Quantitative analysis of the mitochondrial proteome in human ovarian carcinomas

Abstract

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.

Mitochondrial Proteomic and Molecular Network Alterations in Human Ovarian Cancers

“…The proteins were extracted from purified mitochondrial samples for iTRAQ-labeled quantitative proteomic analysis. The detailed procedure was described in our previous publications [14,15].…”

“…The iTRAQ reporter-ion intensities were used to quantify each protein and determine each mtDEPs. The detailed procedure was described in our previous publications [14,15].…”

“…iTRAQ-labeling coupled with SCX-LC-MS/MS identified 5115 proteins in mitochondrial samples prepared from human ovarian cancer and control ovary tissues, with at least one peptide sequence matches (PSMs). All of identified proteins was collected in the supplemental Table 1 in our previous publication [15]. Those 5115 proteins mainly distributed within pI 3.81-12.25 and molecular weight (MW) 2.6-1158.2 kDa, and in multiple cell components including cell junction (0.8%), cell part (42.7%), extracellular matrix (0.6%), macromolecular complex (17.8%), organelle (28.2%), and synapse (0.3%) (Figure 1).…”

“…Therefore, mitochondria play important roles in tumorigenesis, proliferation, angiogenesis, invasiveness, and metastasis of cancer cells [14,15]. Proteins are the important performer in maintaining mitochondrial morphology and functions.…”

“…Mitochondrial proteomics is an effective approach to systematically investigate the role of mitochondria in ovarian cancer for discovery of reliable mitochondrial protein biomarkers to insight into the molecular mechanism and determination of therapeutic target to mitochondria for ovarian cancers. Quantitative proteomic methods commonly include two-dimensional gel electrophoresis (2DGE) [28,29] or two-dimensional difference in-gel electrophoresis (2D DIGE) [30] comparative proteomics, and gelfree-based quantitative proteomics [14,15], for example, isobaric tags for relative and absolute quantification (iTRAQ ) [31,32], tandem mass tag (TMT) [33], or label-free-based quantitative proteomics [34,35], with different advantages and disadvantages, respectively. Those quantitative proteomic methods can achieve a high-throughput and high-sensitive identification of mitochondrial proteins and post-translational modifications.…”