Proteogenomic characterization of pancreatic ductal adenocarcinoma.

Academic Article

Abstract

  • Pancreatic ductal adenocarcinoma (PDAC) is a highly aggressive cancer with poor patient survival. Toward understanding the underlying molecular alterations that drive PDAC oncogenesis, we conducted comprehensive proteogenomic analysis of 140 pancreatic cancers, 67 normal adjacent tissues, and 9 normal pancreatic ductal tissues. Proteomic, phosphoproteomic, and glycoproteomic analyses were used to characterize proteins and their modifications. In addition, whole-genome sequencing, whole-exome sequencing, methylation, RNA sequencing (RNA-seq), and microRNA sequencing (miRNA-seq) were performed on the same tissues to facilitate an integrated proteogenomic analysis and determine the impact of genomic alterations on protein expression, signaling pathways, and post-translational modifications. To ensure robust downstream analyses, tumor neoplastic cellularity was assessed via multiple orthogonal strategies using molecular features and verified via pathological estimation of tumor cellularity based on histological review. This integrated proteogenomic characterization of PDAC will serve as a valuable resource for the community, paving the way for early detection and identification of novel therapeutic targets.
  • Authors

    Published In

  • Cell  Journal
  • Keywords

  • CPTAC, KRAS, endothelial cell, glycoproteins, immune-cold tumors, kinase inhibitors, neoplastic cellularity, pancreatic ductal adenocarcinoma, proteogenomics, tumor subtyping, Adenocarcinoma, Adult, Aged, Aged, 80 and over, Algorithms, Carcinoma, Pancreatic Ductal, Cohort Studies, Endothelial Cells, Epigenesis, Genetic, Female, Gene Dosage, Genome, Human, Glycolysis, Glycoproteins, Humans, Male, Middle Aged, Molecular Targeted Therapy, Pancreatic Neoplasms, Phenotype, Phosphoproteins, Phosphorylation, Prognosis, Protein Kinases, Proteogenomics, Proteome, Substrate Specificity, Transcriptome
  • Digital Object Identifier (doi)

    Author List

  • Cao L; Huang C; Cui Zhou D; Hu Y; Lih TM; Savage SR; Krug K; Clark DJ; Schnaubelt M; Chen L
  • Start Page

  • 5031
  • End Page

  • 5052.e26
  • Volume

  • 184
  • Issue

  • 19