LUAD accounts for nearly 40% of all lung cancer cases, and the prognosis of LUAD patients remains unsatisfactory.2,5 Therefore, developing effective biomarkers with high specificity and sensitivity is of significance to improve the survival of LUAD patients, especially in the era of immunotherapy. Nowadays, with the development of the technology of high-throughput sequencing, many studies have indicated the prognostic value of genome-wide biomarkers in malignant tumors, such as signatures of messenger RNAs (mRNAs), microRNAs (miRNAs), and lncRNAs.27–29 In particular, immune-related signatures have been proved to have effectively predictive value in the treatment and prognosis of cancers including LUAD.16–20 However, most of these signatures depend on the exact expression levels of transcripts, which weakens their clinical application value due to the heterogeneity of gene expression data.
In this study, we innovatively conducted a new method of cyclically single pairing along with a 0-or-1 matrix to construct a novel prognostic signature of irlncRNA pairs in LUAD. This novel signature does not require quantitative expression levels of lncRNAs, but only needs to detect the higher or lower expression level of the two lncRNAs in each lncRNA pair, which improves its clinical practicability. Totally, 8 DEirlncRNA pairs were selected to construct the prediction model of LUAD, which was proved to be efficient to predict the survival of LUAD patients. Among these DEirlncRNA included in the model, some have been revealed to be related to the development of cancers, such as LINC00958, FOXF1 adjacent non-coding developmental regulatory RNA (FENDRR), LINC01116, and LINC00941.
LncRNA LINC00958 was initially identified as an oncogene in bladder cancer,30 and subsequent studies revealed the overexpression of LINC00958 in many other malignant tumors, such as hepatocellular carcinoma, pancreatic cancer, gastric cancer, glioma, and cervical cancer.31–35 In NSCLC, Luo et al. demonstrated that LINC00958 was highly expressed in both LUAD and lung squamous cell carcinoma (LUSC) cell lines and it could facilitate the proliferation and migration of NSCLC cells, which was mediated by JNK/c-JUN signaling pathway.36
LncRNA FENDRR, as a potential tumor suppressor, has been revealed to be downregulated in different cancers, such as gastric cancer, breast cancer, hepatocellular carcinoma as well as NSCLC.37–40 Zhang et al. demonstrated that FENDRR was downregulated in both NSCLC cells and tissues and was negatively related to the prognosis of NSCLC patients. Up-expression of FENDRR could inhibit the aggressiveness phenotypes of NSCLC cells, such as proliferation, migration and invasion, via directly binding to miR-761 and regulating the expression of tissue inhibitor of metalloproteinases 2 (TIMP2).40 Besides, Munteanu et al. indicated that FENDRR might also regulate the immune response in macrophages. In detail, the overexpression of FENDRR could enhance interferon γ (IFN γ) induced M1 macrophage polarization by modulating signal transducer and activator of transcription 1 (STAT1) activation pathway.41
LncRNA LINC01116 was found to be dysregulated in various human cancers, such as glioma, prostate cancer, breast cancer, and osteosarcoma.42–45 And recent studies also suggested that LINC01116 plays an oncogenic role in lung cancer. For instance, Zeng et al. demonstrated the upregulation of LINC01116 in LUAD tissues and cell lines, and short interfering RNAs (siRNAs) induced LINC01116 knockdown could inhibit the cell proliferation, migration, and epithelial-mesenchymal transition (EMT) of LUAD cells.46 And Wang et al. found that LINC0116 overexpression contributed to cisplatin resistance in LUAD.47 Besides, LINC01116 also played a significant role in gefitinib resistance of NSCLC via regulating the expression of interferon-induced protein 4 (IFI4).48
LncRNA LINC00941, also known as MSC upregulated factor (lncRNA-MUF), was first identified as an oncogene in gastric cancer by Luo et al. They found that LINC00941 was overexpression in the tissues of gastric cancer compared with adjacent normal tissues and its aberrant expression was related to invasion depth, TNM stage, and lymphatic metastasis.49 Consistently, Liu et al. indicated that silence of LINC00941 could inhibit the proliferation, migration, and invasion of gastric cancer cells.50 Meanwhile, Wang et al. found that LINC00941 could act as a competing endogenous RNA (ceRNA) by sponging miR-335-5p to regulate ROCK1-mediated LIMK1/Cofilin-1 signaling, which contributed to the proliferation, migration, invasion, and EMT of pancreatic cancer cells.51 And in LUAD, LINC0094 could regulate focal adhesion and PI3K-AKT signaling pathway, and its elevated expression level was related to decreased survival of LUAD patients.52
To evaluate the efficacy and accuracy of this prediction model, we performed 1-, 3-, and 5-year ROC curve analysis and the results showed that this model was efficient in predicting the prognosis of LUAD patients since AUC values were all over 0.70. And based on the optimal cut-off risk score identified by Youden Index, LUAD patients were divided into high-risk and low-risk subgroups, and K-M analysis revealed that this risk model exhibited great power in distinguishing good or poor survival of LUAD patients. In addition, the risk score of the model was found to be an independent prognostic factor for LUAD patients. Moreover, in order to estimate the clinical significance of the model, we performed chi-square test and Wilcoxon rank-sum test to explore the correlation between risk model and clinicopathological characteristics of LUAD patients, which indicated that the risk model was significantly associated with the clinical stage of patients including T stage, N stage, and M stage. All these results implied that this risk model performed well in predicting the prognosis of LUAD patients and these survival-related irlncRNAs included in the model might be used as novel therapeutic targets for LUAD treatment in the future.
