Multi-Omics Analysis Based on Integrated Genomics, Epigenomics and Transcriptomics in Pancreatic Cancer

Abstract

Aim: Integrated analysis of genomics, epigenomics, transcriptomics and clinical information contributes to identify specific molecular subgroups and find novel biomarkers for pancreatic cancer. Materials & methods: The DNA copy number variation, the simple nucleotide variation, methylation and mRNA data of pancreatic cancer patients were obtained from The Cancer Genome Atlas. Four molecular subgroups (iC1, iC2, iC3 and iC4) of pancreatic cancer were identified by integrating analysis. Results: The iC1 subgroup harbors better prognosis, higher immune score, lesser DNA copy number variation mutations and better genomic stability compared with iC2, iC3 and iC4 subgroups. Three new genes ( GRAP2, ICAM3 and A2ML1) correlated with prognosis were identified. Conclusion: Integrated multi-omics analysis provides fresh insight into molecular classification of pancreatic cancer, which may help discover new prognostic biomarkers and reveal the underlying mechanism of pancreatic cancer.

A Prognostic Prediction Model Developed Based on Four CpG Sites and Weighted Correlation Network Analysis Identified DNAJB1 as a Novel Biomarker for Pancreatic Cancer

“…Previous studies have proposed various risk stratification models for the diagnosis, prognosis, and recurrence of pancreatic cancer, which exhibited better efficiency than the classical TNM stage (43)(44)(45). The rapid development of sequencing techniques has enabled the access to multi-omics data and high-quality clinical information through different databases, such as TCGA, ICGC, and Gene Expression Omnibus (17,46,47). These resources provide novel insights into the initiation and progression of multiple cancers.…”

“…In the RNA-Seq data, the genes with missing values in >50% of the total samples were deleted. The silent mutation and mutation in the intron region of single nucleotide variation data were deleted (17). The detailed information of the pancreatic cancer samples obtained from TCGA and ICGC databases is shown in Supplementary Tables 1, 2, respectively.…”

Prognostic value of Glypican family genes in early-stage pancreatic ductal adenocarcinoma after pancreaticoduodenectomy and possible mechanisms

“…For pancreatic cancer, the transcription factor, hif-2α, can speed up metabolism and promote tumor proliferation and high level of hif-2α correlates with worse patients OS (61,62). Methylation status of GRAP2, ICAM3, A2ML1, MUC1 and MUC4 can in uence expression of these genes, which is associated with survival of pancreatic cancer (63,64). Phosphatidylserine is related to the apoptosis of pancreatic cancer cells with the intervention of microparticles (65).…”

Prognostic value of Glypican family genes in early-stage pancreatic ductal adenocarcinoma after pancreaticoduodenectomy and possible mechanisms

“…In pancreatic cancer, the transcription factor hif-2α can speed up metabolism and promote tumor proliferation and high level of hif-2α correlates with worse OS (61,62). The methylation status of GRAP2, ICAM3, A2ML1, MUC1, and MUC4 can in uence the expression of these genes, which is associated with survival of pancreatic cancer (63,64). Phosphatidylserine is related to apoptosis of pancreatic cancer cells with the involvement of microparticles (65).…”