Open Access

A signature of tumor immune microenvironment genes associated with the prognosis of non‑small cell lung cancer

  • Authors:
    • Jia Li
    • Xin Li
    • Chenyue Zhang
    • Chenxing Zhang
    • Haiyong Wang
  • View Affiliations

  • Published online on: January 14, 2020     https://doi.org/10.3892/or.2020.7464
  • Pages: 795-806
  • Copyright: © Li et al. This is an open access article distributed under the terms of Creative Commons Attribution License.

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Abstract

Establishing a prognostic genetic signature closely related to the tumor immune microenvironment (TIME) to predict clinical outcomes is necessary. Using the Gene Expression Omnibus (GEO) database of a non‑small cell lung cancer (NSCLC) cohort and the immune score derived from the Estimation of Stromal and Immune cells in Malignant Tumours using Expression data (ESTIMATE) algorithm, we applied the least absolute shrinkage and selection operator (LASSO) Cox regression model to screen a 10‑gene signature among the 448 differentially expressed genes and found that the risk prediction models constructed by 10 genes could be more sensitive to prognosis than TNM (Tumor, Lymph node and Metastasis) stage (P=0.006). The CIBERSORT method was applied to quantify the relative levels of different immune cell types. It was found that the ratio of eosinophils, mast cells (MCs) resting and CD4 T cells memory activated in the low‑risk group was higher than that in the high‑risk group, and the difference was statistically significant (P=0.003, P=0.014 and P=0.018, respectively). Inconsistently, the ratio of resting natural killer (NK) cells and activated plasma cells in the low‑risk group was significantly lower than that in the high‑risk group (P=0.05 and P=0.009, respectively). Kaplan‑Meier survival results showed that patients of the high‑risk group had significantly shorter overall survival (OS) than those of the low‑risk group in the training set (P<0.001). Furthermore, Kaplan‑Meier survival showed that patients of the high‑risk group had significantly shorter OS than those of the low‑risk group (P=0.0025 and P=0.0157, respectively) in the validation set [GSE31210 and TCGA (The Cancer Genome Atlas)]. The 10‑gene signature was found to be an independent risk factor for prognosis in univariate and multivariate Cox proportional hazard regression analyses (P<0.001). In addition, it was found that the risk model constructed by the 10‑gene signature was related to the clinical related factors in logistic regression analysis. The genetic signature closely related to the immune microenvironment was found to be able to predict differences in the proportion of immune cells (eosinophils, resting MCs, memory activated CD4 T cells, resting NK cells and plasma cells) in the risk model. Our findings suggest that the genetic signature closely related to TIME could predict the prognosis of NSCLC patients, and provide some reference for immunotherapy.

Introduction

Lung cancer ranks first among all malignant tumors in regards to morbidity and mortality worldwide, with 2.1 million new lung cancer cases and 1.8 million deaths expected worldwide in 2018 (1). Non-small cell lung cancer (NSCLC) accounts for 85% of all lung cancer cases, and targeted therapy and immunotherapy for NSCLC treatment are developing rapidly (2,3). Accurate judgment and prognostic assessment are important factors influencing the appropriate treatment for each individual case. The current TNM staging system has been tested over time and remains the most powerful prognostic instrument for lung cancer (4). However, due to the heterogeneity of the tumor itself and the complexity of the pathogenesis, even patients with the same TNM stage and treatment may exhibit various clinical outcomes (5). The current direction is to combine TNM with other prognostic factors to create a comprehensive prognostic indicator for NSCLC.

The tumor immune microenvironment (TIME) consists of immune cells, mesenchymal cells, endothelial cells, inflammatory mediators, and extracellular matrix (ECM) molecules (6,7). The type, density and location of immune cells in TIME play an important role in the development of the disease and have been proposed to be valuable for the diagnosis and prognostic assessment of tumors (8). Therefore, immunological structures based on TIME should be used as a separate component in the classification system (9). Immunological analysis of the TIME (immunoscore) shows great promise for improved prognosis and prediction of response to immunotherapy. Several reports have demonstrated that immune scores and stromal scores calculated based on the ESTIMATE algorithm could predict the infiltration of non-tumor cells, by analyzing specific gene expression signature of immune and stromal cells (1013).