In recent years, the treatment of lung cancer has entered the era of immunotherapy. However, not all patients with lung cancer can benefit from the treatment of immunotherapeutic agents, and the response rate of LUAD patients to immunotherapy remains unsatisfactory.5 Tumor infiltrating immune cells in TME participate in various biological processes of malignant tumors, and the interaction between infiltrating immune cells and cancer cells can influence the malignant phenotypes of cancers.53,54 In this study, we comprehensively estimated the tumor-infiltrating immune cells of LUAD samples by using seven acceptable methods including xCell, TIMER, quanTIseq, MCP-counter, EPIC, CIBERSORT-ABS, and CIBERSORT,25,26 and then analyzed the relationship between tumor-infiltrating immune cells and the risk model. The correlation analysis indicated that the high-risk subgroup was more negatively related to tumor-infiltrating immune cells, such as CD8 + T cells and monocytes. CD8 + T cells are key effectors in anti-tumor immunity, and the frequency of CD8 + T cells is positively associated with the survival of patients with lung cancer, melanoma, and breast cancer.55,56 In addition, the infiltration of CD8 + T cells in TME is related to improved responses of cancer patients treated with immune checkpoint inhibitors (ICIs). For instance, Wong et al. demonstrated that melanoma patients with high CD8 + T cell count experienced prolonged survival when treated with anti-PD-1 therapy.57 In addition, monocytes are a subtypes of innate immune cells, which also play significant roles in anti-tumor immunity by various mechanisms, such as phagocytosis, apoptosis, and cell contact-mediated antibody-dependent cellular cytotoxicity (ADCC).58,59 The role of CD8 + T cells and monocytes in anti-tumor immunity was consistent with our results of correlation analysis, which indicated that LUAD patients in low-risk subgroup have more CD8 + T cells and monocytes infiltration. Besides, we also found that the risk scores of LUAD patients were significantly related to the expression levels of CTLA4 gene and HAVCR2 gene, which have been proved to be potential biomarkers associated with the treatment of ICIs.60,61
To further evaluate the clinical application value of the risk model in the treatment of LUAD, we calculated the IC50 of several common anti-tumor drugs and compared the differences of drug sensitivity between patients with high-risk and low-risk subgroups. We found that high-risk LUAD patients have higher sensitivity (lower IC50) of anti-tumor drugs including paclitaxel, docetaxel, gemcitabine, vinorelbine, etoposide, and erlotinib. This relationship between risk model and drug sensitivity might be used to guide the selection and administration of anti-tumor drugs in clinical practice, which needs to be further investigated in the future.
However, there are some shortcomings in this study. First, the RNA-seq data of LUAD cohort was only downloaded from TCGA database. Although we performed various methods to validate the accuracy and efficiency of our prognostic prediction model, additional external cohorts are needed to confirm it in the future. Second, the tumor-infiltrating immune cells of LUAD samples were estimated by different quantification methods based on the RNA-seq data, which need to be experimentally validated. Finally, the clinical application value of our risk model, such as its relationship with anti-tumor drug sensitivity, has not been clinically verified. Further studies with larger sample size of LUAD patients are required to confirm our results in the future.
In conclusion, we innovatively constructed a novel signature of DEirlncRNA pairs in LUAD, which did not depend on specific expression levels of lncRNAs. This signature performed well in predicting the prognosis of LUAD patients and might be used to guide the administration of patients with LUAD in clinical practice. Future studies, preferably with a large sample size, are needed to verify our findings.