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

Figures & data

Table 1. Clinical characteristics of prostate cancer patients

Clinicopathological variables	n = 498
Age
< 60 years	203 (40.8%)
≥ 60 years	295 (59.2%)
Subtype
Acinar Type	483 (97.0%)
Other	15 (3.0%)
Gleason score
5–7	293 (58.8%)
8–10	205 (41.2%)
Tumor size
T1 + T2	188 (37.8%)
T3 + T4	303 (60.8%)
Recurrence	91 (18.3%)
Death	10 (2.0%)

Table 2. Characteristics of CpG sites selected by LASSO

CG_ID	Gene_Symbol	CG_Chromosome_location	Position_to_TSS	CGI_Coordinate	Feature_Type
cg00496102	RP5-1159O4.1	chr7: 7,565,607–7,565,608	TSS1500	chr7:7,566,741–7,567,392	N_Shore
cg02893550	CTD-2555A7.2	chr16: 89,053,010–89,053,011	TSS200	chr16:89,052,898–89,053,256	Island
cg03482458	GTSE1-AS1	chr22: 46,296,314–46,296,315	TSS1500	chr22:46,296,313–46,297,452	Island
cg06313119	FGF14-AS2	chr13: 102,394,386–102,394,387	TSS1500	chr13:102,394,330–102,394,876	Island
cg06457534	RP11-201M22.1	chr11: 91,803,313–91,803,314	TSS200	chr11:92,224,469–92,226,866
cg06942685	AC006116.21	chr19: 56,368,063–56,368,064	TSS200	chr19:56,368,048–56,368,626	Island
cg09671962	LINC01122	chr2: 58,428,328–58,428,329	TSS200	chr2:58,428,308–58,428,977	Island
cg14034476	AC005786.5	chr19: 3,556,720–3,556,721	TSS1500	chr19:3,556,964–3,558,295	N_Shore
cg14245102	MEG3	chr14: 100,826,630–100,826,631	TSS1500	chr14:100,826,526–100,826,764	Island
cg15736169	LINC00403	chr13: 112,106,711–112,106,712	TSS1500	chr13:112,106,551–112,106,799	Island
cg19930288	WWC2-AS2	chr4: 183,100,149–183,100,150	TSS1500	chr4:183,097,677–183,100,226	Island
cg21741562	LINC00506	chr3: 87,089,237–87,089,238	TSS200	chr3:87,089,075–87,089,396	Island
cg22408108	AC091801.1	chr7: 3,175,654–3,175,655	TSS1500	chr7:3,300,722–3,302,101
cg23643814	RP11-74E22.8	chr17: 2,724,291–2,724,292	TSS1500	chr17:2,724,007–2,725,008	Island
cg23679434	CTB-83J4.1	chr19: 54,224,165–54,224,166	TSS1500	chr19:54,207,238–54,207,507
cg24514600	PVT1	chr8: 127,793,168–127,793,169	TSS1500	chr8:127,793,835–127,794,653	N_Shore

CGI, CpG island.

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. 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. 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. (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. Kaplan-Meier analyses with high-risk or low-risk score of methylation beta-values of single CpG site in the classifier

Figure 6. Functional enrichment analysis of lncRNA co-expression genes

1. Gene Oncology (GO) enrichment

2. KEGG pathway enrichment.