For the first time in the present study, using the Gene Expression Omnibus (GEO) database of the NSCLC cohort and the immune score derived from the ESTIMATE algorithm, we extracted a genetic signature closely related to the TIME that predict the prognosis of lung cancer patients. Then the CIBERSORT method was used to quantify the relative levels of different immune cell types in complex gene expression mixtures. Furthermore, the validity and reliability of the gene signature were further verified. Our findings suggest that the genetic signature closely related to TIME is able to predict the prognosis of NSCLC patients, and provide some reference for immunotherapy.

Materials and methods

Data source and processing

Gene-expression profiling data of NSCLC patients were downloaded from Gene Expression Omnibus datasets (GEO; GSE103584 and GSE31210) and The Cancer Genome Atlas (TCGA; http://tcga-data.nci.nih.gov/tcga/). Microarray analysis of 130 NSCLC patients in GSE103584 was based on CancerSCAN panel (14). Dataset GSE103584 was used as a training set for model construction, and data in GSE31210 (15) and TCGA were applied to verify the validity of the model.

ESTIMATE algorithm-derived immune scores

Immune scores were calculated by applying the ESTIMATE algorithm using gene expression data.

The algorithm was publicly available through the SourceForge software repository (https://sourceforge.net/projects/estimateproject/) (13). The algorithm was based on single-sample gene set enrichment analysis and generates immune score (indicating the infiltration of immune cells in tumor tissue).

Differential gene screening related to immune scores and enrichment analysis of differentially expressed genes

The immune score for each sample in the training set was calculated according to the ESTIMATE algorithm, and the best cutoff value was generated using X-tile plots (16). Data analysis was performed using packaging limma (17). The relapse-free survival is defined as time from randomization to the first reucurrence or death. The overall survival is defined as the time from the initial confirmed diagnosis to the death of any cause. Fold change >1.5 and adj. P<0.05 were set as the cutoff value for screening differentially expressed genes. First, the low immune score and high immune score samples were normalized by the limma package, and then the differential genes were screened to obtain 448 differentially expressed genes.

Functional enrichment analysis of the differential genes was performed using Database for Annotation, Visualization and Integrated Discovery (DAVID) (18) and GO categories were identified by their biological processes (BP), molecular functions (MF) and cellular components (CC). The DAVID database was also used for pathway enrichment analysis with reference to the Kyoto Encyclopedia of Gene and Genomic (KEGG) pathway. False discovery rate (FDR) <0.05 was used as the cutoff.

Screening for prognosis-related genes and building risk models

LASSO is a superior high-dimensional regression classifier and was used to select the key genes influencing patient outcomes (19). LASSO 1000 iterations were performed using the publicly available R package glmnet (20). Multiple genomes containing the optimal solution were received after multiple dimensionality reduction. At the same time, for the stability and accuracy of the results, a random sampling method of leave-one-out cross-validation (LOOCV) was used to select a set of genes to construct a prognostic model (19).

According to the selected genetic model, a risk formula of risk score was constructed to evaluate the high-risk and low-risk groups. The formula for obtaining the score is Σiωiχi, where ωi and χi are the coefficients and expressed value of each gene. The risk score for each sample in the data in the training set was calculated according to the formula, and the best cutoff value was generated using X-tile plots (16). This threshold was set to classify patients: Higher than the best cutoff for the low-risk group and lower than the risk score for the high-risk group.

Estimating the composition of immune cells

To estimate the immune cell composition in the sample, the analytical platform CIBERSORT (https://cibersort.stanford.edu/) was used to quantify the relative levels of distinct immune cell types within a complex gene expression mixture (21). The analysis was performed with an arrangement of 100 default statistical parameters. The activation and quiescence state of the same type of immune cells were analyzed as a whole. CIBERSORT's deconvolution of gene expression data provides valuable information about the composition of immune cells in a sample.

