Patient characteristics
The study investigated 481 patient samples, including 432 LSCC and 49 normal tissues. Table 1 lists detailed clinical characteristics, including gender, race, age at diagnosis, and disease stage. Of the enrolled patients, 26.2% were female, and 78.4% were order than 60 years. The most common tumor grades were I (49.3%) and II (32.4%). A total of 936 differentially expressed lncRNAs, including 687 upregulated and 249 downregulated lncRNAs, were identified between LSCC and normal tissues in Figure 1.
The relationship between lncRNA expression and LSCC patient OS
We began by using univariate and multivariate Cox proportional hazard regression models in order to identify those lncRNAs which were associated with LSCC patient prognosis. In total, we identified three candidate lncRNAs in these LSCC patients (p < 0.01; Fig 2). A multivariate model confirmed that the expression of the lncRNAs LINC02555 (HR = 1.08, p = 0.025), APCDD1L-DT (HR = 1.10, p = 0.004), and OTX2-AS1 (HR = 0.89, p = 0.006) were all independently associated with LSCC patient OS. Kaplan-Meier survival curves and log-rank tests were further used to examine the relationship between these lncRNAs and patient survival. We found that two of the tested lncRNAs (LINC02555 and APCDD1L-DT) were negatively associated with LSCC patient OS, whereas the lncRNA OTX2-AS1 was positively correlated with OS (Fig. 3).
The prognostic utility of the three lncRNA signature
Using this three lncRNA signature, we were able to assign risk scores to patient samples , after which these samples were separated into high- and low-risk groups based upon the median risk score value (n = 216 samples/group). We then found that patients in the high-risk group had a significantly shorter OS than did patients in the low-risk group (p < 0.001) (Fig 4a). We then used an ROC analysis in order to assess the prognostic utility of this three lncRNA signature. The AUC values for these curves as predictors of LSCC patient 3- and 5-year survival were 0.67 and 0.62, respectively, corresponding to an effective survival prediction (Fig 4b). Patients in the high-risk group expressed higher levels of the lncRNAs LINC02555 and APCDD1L-DT on average relative to low risk patients, whereas low-risk patients expressed higher levels of OTX2-AS1 lncRNA.
Functional enrichment analysis and PPI networks
In order to identify potential targets for these three lncRNAs which were associated with LSCC patient prognosis, we conducted a co-expression analysis as detailed in the Materials and Methods section. We then performed GO and KEGG pathway analyses on these co-expressed genes in order to unravel their potential physiological roles (Fig 5). These co-expressed genes were primarily enriched in genes associated with biological processes such cell adhesion molecule binding, ubiquitin-like protein ligase binding, protein serine/threonine kinase activity, ubiquitin protein ligase binding, actin binding, ATPase activity, phospholipid binding, and phosphoric ester hydrolase activity. These genes were additionally significantly enriched in KEGG pathways including endocytosis, focal adhesion, MAPK signaling, lysosomes, neurotrophin signaling, ubiquitin mediated proteolysis, axon guidance, herpes simplex virus 1 infection, and the cell cycle. Furthermore, PPI networks were also obtained using the STRING tool. As mentioned in Fig 5c, INS, GCG, GCGR, GLP1R, IAPP, P2RY1, CRH and FFAR1 had the most connections with other members of the module and were thus the most noteworthy nodes in this network.