Abstract
BackgroundThe incidence rate of non-small cell lung cancer (NSCLC) has been increasing worldwide, and the correlation of circadian rhythm disruption with a raised risk of cancer and worse prognosis has been shown by accumulating evidences recently. On the other hand, drug resistance and the impact of tumor heterogeneity have been inevitable in NSCLC therapy. These both lead to an urgent need to identify more useful prognostic and predictive markers for NSCLC diagnosis and treatment, especially on the aspect of circadian clock genes.MethodsThe expression of the main clock genes in cancer was probed with TIMER and Oncomine databases. The prognostic value of key clock genes was probed systematically with the Kaplan–Meier estimate and Cox regression on samples from TCGA database. RT-qPCR was performed on patient tissue samples to further validate the results from databases. The functional enrichment analysis was performed using the “ClusterProfiler” R package, and the correlation of key clock genes with tumor mutation burden, immune checkpoint, and immune infiltration levels were also assessed using multiple algorithms including TIDE, TIMER2.0, and XCELL.ResultsTIMELESS was significantly upregulated in lung tissue of clinical lung cancer patients as well as TCGA and Oncomine databases, while RORA was downregulated. Multivariate Cox regression analysis indicated that TIMELESS (P = 0.004, HR = 1.21 [1.06, 1.38]) and RORA (P = 0.047, HR = 0.868 [0.755, 0.998]) has a significant correlation with overall survival in NSCLC. Genes related to TIMELESS were enriched in the cell cycle and immune system, and the function of RORA was mainly focused on oncogenic signaling pathways or glycosylation and protein activation. Also, TIMELESS was positively correlated with tumor mutation burden while RORA was negatively correlated with it. TIMELESS and RORA were also significantly correlated with immune checkpoint and immune infiltration levels in NSCLC. Additionally, TIMELESS showed a significant positive relationship with lipid metabolism.ConclusionsTIMELESS and RORA were identified as key clock genes in NSCLC, and were independent prognostic factors for overall survival in NSCLC. The function of them were assessed in many aspects, indicating the strong potential of the two genes to serve as biomarkers for NSCLC progression and prognosis.
Highlights
As the most common cancer type, lung cancer caused most cancer-related deaths worldwide, accounting for about 1.4 million deaths per year [1]
Datasets and data availability The sex, age, survival, status, topography and tumornode-metastasis (TNM) stage of lung adenocarcinoma (LUAD) and lung squamous cell carcinoma (LUSC) samples were extracted from The Cancer Genome Atlas (TCGA: https://cancergenome.nih.gov) with the exclusion patients without sufficient data were excluded from subsequent analyses
The mRNA levels of five clock genes (TIMELESS, receptor A (RORA), period circadian regulator 1 (PER1), Period circadian regulator 2 (PER2), Cryptochrome circadian regulator 2 (CRY2)) are significantly altered in several kinds of cancer The transcription level of clock genes in tumor and normal tissues was assessed with Oncomine database (Fig. 1A). we found that the TIMELESS expression level was upregulated in most of the significantly altered datasets (77 of 84 datasets, 91.7%), especially in breast cancer and lung cancer, whereas the expression levels of RORA, PER1, PER2, and CRY2 were downregulated in most of the significantly altered datasets (63 of 73 datasets, 86.3%; 44 of 49 datasets, 89.8%; 44 of datasets, 91.7%; of 52 datasets, 94.2%)
Summary
As the most common cancer type, lung cancer caused most cancer-related deaths worldwide, accounting for about 1.4 million deaths per year [1]. The need to identify more useful prognostic and predictive markers or targets for the diagnosis and treatment of NSCLC is more and more urgent. The incidence rate of non-small cell lung cancer (NSCLC) has been increasing worldwide, and the correlation of circadian rhythm disruption with a raised risk of cancer and worse prognosis has been shown by accumulating evidences recently. Drug resistance and the impact of tumor heterogeneity have been inevitable in NSCLC therapy. These both lead to an urgent need to identify more useful prognostic and predictive markers for NSCLC diagnosis and treatment, especially on the aspect of circadian clock genes
Sign-in/Register to view highlights & summary Sign-in/Register to access full text options 
Free) 
Talk to us
Join us for a 30 min session where you can share your feedback and ask us any queries you have
Schedule a call
