Integration of quantitative proteomics and metabolomics reveals tissue hypoxia mechanisms in an ischemic-hypoxic rat model

Tissues hypoxia caused by hemorrhage is a common complication in many clinical diseases. However, its pathological mechanism remains largely unknown. To partly address this issue, an ischemic-hypoxic rat model was established and the plasma proteomic and metabolic profiles were quantified and analyzed using TMT-based quantitative proteomics and metabolomics. The analysis revealed a total of 177 differentially expressed proteins and 32 metabolites that were uniquely altered in the hypoxic rat plasma, compared to the control. Bioinformatics analysis showed that these altered proteins and metabolites were involved in a wide range of biological processes. Twelve of the 177 differentially expressed proteins were involved in PI3K-Akt signaling, a pathway that has been reported to be strongly associated with tissue hypoxia. Other signaling pathways such as complement and coagulation cascades, GnRH signaling, relaxin signaling, protein processing in endoplasmic reticulum, as well as AGE-RAGE signaling were markedly altered in the ischemic-hypoxic response, implying their potential roles in tissue hypoxia. A joint analysis of proteome and metabolome showed that the significantly altered metabolites such as guanine, tryptamine, dopamine, hexadecenoic, l-methionine, and fumarate may have participated in the pathogenesis of tissue hypoxia. Further, we found that changes in the levels of metabolites matched the changes in protein abundance within the same pathway. Overall, this study presents an overview of the molecular networks in ischemic-hypoxic pathology and offers biochemical basis for further study on the mechanism of tissue hypoxia. We employed an integrated metabonomic-proteomic method to systematically analyze the profiles of metabolites and proteins in an ischemic-hypoxic rat model. Bioinformatics and enrichment analysis showed that the differentially expressed proteins were mainly involved in complement and coagulation cascades, PI3K-Akt signaling, GnRH signaling, relaxin signaling, protein processing in endoplasmic reticulum, and AGE-RAGE signaling. Moreover, a panel of 12 candidate proteins involved in PI3K-Akt signaling (i.e., Vtn, Hsp90b1, Ywhae, Tnc, Ywhaz, Thbs4, Lamc1, Col1a1, Il2rg, Egfr, Newgene 621,351, and Tfrc) may serve as the potential biomarkers to predict tissue hypoxia.