Dong-Gi Mun, Jinhyuk Bhin, Sangok Kim, Hyunwoo Kim, Jae Hun Jung, et al., Cancer Cell (2019) Vol. 35, Issue 1, p111-124 https://doi.org/10.1016/j.ccell.2018.12.003
We report proteogenomic analysis of diffuse gastric cancers (GCs) in young population. Phosphoproteome data elucidated signaling pathways associated with somatic mutations based on mutation-phosphorylation correlations. Moreover, correlations between mRNA and protein abundances provided potential oncogenes and tumor suppressors associated with patient survival. Furthermore, integrated clustering of mRNA, protein, phosphorylation, and N-glycosylation data identified four subtypes of diffuse GCs. Distinguishing these subtypes was possible by proteomic data. Four subtypes were associated with proliferation, immune response, metabolism, and invasion, respectively; and associations of the subtypes with immune- and invasion-related pathways were identified mainly by phosphorylation and N-glycosylation data. Therefore, our proteogenomic analysis provides additional information beyond genomic analyses, which can improve understanding of cancer biology and patient stratification in diffuse GCs.
Mass Spectrometry Data Sets, Provided Below
Peptides from tumor and adjacent normal tissues of early-onset gastric cancer (EOGC) patients were labeled with 4-plex iTRAQ reagent (AB Sciex) according to the manufacturer’s instructions. For each of the first 50 patients, two independent biological replicates of peptide samples from the pair of tumor and adjacent normal tissues were merged into one peptide pool (i.e., 800 µg/replicate), respectively, and each of two 800 µg samples of normal and tumor peptides was labeled with 114/116 and 115/117 iTRAQ reagents, respectively. For the rest 30 patients, the peptide samples for two pairs of tumor and adjacent normal tissues from two patients were merged into one peptide pool (800 µg each), respectively. The normal and tumor peptides of a patient were labeled with 114 and 115 iTRAQ reagents, respectively, while the normal and tumor peptides of another patient were labeled with 116 and 117 iTRAQ reagents.
There are a total of 65 iTRAQ experiments for global proteome analyses (3.48 TB raw data, 1560 files), 65 iTRAQ experiments for phosphoprotome (1.19 TB raw data, 780 files) and glycoproteome (1.35 TB raw data, 779 files).
EOGC (early-onset gastric cancer) Patient Samples
iTRAQ Mass Spectrometry Patient SampleID Mapping
NCBI GEO (Gene Expression Omnibus): Patient sample ID mapping for genomic data
NCBI BioProject PRJNA508414; GEO: GSE122401
NCBI SRA (Sequence Read Archive) Study: Transcriptome Analysis
NCBI SRA Run Selector: Patient sample clinical table
(ALL): Selection of this box downloads all data in the row
(raw): The original mass spectrometry(MS) instrument files
(mzML): HUPO-PSI standard raw data files generated from the original MS instrument files
(PSM): Peptide-Spectrum Match data