4D label-free proteomic analysis of vitreous from patients with rhegmatogenous retinal detachment

Abstract

AIM: To identify metabolites, proteins, and related pathways involved in the etiology of rhegmatogenous retinal detachment (RRD) for use as biomarkers in diagnosing and treating RRD. METHODS: Vitreous specimens were collected and liquid chromatography-tandem mass spectrometry analysis was performed using the four-dimensional label-free technique. Statistically significant differentially expressed proteins, gene ontology (GO) terms, Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway representations, and protein interactions were analyzed. RESULTS: Nine specimens were subjected to proteomic analysis. In total, 161 proteins were identified as differentially expressed proteins (DEPs), including 53 upregulated proteins and 108 downregulated proteins. GO functional analysis revealed that some DEPs were enriched in neuron-related terms and membrane protein terms. Moreover, KEGG analysis indicated that the cell adhesion molecule metabolic pathway was associated with the greatest number of DEPs. Finally, the evaluation of protein-protein interaction network revealed that DEPs were clustered in neuronal adhesion, apoptosis, inflammation and immune responses, correct protein folding, and glycolysis. CONCLUSION: Proteomic profiling is useful for the exploration of molecular mechanisms that underlie RRD. This study reveals increased expression levels of proteins related to heat shock protein content, glycolysis, and inflammatory responses in RRD. Knowledge regarding biomarkers of RRD pathogenesis may help to prevent the occurrence of RRD in the future.

Integrated 4D label-free proteomics and data mining to elucidate the effects of thermal processing on crisp grass carp protein profiles

“…7 mm, volume 3 ml, Sigma), concentrated by vacuum centrifugation, and reconstituted in 40 μl of 0.1% (v/v) formic acid. The peptide content was estimated by the UV light spectral density at 280 nm ( Huo et al, 2023 ).…”

“…The integrated application of this technology not only greatly expands the coverage and resolution of protein detection but also enhances the dynamic range of analysis through improvements in time and spatial resolution, allowing researchers to capture subtle changes in protein expression. These changes could be key indicators of environmental stress ( Wang et al, 2021b ), changes in nutritional status ( Wang et al, 2023 ), or disease progression ( Huo et al, 2023 ). 4D label-free proteomics technology provides us with an unprecedented macroscopic perspective to comprehensively understand the biological traits of CGC at the protein level.…”

Proteomic study of vitreous in proliferative diabetic retinopathy patients after treatment with aflibercept: a quantitative analysis based on 4D label-free technique

“…The purpose of this experiment is to address the problem of drug resistance after the widespread use of anti-VEGF therapeutic drugs. In our previous experiments, we have analyzed the vitreous fluid samples of patients with foramen ovale retinal detachment by 4D-DIA, and found that DEPs were mainly enriched in the cell adhesion pathway compared with the control group, and that DEPs were associated with the heat shock protein content, glycolysis, and acute inflammatory processes, which provided a reference for finding biomarkers for the pathogenesis of rhegmatogenous retinal detachment [9] . DDA technique, which is capable of capturing information on all acquired ions, reduces randomness in the detection process, has higher reproducibility and stability, and increased accuracy.…”