Dataset of quantitative proteomic analysis to understand aging processes in rabbit liver

Identification of Target Proteins Involved in Cochlear Hair Cell Progenitor Cytotoxicity following Gentamicin Exposure

Given the non-labile, terminal differentiation of inner-ear sensory cells, preserving their function is critical since sensory cell damage results in irreversible hearing loss. Gentamicin-induced cytotoxicity is one of the major causes of sensory cell damage and consequent sensorineural hearing loss. However, the precise molecular mechanisms and target proteins involved in ototoxicity are still unknown. The objective of the present study was to identify target proteins involved in gentamicin-induced cytotoxicity to better characterize the molecular pathways involved in sensory cell damage following ototoxic drug administration using House Ear Institute-Organ of Corti 1 (HEI-OC1) cells and high-performance liquid chromatography coupled with tandem mass spectrometry (HPLC-MS/MS). We identified several unique proteins involved in gentamicin-induced cytotoxicity, expression of which were further confirmed using confocal microscopy. Further investigation of these pathways can inform the design and discovery of novel treatment modalities to prevent sensory cell damage and preserve their function.

Plasma proteome profiling using tandem mass tag labeling technology reveals potential biomarkers for Parkinson's disease: a preliminary study

PURPOSE

Parkinson's disease (PD) is the second most frequently occurring progressive neurodegenerative disorder. Biomarkers are useful indicators for tracking disease progression, early diagnosis, and intervention of disease progression. We aimed to develop plasma biomarker panel which maybe aid to predict the onset and progression of PD.

EXPERIMENTAL DESIGN

Tandem mass tag (TMT) mass spectrometry was applied using an Orbitrap Lumos mass spectrometer to analyze plasma protein expression in patients diagnosed with PD and healthy controls.

RESULTS

In total, 555 proteins were quantified. Using a cut-off of p < 0.05 and a fold change of >1.2 for the variation in expression, 25 proteins were differentially expressed between the PD and control groups. Sixteen proteins were upregulated and nine were downregulated. Several proteins, including Chitinase-3-like protein 1 (CHI3L1) and thymosin beta-4 (TMSB4X) were implicated in PD pathogenesis.

CONCLUSIONS

The data from the TMT-based proteomic profiling of plasma samples in PD may help advance the understanding of the molecular mechanisms of PD and identify potential novel biomarkers of PD for further characterization.

Proteomic Analysis of Hypoxia-Induced Senescence of Human Bone Marrow Mesenchymal Stem Cells

Methods

Hypoxia in hBMSCs was induced for 0, 4, and 12 hours, and cellular senescence was evaluated by senescence-associated β-galactosidase (SA-β-gal) staining. Tandem mass tag (TMT) labeling was combined with liquid chromatography-tandem mass spectrometry (LC-MS/MS) for differential proteomic analysis of hypoxia in hBMSCs. Parallel reaction monitoring (PRM) analysis was used to validate the candidate proteins. Verifications of signaling pathways were evaluated by western blotting. Cell apoptosis was evaluated using Annexin V/7-AAD staining by flow cytometry. The production of reactive oxygen species (ROS) was detected by the fluorescent probe 2,7-dichlorodihydrofluorescein diacetate (DCFH-DA).

Results

Cell senescence detected by SA-β-gal activity was higher in the 12-hour hypoxia-induced group. TMT analysis of 12-hour hypoxia-induced cells identified over 6000 proteins, including 686 differentially expressed proteins. Based on biological pathway analysis, we found that the senescence-associated proteins were predominantly enriched in the cancer pathways, PI3K-Akt pathway, and cellular senescence signaling pathways. CDK1, CDK2, and CCND1 were important nodes in PPI analyses. Moreover, the CCND1, UQCRH, and COX7C expressions were verified by PRM. Hypoxia induction for 12 hours in hBMSCs reduced CCND1 expression but promoted ROS production and cell apoptosis. Such effects were markedly reduced by the PI3K agonist, 740 Y-P, and attenuated by LY294002.

Conclusions

Hypoxia of hBMSCs inhibited CCND1 expression but promoted ROS production and cell apoptosis through activating the PI3K-dependent signaling pathway. These findings provided a detailed characterization of the proteomic profiles related to hypoxia-induced senescence of hBMSCs and facilitated our understanding of the molecular mechanisms leading to stem cell senescence.