Validation of the validity and reliability

Univariate survival analysis of the gene signature was assessed by using survival in R language (P<0.05) (22). Then survival receiver operating characteristic curve (ROC) was used to complete the area under the curve (AUC) of gene signature and TNM classification (23). External data from GSE31210 and TCGA were applied to verify the reliability of the gene signature's impact on the prognosis of the patients.

The univariate and multivariate Cox proportional hazard regression analyses were used to evaluate independent prognostic factors associated with survival. Gene signature, age, sex, smoking status, T stage T, N stage, histology, grade, epidermal growth factor receptor (EGFR) mutation status and adjuvant chemotherapy were employed as covariates. In addition, the logistic regression analysis were used to analyze the association between the clinical related factors and risk model of gene signature construction.

Results

Correlation between immune score and overall survival in patients with NSCLC

There were 13,035 gene expression profiles obtained from 130 tumor samples in the dataset GSE103584 (Table SI). After normalizing the data of 130 samples, the immune score, stromal score, and estimate score were calculated by immunocyte-related genes (Table SII). The 21 low immune score samples and 109 high immune score samples were divided by X-tile plots (Fig. 1A and B, P<0.001). Kaplan-Meier survival curves showed that the relapse-free survival of patients with the high score group of immune scores was longer than that when compared with the patients in the low score group (Fig. 1C, P<0.001). Consistently, patients with high immune scores also showed longer overall survival compared to the patients with low scores (Fig. 1D, P=0.017).

Differential gene screening related to immune scores and enrichment analysis of the differential genes

To reveal the correlation of gene expression profiles with immune scores, we compared the gene microarray data of all 130 cases obtained in the dataset GSE103584. The low immune score and high immune score samples were normalized by the limma package and 448 differential genes were extracted from the comparison of high vs. low immune score groups. Heatmaps showed distinct gene expression profiles of cases in the low vs. high low immune score groups (Fig. 2A).

To analyze the potential functions of differential genes, we performed functional enrichment analysis on 448 differentially expressed genes. The Gene Ontology (GO) terminology was identified. The top 10 positions of the GO term for biological processes, cellular component terms and molecular functions are listed (Fig. 2B). The top GO terms included ‘extracellular matrix organization’ and ‘extracellular structure organization’ closely related to the immune microenvironment of tumors. In addition, pathway enrichment analysis with reference to KEGG mainly focused on ‘protein digestion and absorption’, ‘AGE-RAGE signaling pathway in diabetic complications’, ‘platelet activation and focal adhesion’ which also had a relationship with immune response (Fig. 2C).

Screening genes associated with prognosis and building risk models

We applied the LASSO Cox regression model to predict and analyze the most valuable prognostic genes among the 448 differential genes in the 130 sample data. A random sampling method of 10-cross validation was used to construct a prognostic model containing 10 genes (Fig. 3A). Through calculation and verification, it was found that the model constructed by 10 genes had the lowest error rate (Fig. 3B). Fig. 3C shows the specific information and coefficients of the 10 genes.

To further validate the accuracy of the risk prediction model, we established a ROC plot of the signature model and TNM stage. As shown in Fig. 3D, we found that risk prediction models were more sensitive to prognosis than the TNM stage (P=0.006).

Estimating the composition of immune cells

We used CIBERSORT to estimate the immune cell composition of the 130 samples and quantify the relative levels of different cell types in a mixed cell population. All results were normalized relative proportions by cell type (Table SIII). As shown in Fig. 4A, B and E, we compared different types of cells in the low-risk group and the high-risk group. It was found that the ratio of eosinophils, mast cells resting and CD4 T cells memory activated in the low-risk group was higher than that in the high-risk group, and the difference was statistically significant (P=0.003, P=0.014 and P=0.018, respectively). Inconsistently, the ratio of NK cells resting and plasma cells activated in the low-risk group was lower than that in the high-risk group (P=0.05 and P=0.009, respectively) (Fig. 4C and D). The results indicated that activation and inhibition of various immune cells existed simultaneously in the tumor microenvironment.

