Mitochondria play important roles in growth, signal transduction, division, tumorigenesis and energy metabolism in epithelial ovarian carcinomas (EOCs) without an effective biomarker. To investigate the proteomic profile of EOC mitochondrial proteins, a 6-plex isobaric tag for relative and absolute quantification (iTRAQ) proteomics was used to identify mitochondrial expressed proteins (mtEPs) in EOCs relative to controls, followed by an integrative analysis of the identified mtEPs and the Cancer Genome Atlas (TCGA) data from 419 patients. A total of 5115 quantified proteins were identified from purified mitochondrial samples, and 262 proteins were significantly related to overall survival in EOC patients. Furthermore, 63 proteins were identified as potential biomarkers for the development of an EOC, and our findings were consistent with previous reports on a certain extent. Pathway network analysis identified 70 signaling pathways. Interestingly, the results demonstrated that cancer cells exhibited an increased dependence on mitophagy, such as peroxisome, phagosome, lysosome, valine, leucine and isoleucine degradation and fatty acid degradation pathways, which might play an important role in EOC invasion and metastasis. Five proteins (GLDC, PCK2, IDH2, CPT2 and HMGCS2) located in the mitochondrion and enriched pathways were selected for further analysis in an EOC cell line and tissues, and the results confirmed reliability of iTRAQ proteomics. These findings provide a large-scale mitochondrial proteomic profiling with quantitative information, a certain number of potential protein biomarkers and a novel vision in the mitophagy bio-mechanism of a human ovarian carcinoma.
Supplementary Table 1. Proteins identified in epithelial ovarian cancer mitochondria relative to controls. (Mitochondrial protein were obtained in 7 EOC tissues and 11 control ovaries with benign gynecologic diseases and identified with iTRAQ-based quantitative proteomics. PSMs = Peptide sequence matches. MW = Molecular weight. Ratio (T/N) = Ratio of tumors to normal controls )
Supplementary Table 2: Level 3 RNA-seq V2 data obtained from the TCGA database of ovarian cancer patients (n=419).
Supplementary Table 3: Clinical data obtained from the TCGA data of ovarian cancer patients (Overall Survival data were extracted from TCGA database including 419 samples and event=0 means survival status).
Supplementary Table 4: 1108 overall survival-related genes were obtained by TCGA database (Overall Survival survival analysis of genes in ovarian cancer was calculated by the Kaplan-Meier method and compared with the log-rank test with R 3.4.2 virsion.)
Supplementary Table 5: 262 significant proteins obtained by overlapping analysis between 5115 identified proteins and TCGA database ( PSMs = Peptide sequence matches. MW = Molecular weight. Ratio (T/N) = Ratio of tumors to normal controls)
Supplementary Table 6: Protein localization according to biological process (BP) analysis.
Supplementary Table 7: The localization of overlapped proteins according to cellular component (CC).
Supplementary Table 8: A series of molecular functions (MFs) involved in 262 overlapped proteins.
Supplementary Table 9: 992 proteins of 5115 proteins were reported to relate with ovary compared to previous literatures(We searched CooLGeN with key words of ovary or ovarian, to identify studies of related genes on ovary. PSMs = Peptide sequence matches. MW = Molecular weight. Ratio (T/N) = Ratio of tumors to normal controls).
Supplementary Table 10: Protein–protein interactions analysised by STRING.
Supplementary Table 11: The mRNA-mRNA significant correlation between each other.
Supplementary Table 12: Chromosomal location of each significant correlation genes obtained by Ensembl. Ratio (T/N) = Ratio of tumors to normal controls
Supplementary Table 13: KEGG pathway analysis mapped the identified proteins to 70 signaling pathways.