Survival Analysis of Multi-Omics Data Identifies Potential Prognostic Markers of Pancreatic Ductal Adenocarcinoma

被引:49
|
作者
Mishra, Nitish Kumar [1 ]
Southekal, Siddesh [1 ]
Guda, Chittibabu [1 ]
机构
[1] Univ Nebraska Med Ctr, Dept Genet Cell Biol & Anat, Omaha, NE 68198 USA
基金
美国国家卫生研究院;
关键词
Dm-CpG: Differentially methylated CpG; DMR: differentially methylated region; DEG: differentially expressed gene; HR: hazard ratio; TCGA: The Cancer Genome Atlas; GDC: The Genomic Data Commons; FDR: false discovery rate; PROMOTES CELL-PROLIFERATION; CPG ISLAND METHYLATION; GENOME-WIDE ANALYSIS; DNA METHYLATION; BREAST-CANCER; R PACKAGE; EXPRESSION; GENE; METASTASIS; OVEREXPRESSION;
D O I
10.3389/fgene.2019.00624
中图分类号
Q3 [遗传学];
学科分类号
071007 ; 090102 ;
摘要
Pancreatic ductal adenocarcinoma (PDAC) is the most common and among the deadliest of pancreatic cancers. Its 5-year survival is only similar to 8%. Pancreatic cancers are a heterogeneous group of diseases, of which PDAC is particularly aggressive. Like many other cancers, PDAC also starts as a pre-invasive precursor lesion (known as pancreatic intraepithelial neoplasia, PanIN), which offers an opportunity for both early detection and early treatment. Even advanced PDAC can benefit from prognostic biomarkers. However, reliable biomarkers for early diagnosis or those for prognosis of therapy remain an unfulfilled goal for PDAC. In this study, we selected 153 PDAC patients from the TCGA database and used their clinical, DNA methylation, gene expression, and micro-RNA (miRNA) and long non-coding RNA (IncRNA) expression data for multi-omics analysis. Differential methylations at about 12,000 CpG sites were observed in PDAC tumor genomes, with about 61% of them hypermethylated, predominantly in the promoter regions and in CpG-islands. We correlated promoter methylation and gene expression for mRNAs and identified 17 genes that were previously recognized as PDAC biomarkers. Similarly, several genes (B3GNT3, DMBT1, DEPDC1B) and IncRNAs (PVT1, and GATA6-AS) are strongly correlated with survival, which have not been reported in PDAC before. Other genes such as EFR3B, whose biological roles are not well known in mammals are also found to strongly associated with survival. We further identified 406 promoter methylation target loci associated with patients survival, including known esophageal squamous cell carcinoma biomarkers, cg03234186 (ZNF154), and cg02587316, cg18630667, and cg05020604 (ZNF382). Overall, this is one of the first studies that identified survival associated genes using multi-omics data from PDAC patients.
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页数:18
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