Validation of the validity and reliability

Survival analysis in R language package was applied to examine the effects of the 10-gene signature on the prognosis of NSCLC patients. Kaplan-Meier survival curves for overall survival were used to represent the survival probabilities of the high-risk group and the low-risk group. The results showed that patients in the high-risk group had shorter overall survival than patients in the low-risk group (Fig. 5A, P<0.001).

Furthermore, external data from GSE31210 and TCGA were applied as a validating set to verify the validity and reliability of the 10-gene signature impact on the prognosis of the NSCLC patients. Kaplan-Meier survival showed that patients in the high-risk group had shorter overall survival than patients in the low-risk group (Fig. 5B, P=0.0025 and Fig. 5C, P=0.0157).

Correlation of the clinical information

The correlation analysis between gene signature and clinical pathological parameters in the training set (GSE103584) is shown in Table I. The high-risk group was found to be significantly associated with all clinical pathological parameters. The univariate and multivariate Cox proportional hazard regression analyses were used to evaluate independent prognostic factors associated with survival. Gene signature, age, sex, smoking status, T stage, N stage N, histology, grade, EGFR mutation status and adjuvant chemotherapy were employed as covariates. It was found that the risk model constructed by the 10-gene signature was an independent risk factor for prognosis (Table II, P<0.001).

Table I.

Correlation analysis between genetic signature and clinical pathological parameters of the NSCLC patients in the training set (GSE103584).

Table I.

Correlation analysis between genetic signature and clinical pathological parameters of the NSCLC patients in the training set (GSE103584).

VariablesLow risk n (%)High risk n (%)P-value
Age (years) <0.001
  <6529 (32.6)8 (19.5)
  >6460 (67.4)33 (80.5)
Sex <0.001
  Female26 (29.2)8 (19.5)
  Male63 (70.8)33 (80.5)
Smoking status <0.001
  Yes75 (84.3)35 (85.4)
  No14 (15.7)6 (14.6)
T stage <0.001
  T0-146 (51.7)12 (29.3)
  T228 (31.5)21 (51.2)
  T313 (14.6)3 (7.3)
  T42 (2.2)5 (12.2)
N stage <0.001
  N076 (85.4)28 (68.3)
  N19 (10.1)3 (7.3)
  N24 (4.5)10 (24.4)
Histology <0.001
  Adenocarcinoma67 (75.3)29 (70.7)
  Squamous21 (23.6)10 (24.4)
  Others1 (1.1)2 (4.9)
Grade <0.001
  I17 (19.1)5 (12.2)
  II44 (49.4)18 (43.9)
  III16 (20.0)11 (26.8)
  Other12 (13.5)7 (17.1)
EGFR status <0.001
  Yes17 (19.1)2 (4.9)
  No49 (55.1)33 (80.5)
  Unknown23 (25.8)6 (14.6)
Adjuvant therapy <0.001
  Yes66 (74.2)14 (34.1)
  No23 (25.8)27 (65.9)

[i] NSCLC, non-small cell lung cancer; EGFR, epidermal growth factor receptor.

Table II.

Univariate and multivariate Cox proportional hazard regression analyses between the risk factors and overall survival of NSCLC patients.

Table II.

Univariate and multivariate Cox proportional hazard regression analyses between the risk factors and overall survival of NSCLC patients.

Univariate analysisMultivariate analysis


VariablesWald χ2P-valueHR (95% CI)P-value
Age (years)0.2530.615 NI
  <65
  >64
Sex0.4320.511 NI
  Female
  Male
Smoking status0.4430.506 NI
  Yes
  No
T stage2.5450.467 NI
  T0-1
  T2
  T3
  T4
N stage4.7060.095 NI
  N0
  N1
  N2
Histology0.3790.827 NI
  Adenocarcinoma
  Squamous
  Others
Grade3.0660.382 NI
  I
  II
  III
  Other
EGFR status0.9750.614 NI
  Yes
  No
  Unknown
Adjuvant therapy0.7660.381 NI
  Yes
  No
Gene signature26.149<0.001 <0.001
  Low risk Reference
  High risk 8.828 (3.831–20.342)<0.001

[i] NSCLC, non-small cell lung cancer; EGFR, epidermal growth factor receptor; CI, confidence interval; NI, not included.

