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. 2021 Dec;12(1):3252-3262.
doi: 10.1080/21655979.2021.1945991.

A DNA methylation profile of long non-coding RNAs can predict OS in prostate cancer

Wei Cheng  1 , Jie Cao  2 , Yong Xia  3 , Xin Lei  2 , Lili Wu  4 , Liang Shi  2   5
Affiliations

A DNA methylation profile of long non-coding RNAs can predict OS in prostate cancer

Wei Cheng et al. Bioengineered. 2021 Dec.

Abstract

Prostate cancer (PCa) is the most common male reproductive tract malignant tumor, accurate evaluation of PCa characterization and prognostic prediction at diagnosis are vital for the effective administration of the disease, especially at the molecular level. In this study, 48 CpG sites with differential methylation associated with overall survival (OS) were screened out between PCa and normal adjacent tissues. 16 CpG sites were selected by the least absolute shrinkage and selection operator (LASSO) and the risk score formula for methylated-based classifier was established. For 16-lncRNAs-CpG-classifier, the area under the curve (AUC) were 0.890, 0.917, and 0.932 at 3 years, 5 years and 7 years, respectively. Kaplan-Meier curves indicated that patients with high-risk scores had worse OS than those with low-risk scores. Prognostic methylation model of lncRNAs was identified from the whole genome in patients with PCa. This novel finding provides a novel insight for screening biomarkers of a prognosis for PCa.

Keywords: Prostate cancer; lncRNAs; methylation; prognostic.

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Conflict of interest statement

The authors have declared that no competing interest exists.

Figures

None
Graphical abstract
Figure 1.
Figure 1.
(a) The raw data of beta-values in methylated CpG site.

  1. The normalized beta-values of methylation of CpG site.

  2. One thousand most variable CpG sites were screened using ‘minfi’

package in R software
Figure 2.
Figure 2.
A CpG sites were selected in LASSO analysis.B LASSO coefficient profiles of the CpG sites.C Hierarchical clustering by differential levels in methylated CpG sites
Figure 3.
Figure 3.
The methylated levels of 8 CpG sites were up-regulated and 8 CpG sites were down-regulated in PCa compared with para-carcinoma tissues
Figure 4.
Figure 4.
(a)Time-dependent ROC analysis was carried out to estimate the predictive effect for OS at varied follow-up periods.(b) SKaplan–Meier analysis was used to estimate the OS in patients. The patients were divided into high-risk group or low-risk group based on the median cutoff point of risk score
Figure 5.
Figure 5.
Kaplan-Meier analyses with high-risk or low-risk score of methylation beta-values of single CpG site in the classifier
Figure 6.
Figure 6.
Functional enrichment analysis of lncRNA co-expression genes

  1. Gene Oncology (GO) enrichment

  2. KEGG pathway enrichment.

See this image and copyright information in PMC

References

    1. Sung H, Ferlay J, Siegel RL, et al. Global cancer statistics 2020: GLOBOCAN estimates of incidence and mortality worldwide for 36 cancers in 185 countries. CA Cancer J Clin. 2021;71(3):209–249. - PubMed
    1. Xu J, Lan Y, Yu F, et al. Transcriptome analysis reveals a long non-coding RNA signature to improve biochemical recurrence prediction in prostate cancer. Oncotarget. 2018;9(38):24936–24949. - PMC - PubMed
    1. Pistore C, Giannoni E, Colangelo T, et al. DNA methylation variations are required for epithelial-to-mesenchymal transition induced by cancer-associated fibroblasts in prostate cancer cells. Oncogene. 2017;36(40):5551–5566. - PubMed
    1. Luo H, Zhao Q, Wei W, et al. Circulating tumor DNA methylation profiles enable early diagnosis, prognosis prediction, and screening for colorectal cancer. Sci Transl Med. 2020;12(524). - PubMed
    1. Lemos AEG, Matos ADR, Ferreira LB, et al. The long non-coding RNA PCA3: an update of its functions and clinical applications as a biomarker in prostate cancer. Oncotarget. 2019;10(61):6589–6603. - PMC - PubMed

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