9%)
|
|
152(80.0%)
|
159(83.2%)
|
|
Ⅲ-Ⅳ
|
41(26.8)
|
34(22.1%)
|
|
38(20.0%)
|
32(16.7%)
|
|
TP53
|
|
|
NA
|
|
|
<0.001
|
Wide type
|
-
|
-
|
|
132(69.5%)
|
155(81.1%)
|
|
Mutant type
|
-
|
-
|
|
58(30.5%)
|
36(18.8%)
|
|
LUAD, adenocarcinoma of lung, TCGA, The Cancer Genome Atlas, GEO, Gene Expression Omnibus, y, years, NA: not available.