In addition, logistic regression analysis was used to analyze the association between the clinical related factors and risk model of 10-gene signature construction. As shown in Table III, we analyzed the risk factors for the risk model of the 10-gene signature construction. Age, sex, smoking status, T stage, N stage, histology, grade, EGFR mutation status and adjuvant chemotherapy were selected in the logistic regression model. T stage, N stage and EGFR mutation status were all independent risk factors in the multivariable analysis. The results showed that the patients with Stage T2 and Stage T4 had a significantly higher risk than those with Stage T0-1 (OR 3.822, 95% CI 1.422–10.269, P=0.008; OR 19.671, 95% CI 2.304–167.949, P=0.006) and the patients with Stage N2 had a significantly higher risk than those with Stage N0 (OR 13.066, 95% CI 2.680–63.700 P=0.001). We also found that the patients without EGFR mutations had a significantly higher risk than those with EGFR mutations (OR 16.150, 95% CI 2.122–122.877, P=0.007).

Table III.

Logistic regression analysis between the clinical related factors and risk model of genetic signature construction (HR=1).

Table III.

Logistic regression analysis between the clinical related factors and risk model of genetic signature construction (HR=1).

Univariate analysisMultivariate analysis


VariablesWald χ2P-valueOR (95% CI)P-value
Age (years)1.0100.315 NI
  <65
  >64
Sex1.6560.198 NI
  Female
  Male
Smoking status0.4780.490 NI
  Yes
  No
T stage10.7200.013 0.009
  T0-1 Reference
  T2 3.822 (1.422–10.269)0.008
  T3 1.218 (0.255–5.823)0.805
  T4 19.671 (2.304–167.949)0.006
N stage8.6520.013 0.006
  N0 Reference
  N1 1.042 (0.229–4.750)0.957
  N2 13.066 (2.680–63.700)0.001
Histology0.1020.950 NI
  Adenocarcinoma
  Squamous
  Others
Grade0.8670.833 NI
  I
  II
  III
  Others
EGFR status7.9800.018 0.010
  Yes Reference
  No 16.150 (2.122–122.877)0.007
  Unknown 5.985 (0.688–52.088)0.105
Adjuvant therapy2.0330.154 NI
  Yes
  No

[i] HR, hazard ratio; OR, odds ratio, CI, confidence interval; EGFR, epidermal growth factor receptor; NI, not included.

Discussion

Malignant solid tumor tissues include not only tumor cells, but also tumor-associated normal epithelial cells and stromal cells, immune cells and vascular cells. Infiltrating immune cells are an integral component of the tumor immune microenvironment (TIME) and play an important role in increasing the effectiveness of immunotherapy (24). This infiltrating immune cell population is usually a heterogeneous mixture of immune cells, including cell types associated with activity and inhibition (25). Because of the need for different types and subtypes of TIME to be identified in the immunotherapy of tumors, their characteristics and differences must be identified (26). In order to ensure substantial progress, bioinformatic techniques are used to assess the composition, functional status and cellular localization of immune cells. Based on gene signature, a more precise classification of patients based on their TIME will better predict overall survival and response to immunotherapeutic agents.

Firstly, we utilized an ESTIMATE algorithm to calculate immune scores and predict the level of infiltrating immune cells by immunocyte-related genes. The 21 low immune score samples and 109 high immune score samples were divided by X-tile plots. Kaplan-Meier survival curves showed that relapse-free survival and overall survival of patients in the high score group of immune scores was longer than the patients in the low score group. Next, 448 differential genes were extracted from the comparison of high vs. low immune score groups and the top Gene Ontology (GO) terms included extracellular matrix organization and extracellular structure organization closely related to the immune microenvironment of tumors. In addition, pathway enrichment analysis with reference to KEGG mainly focused on ‘protein digestion and absorption’, ‘AGE-RAGE signaling pathway in diabetic complications’, ‘platelet activation and focal adhesion’ which also had a relationship with immune response.

