IrlncRNAs in ovarian cancer
Figure 1 shows the flow diagram of this study. Transcriptome data of ovarian cancer downloaded from TCGA and GTEx included 88 normal samples and 379 cancer samples. 2483 immune-related genes were obtained from the ImmPort database. The co-expression analysis of immune genes and lncRNAs obtained 616 immune-related lncRNAs was shown in Table S1 (p < 0.001).
Establishment of risk assessment signature by Differentially Expressed irlncRNA (DEirlncRNA) pairs
We obtained 145 DEirlncRNAs in the subsequent differential analysis. 137 of the 145 DEirlncRNAs were up-regulated and 8 of them were down-regulated (Fig. 2A and B). Based on the 145 DEirlncRNAs, a 0–1 matrix was constructed through a single cycle comparation, and 8613 valid pairs of DEirlncRNA were obtained. Single factor test and Lasso regression analysis were used to optimize and screen the DEirlncRNA pairs (Fig. 3A). So as to avoid over-fitting and improve the accuracy of the signature, we used the cross-validation and finally gained 29 DEirlncRNA pairs (Fig. 3B).
A total number of 374 available ovarian cancer patients’ samples from the TCGA database were used to calculate the risk scores, and the 29 DEirlncRNA pairs were used to calculate the areas under curve (AUCs) for each ROC curve. In order to confirm the optimality, we performed the 1-, 3-, and 5-year ROC curves and found the maximum area under the curves belonged to the 5-year ROC curve, which was selected to distinguish the high and low risk groups of the signature (Fig. 3C and D). Finally, we obtained 235 cases in the high-risk group and 139 cases in the low-risk group (Fig. 3E). Further, we verified the signature based on prognosis. The risk coefficient was positively related to the mortality, and the Kaplan-Meier analysis also confirmed that the low-risk group patients had a longer survival.
Validation of the clinical-based risk assessment signatures
In order to figure out the relationship between the risk signature and different clinicopathological factors, we performed the Wilcoxon signed-rank test and the results showed the risk was significantly related to age (p < 0.05), survival status (p < 0.0001) and residual tumor lesions (p < 0.05, Fig. 4A-C). There was no significant correlation with OC grade and stage (Fig. 4D and E). However, there was some difference between the stage Ⅰ-Ⅱ and stage Ⅳ (p = 0.085).Next, we verified the risk signature as an independent prognostic factor for ovarian cancer through the univariate and multivariate Cox regression analyses. The results indicated that age (p < 0.001, HR = 1.023, 95%CI [1.010–1.036]), residual tumor lesions (p < 0.001, HR = 2.209, 95%CI [1.596–3.110]) and riskScore (p < 0.001, HR = 1.142, 95% CI [1.117–1.167]) was related to overall survival in univariate Cox regression analysis (Fig. 4F). In multivariate Cox regression analysis, riskScore can be used as an independent predictor of prognosis (Fig. 4F, p < 0.001, HR = 1.136, 95% CI [1.111–1.161]).
Application of risk assessment signature in chemo-sensitivity
Furthermore, we also analyzed the efficacy of common chemotherapy drugs for ovarian cancer by using the half-inhibition rate (IC50). From the box diagram, we can find that the low-risk group had higher sensitivity to chemotherapy. Among them, platinum (p < 0.001) and paclitaxel (p < 0.05), the most conventional chemotherapy drugs for ovarian cancer, had statistical differences (Fig. 5A and B). PARP inhibitors, a novel chemotherapy agent for ovarian cancer, also showed lower IC50 values in the low-risk group (Fig. 5C, p < 0.05). Besides, vinblastine (p < 0.001) and camptothecin (p < 0.0001) also differed in drug sensitivity among patients at different risk (Fig. 5D and E). Docetaxel, although not statistically significant, did show different drug sensitivities in different risk groups (Fig. 5F, p = 0.065). This suggests the possibility of the label as a predictor of chemotherapeutic drug sensitivity.
Correlation of tumor immunotherapy and risk assessment signature
Clinical application of immunotherapy has attracted widespread attention in ovarian cancer. We investigated whether this risk signature was correlated with tumor-infiltrating immune cells (Fig. 6A). The figure shows differences in the expression of immune cells in the high and low risk groups, we found that the low-risk group has positive correlation with specific immune cells, such as B cells and T cells (Fig. 6B-D), while has negative correlation with non-specific immune cells, such as neutrophils, macrophages and mast cells (Fig. 6E-G). This suggests the possibility of the risk signature on immunotherapy in ovarian cancer.