Genome-wide Analysis Of Cell-free DNA Methylation Profiling For The Early Diagnosis Of Pancreatic Cancer

Pancreatic cancer is one of the most malicious cancers in the world which takes about 18 years to develop from early gene mutation,carcinogenesis to invasive pancreatic cancer.This provides a wide time frame for early pancreatic cancer detection.Patients are of no any early symptom until advanced stage,leading to the hard challenge of being detected at early stage.Almost 80% pancreatic ductal adenocarcinoma(PDAC)patients are of no any early symptom until advanced stage with a 5-year survival as low as 9%.Therefore,it would be important to identify both sensitive and specific biomarkers for screening high risk groups of pancreatic cancer patients.In recent years,circulating cell-free DNA(cf DNA)methylation detection attracts much more attention for noninvasive and early cancer diagnosis.We performed a genome-wide cf DNA methylation profiling study of pancreatic cancer patients by methylated DNA immunoprecipitation coupled with high-throughput sequencing(Me DIP-seq).There were 775 differentially methylated regions(DMRs)locating in promoter regions were identified in pancreatic cancer patients with 761 hypermethylated and 14 hypomethylated regions;meanwhile,761 DMRs in CpG islands(CGIs)were identified in PDAC patients which contained 27 hypomethylated and 734 hypermethylated regions(p-value < 0.0001).143 hypermethylated DMRs were further selected which located in promoter regions and completely overlapped with CGIs.In order to obtain markers for pancreatic cancer diagnosis,we annotated 143 DMRs to 131 probes on an Illumina HM450 K Bead Chip Array.Then,696 cases of Illumina methylation data were downloaded from TCGA and GEO databases,including 339 patients with pancreatic cancer and 357 healthy individuals.After performing the least absolute shrinkage and selection operator(LASSO)method,a total of 8 probes from 8 genes were found to fairly distinguish PDAC patients from the healthy individuals,including TRIM73,FAM150 A,EPB41L3,SIX3,MIR663,MAPT,LOC100128977 and LOC100130148.In addition,we used bisulfite sequencing PCR(BSP)to preliminarily verify the practical diagnostic ability of 8 biomarkers.The results showed that 8 methylation biomarkers in pancreatic cancer patients and normal people did exist differences.In brief,this work identified a set of 8 differentially methylated markers which may be potentially applied in invasive diagnosis of pancreatic cancer.