Furthermore, we applied the LASSO Cox regression model to screen a 10-gene signature among the 448 differential genes and found that risk prediction models constructed by 10 genes were more sensitive to prognosis than TNM stage. That is the 10 differential gene signature including neural cell adhesion molecule 2 (NCAM2), caldesmon 1 (CALD1), neuron navigator 3 (NAV3), kinase insert domain receptor (KDR), islet cell autoantigen 1-like (ICA1L), CLN5 intracellular trafficking protein (CLN5), zinc finger and BTB domain containing 34 (ZBTB34), PML-RARA regulated adaptor molecule 1 (PRAM1), sulfatase 1 (SULF1) and translocase of outer mitochondrial membrane 6 (TOMM6) may influence the survival time of NSCLC patients.

Moreover, survival analysis in R language pack was applied to examine the effects of the 10-gene signature on the prognosis of NSCLC patients. Kaplan-Meier survival curves for overall survival showed that patients in the high-risk group had shorter over survival than patients in the low-risk group. Then, external data from GSE31210 and The Cancer Genome Atlas (TCGA) were applied as a validating set to verify the validity and reliability of the 10-gene signature impact on the prognosis of the patients. Kaplan-Meier survival showed that indeed patients in the high-risk group had shorter overall survival than patients in the low-risk group.

We not only confirmed the stability and accuracy of the 10-gene signature, but also found it was closely associated with other clinical information. The univariate and multivariate Cox proportional hazard regression analyses were used to evaluate independent prognostic factors associated with survival. It was found that the risk model constructed by the 10-gene signature was an independent risk factor for prognosis (Table III). In addition, logistic regression analysis was used to analyze the association between the clinical related factors and risk model of 10-gene signature construction. T stage, N stage and EGFR mutation status were all independent risk factors in the multivariable analysis. The results showed that the patients with Stage T2 and T4 had a significantly higher risk than those with Stage T0-1 and the patients with Stage N2 had a significantly higher risk than those with Stage N0. We also found that the patients without EGFR mutations had a significantly higher risk than those with EGFR mutations. These results suggest that our characteristics may contribute to the clinical management of NSCLC.

Finally, we used CIBERSORT to estimate the immune cell composition of 130 samples and quantify the relative levels of the different cell types in a mixed cell population and compared the different types of cells in the low-risk group and the high-risk group. Surprisingly, it was found that the ratio of eosinophils, mast cells resting and CD4 T cells memory activated in the low-risk group was higher than that in the high-risk group, and the difference was statistically significant. Inconsistently, the ratio of NK cells resting and plasma cells activated in the low-risk group was lower than that in the high-risk group. The results indicated that activation and inhibition of various immune cells existed simultaneously in TIME. The 10-gene signature was used to analyze the composition of immune cells helping to clarify the role of TIME and increase our understanding of molecular phenotype. The success of cancer immunotherapy has revolutionized cancer treatment and has used TIME parameters (immune cell composition and proportion) as predictive immunotherapy markers (8). Detailed characterization of the immune cell composition in tumors may be the basis for determining the prognostic and predictive biomarkers of immunotherapy (27,28). Therefore, incorporating TIME parameters into a gene signature can be more conducive to individualized treatment options (29). Studies have reported that the expression levels of various proliferation-related genes are related to the response to immune checkpoint inhibitors in NSCLC (30). In addition, JAK1/2 mutations are associated with resistance to anti-PD-1/PD-L1 antibodies and MDM2/MDM4 and EGFR changes may be associated with hyperprogression (3133). Here, the 10-gene signature closely related to TIME could predict the prognosis of lung cancer patients, and provide some reference for immunotherapy.

