Knockdown of Glycolysis-Related LINC01070 Inhibits the Progression of Breast Cancer

Abstract

Accumulative evidence confirms that glycolysis and long non-coding RNAs (lncRNAs) are closely associated with tumor development. The aim of this study was to construct a novel prognostic model based on glycolysis-related lncRNAs (GRLs) in breast cancer patients. By performing Pearson correlation analysis and Lasso regression analysis on differentially expressed genes and lncRNAs associated with glycolysis in the Cancer Genome Atlas (TCGA) and Gene Set Enrichment Analysis (GSEA) datasets, we identified nine GRLs and constructed associated prognostic risk signature. Kaplan-Meier survival analysis and univariate and multivariate Cox analysis showed that patients in the low-risk group had a better prognosis. The receiver operator characteristics (ROC) curves showed that the area under the curve (AUC) of the prognostic risk signature predicting patients' overall survival at 1-, 3- and 5- years was 0.78, 0.71, and 0.71, respectively. Moreover, the validation curves also showed that the signature had better diagnostic efficacy and clinical predictive power. Furthermore, clone formation assay, EdU assay, and Transwell assay showed that knockdown of LINC01070 inhibited breast cancer progression. We developed a prognostic risk-associated GRLs signature that can accurately predict the breast cancer patient's prognostic status, and LINC01070 can be used as a potential biomarker for the prognosis of breast cancer patients.

Keywords: breast cancer; glycolysis; linc01070; lncrnas; nomogram; risk model.

Figure 1. The workflow of this study.

Abbreviations: TCGA, The Cancer Genome Atlas; GSEA: Gene Set Enrichment Analysis; lncRNA: long non-coding RNAs

Figure 2. Differential GRGs and Differential GRLs were selected between breast cancers and normal tissues.

A. 27 differential GRGs were detected between 3,693 DEGs and 304 GRGs. B, C. Volcano plot and heatmap of 27 differential GRGs were labeled. D. 41 differential GRLs were detected between 1,287 DELs and 271 GRLs. E, F. Volcano plot and heatmap of 41 differential GRLs were labeled. Abbreviations: DEG, differentially expressed lncRNA; GRL, glycolysis-related lncRNA; GRG, glycolysis-related genes

Figure 3. Construction of a risk signature consisting of nine differential GRLs.

A. Lasso coefficient profiles of the 41 differential lncRNAs. B. Mean-squared error plot of the lowest point of the red curve. C, D. All patients were divided into high-risk and low-risk groups using the median risk score as the cut-off point in the training (C) and validation (D) groups. Abbreviations: GRL, glycolysis-related lncRNAs; lncRNA: long non-coding RNAs

Figure 4. The risk score model and Cox proportional hazards regression model for predicting prognosis of breast cancer patients.

A, B. Risk score model for predicting prognosis in the training (A) and validation (B) groups. C. Univariate cox proportional hazards regression model of variables for overall survival. D. Multivariate cox proportional hazards regression model of variables for overall survival.

Figure 5. Construction of nomogram prediction models.

A. Nomogram for predicting 1-year, 3-year and 5-year survival. B. Receiver operating characteristic (ROC) curves for survival at 1, 3 and 5 years. C. Calibration curves for predicting survival probabilities at 1, 3 and 5 years.

Figure 6. Functional enrichment analysis of the risk model by GSEA analysis.

Abbreviation: GSEA, Gene Set Enrichment Analysis; GPCR, G-protein-coupled receptors

Figure 7. Kaplan-Meier survival curves for 9 differential GRLs in breast cancer patients.

A. AC120498.10. B. AC002546.1. C. AC134312.5. D. LINC01070. E. AL357093.2. F. AP001922.3. G. ALDH1L1.AS2. H. TRHDE.AS1. I. KIF26B.AS1.

Figure 8. Knockdown of LINC01070 inhibited breast cancer progression.

A. Growth ability of BT-549 cells (H) transfected with si-NC and si-LINC01070 assessed by clone formation assay. B. Growth ability of BT-549 cells (H) transfected with si-NC and si-LINC01070 assessed by EdU assay. C. Migration and invasion ability of BT-549 cells (H) transfected with si-NC and si-LINC01070 assessed by Transwell assay. p value is considered significant (**p<0.05, ***p<0.001).

Figure 9. lncRNA-microRNA-mRNA prediction network.