Notably, among the 10-gene signature, only the gene KDR is involved in tumor immunity and most of the genes (NCAM2, CALD1, NAV3, PRAM-1 and SULF1) are closely related to tumors and can be used as novel tumor biomarkers. There are also two other genes (ICA1L, CLN5) that have been reported to have related functions, but no reports exist on tumors and immunity. The TOMM6 gene has not been reported. NCAM2 is a close homolog of the neuronal cell adhesion molecule NCAM1 and stimulates neurite outgrowth through FGFR-dependent activation of the Ras/MAPK pathway (34,35). Several studies have reported that NCAM2 can be used as a new therapeutic target for cancer, especially prostate cancer and breast cancer (3638). CALD1 is a novel target of the TEA domain family member (39). Moreover, CALD1 encodes the caldesmon protein, which is a calmodulin-binding and cytoskeleton-associated protein and regulates cell motility, such as migration and invasion (40,41). It has been suggested that CALD1 may indicate a general splicing event associated with cancer (41,42) and was also identified as a potential prognostic molecular marker for bladder and colon cancer (4345).

NAV3 is a novel cancer-associated gene located at chromosome 12q21 and belongs to the ‘hill’ genes of genomic landscaping associated with cancer (46). Accumulating evidence suggests that the NAV3 gene is a key player in a variety of cancers, with downregulation of NAV3 found in 40% of primary neuroblastomas and adrenocortical carcinomas (47,48). NAV3 mutations have been found in melanoma, pancreatic cancer, breast cancer and colon cancer (49). We also found NAV3 gene copy number changes (deletions/amplifications) in other cancer types of epithelial origin (50) and NAV3 gene allelic loss was found to be associated with several subtypes of cutaneous T-cell lymphoma (51,52). KDR, also known as VEGFR2, is expressed in endothelial cells (ECs) to promote EC growth and survival, thereby initiating angiogenesis (53). Research has shown that T cell KDR is an important molecule in immunity, and it was found that KDR was induced to be expressed in activated CD4 and CD8 T cells in vitro (54). In addition, KDR was also demonstrated to be expressed on T cells after interaction with tumor necrosis factor (TNF)-activated ECs, and have a function in transendothelial migration (55).

ICA1L is highly expressed in sperm cells and is closely related to male infertility (56). CLN5 mutations cause neurodegenerative diseases, and symptoms include mainly seizures, visual failure, motor decline, and progressive cognitive deterioration (57). ZBTB34 encodes a nuclear protein and functions as a potential transcriptional repressor. The transcript of ZBTB34 appears in a variety of adult tissues related to the immune, nervous, muscle and endocrine systems suggesting that ZBTB34 is a ubiquitously expressed protein that may function universally in transcriptional regulation (58). PRAM-1 is an intracellular adaptor molecule that is upregulated during the induced granulocytic differentiation of promyelocytic leukemic cells and during normal human myelopoiesis (59). PRAM-1 is involved in a signaling pathway induced by retinoic acid in acute promyelocytic leukemia (APL) cells (60). SULF1 plays a key role in the pathogenesis of various types of human cancer, and SULF1 protein is secreted to the cell surface to regulate the sulfation of heparan sulfate proteoglycans (HSPGs) (61,62). SULF1 was also found to be a novel prognostic marker and predictor of lymph node metastasis in patients with gastric cancer (63). From the above results, we can conclude that our gene signature not only identified new promising biomarkers, but also may provide a direction for the study of TIME mechanisms.

In summary, the present research has the following novelty and innovation. First, multiple bioinformatic analysis methods were used to extracted a 10-gene signature closely related to TIME. Second, the risk model constructed by the 10-gene signature was able to predict the prognosis of NSCLC patients and was more sensitive for predicting prognosis than TNM stage. Third, the 10-gene signature was found to be closely related to TIME parameters (immune cell composition and proportion) and provides a certain reference for the immunotherapy of NSCLC. Fourth, some previously ignored genes in the 10-gene signature may become potential novel markers for NSCLC. However, the present study also has certain limitations. First, the study consisted solely of bioinformatics research, and there was no validation of clinical sample data. Second, the study only verified the validity and reliability of the 10-gene signature impact on the overall survival of the patients, but did not verify relapse-free survival. Third, the sample size requires further expansion to verify the accuracy of the 10-gene signature and truly clarify its clinical value.

Supplementary Material

Supporting Data
Supporting Data
Supporting Data

Acknowledgements

Not applicable.

Funding

This study was supported jointly by Special funds for Taishan Scholars Project (grant. no. tsqn201812149), Academic promotion programme of Shandong First Medical University (2019RC004).

Availability of data and material

We declared that materials described in the manuscript, including all relevant raw data, are freely available to any scientist wishing to use them for non-commercial purposes, without breaching participant confidentiality.

Authors' contributions

HW designed the project and proposed the research concept. XL carried out the data search and downloading and literature collection. CZ conducted the bioinformatic analysis and CZ constructed the graphic images and data charts and performed the statistical processing. JL wrote the manuscript. All authors read and approved the manuscript and agree to be accountable for all aspects of the research in ensuring that the accuracy or integrity of any part of the work are appropriately investigated and resolved.

Ethics approval and consent to participate

This study was approved by the Ethics Committee of Shandong Cancer Hospital and Institute and was consistent with the Helsinki Declaration. This study was mainly based on the Gene Expression Omnibus datasets (GEO; GSE103584,GSE31210) and The Cancer Genome Atlas (TCGA, http://tcga-data.nci.nih.gov/tcga/). Personal privacy information was not involved, thus informed consent was not needed.

Patient consent for publication

Not applicable.

Competing interests

The authors declare that they have no competing interests.

Glossary

Abbreviations

Abbreviations:

TIME

tumor immune microenvironment

TCGA

The Cancer Genome Atlas

GEO

Gene Expression Omnibus

NSCLC

non-small cell lung cancer

ESTIMATE

Estimation of Stromal and Immune cells in Malignant Tumours using Expression data

LASSO

least absolute shrinkage and selection operator

TNM

Tumor, Lymph Node and Metastasis

NK

natural killer

OS

overall survival

ECM

extracellular matrix

EGFR

epidermal growth factor receptor

GO

Gene Ontology

DAVID

Database for Annotation, Visualization and Integrated Discovery

BP

biological processes

MF

molecular functions

CC

cellular components

KEGG

Kyoto Gene and Genomic Encyclopedia

LOOCV

leave-one-out cross-validation

ROC

receiver operating characteristic

AUC

area under the curve

NCAM2

neural cell adhesion molecule 2

NAV3

neuron navigator 3

KDR

kinase insert domain receptor

ICA1L

islet cell autoantigen 1-like

CLN5

intracellular trafficking protein

ZBTB34

zinc finger and BTB domain containing 34

PRAM1

PML-RARA regulated adaptor molecule 1

TOMM6

translocase of outer mitochondrial membrane 6

ICI

immune checkpoint inhibitors

MCs

mast cells

CTL

cytotoxic T lymphocytes

MM

malignant melanoma

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March 2020
Volume 43 Issue 3

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APA
Li, J., Li, X., Zhang, C., Zhang, C., & Wang, H. (2020). A signature of tumor immune microenvironment genes associated with the prognosis of non‑small cell lung cancer. Oncology Reports, 43, 795-806. https://doi.org/10.3892/or.2020.7464
MLA
Li, J., Li, X., Zhang, C., Zhang, C., Wang, H."A signature of tumor immune microenvironment genes associated with the prognosis of non‑small cell lung cancer". Oncology Reports 43.3 (2020): 795-806.
Chicago
Li, J., Li, X., Zhang, C., Zhang, C., Wang, H."A signature of tumor immune microenvironment genes associated with the prognosis of non‑small cell lung cancer". Oncology Reports 43, no. 3 (2020): 795-806. https://doi.org/10.3892/or.2020.7464