DIA Comparative Proteomic Analysis of Retro-oil Fluid and Vitreous Fluid From Retinal Detachment Patients

Shu, Yiyang; Gao, Min; Zhou, Yifan; Liu, Haiyun; Sun, Xiaodong

doi:10.3389/fmolb.2021.763002

Cited by 8 publications

(3 citation statements)

References 27 publications

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“…Proteins related to the reorganization of cell adhesion molecules and apoptosis were upregulated in RRD [16] . Other studies have shown that the proteins neurexin, selectin, and neuronal cell adhesion molecule were significantly downregulated in patients with RRD, compared with controls [17] . After the onset of RRD, retinal pigment epithelium cells lose their epithelial properties and form fibrous membranes on the retinal surface [18] .…”

Section: Protein-protein Interaction Networkmentioning

confidence: 85%

“…Elevated levels of α-enolase and upregulation of glycolysis were observed in extracts from rabbits with retinal detachment [31] . The hypoxia-inducible factor (HIF)-1 signaling pathway and glycolytic metabolism were enriched in human vitreous humor [17] . Other studies have shown that glycolysis, photoreceptor death, and Wnt and mitogenactivated protein kinase (MAPK) signaling are activated during RRD; these pathways promote retinal cell survival.…”

Section: Protein-protein Interaction Networkmentioning

confidence: 99%

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

Huo¹,

Yang²,

Wang³

et al. 2023

Int J Ophthalmol

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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.

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Section: Protein-protein Interaction Networkmentioning

confidence: 85%

Section: Protein-protein Interaction Networkmentioning

confidence: 99%

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

Huo¹,

Yang²,

Wang³

et al. 2023

Int J Ophthalmol

View full text Add to dashboard Cite

show abstract

“…Recent advances in mass spectrometry instrumentation and analytical tools have increased sensitivity in complex clinical matrices and enabled more robust label-free quantitation [29][30][31][32][33][34]. To deeply profile the human fecal proteome, proteins were extracted from stool, proteolytically digested, and resulting peptides were quantified using a data-independent acquisition LC-MS/MS (DIA-MS) approach.…”

Section: Introductionmentioning

confidence: 99%

Comprehensive Profiling of the Human Fecal Proteome from IBD Patients with DIA-MS Enables Evaluation of Disease-Relevant Proteins

Harder,

Lekkerkerker,

Casavant

et al. 2024

Preprint

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Inflammatory bowel disease (IBD), which includes ulcerative colitis (UC) and Crohn’s disease (CD), is characterized by chronic gastrointestinal inflammation. A high unmet need exists for non-invasive biomarkers in IBD to detect mucosal inflammation to monitor changes in disease severity and guide treatment decisions. Fecal proteomics has the potential to allow frequent, non-invasive monitoring of biomarkers in stool of IBD patients, however the fecal proteome remains under explored. Here a data-independent acquisition LC-MS/MS approach was used to profile the human fecal proteome in two independent cohorts of IBD patients and healthy controls (HC) to identify non-invasive biomarkers reflective of disease activity. 688 human proteins were quantified, with 523 measured in both cohorts. In UC stool 96 proteins were differentially abundant and in CD stool 126 proteins were differentially abundant compared to HC stool (absolute log2 fold change >1, p-value <0.05). Many of these fecal proteins are associated with infiltrating immune cells and ulceration/rectal bleeding, which are hallmarks of IBD pathobiology. Mapping of the identified fecal proteins to a whole blood single-cell RNA sequencing data set revealed the involvement of various immune cell subsets to the IBD fecal proteome. Findings from this study not only confirmed the presence of established fecal biomarkers for IBD, such as calprotectin and lactoferrin, but also revealed new fecal proteins from multiple pathways known to be dysregulated in IBD. These novel proteins could serve as potential non-invasive biomarkers to monitor specific aspects of IBD disease activity which could expedite clinical development of novel therapeutic targets.

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Comprehensive profiling of the human fecal proteome from IBD patients with DIA‐MS enables evaluation of disease‐relevant proteins

Harder,

Lekkerkerker,

Casavant

et al. 2024

Proteomics Clinical Apps

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PurposeInflammatory bowel disease (IBD), which includes ulcerative colitis (UC) and Crohn's disease (CD), is characterized by chronic gastrointestinal inflammation. A high unmet need exists for noninvasive biomarkers in IBD to monitor changes in disease activity and guide treatment decisions. Stool is an easily accessed, disease proximal matrix in IBD, however the composition of the IBD fecal proteome remains poorly characterized.Experimental DesignA data‐independent acquisition LC‐MS/MS approach was used to profile the human fecal proteome in two independent cohorts (Cohort 1: healthy n = 5, UC n = 5, CD n = 5, Cohort 2: healthy n = 20, UC n = 10, and CD n = 10) to identify noninvasive biomarkers reflective of disease activity.Results688 human proteins were quantified, with 523 measured in both cohorts. In UC stool 96 proteins were differentially abundant and in CD stool 126 proteins were differentially abundant compared to healthy stool (absolute log2 fold change > 1, p‐value < 0.05). Many of these fecal proteins are associated with infiltrating immune cells and ulceration/rectal bleeding, which are hallmarks of IBD pathobiology. Mapping the identified fecal proteins to a whole blood single‐cell RNA sequencing data set revealed the involvement of various immune cell subsets to the IBD fecal proteome.Conclusions and Clinical RelevanceFindings from this study not only confirmed the presence of established fecal biomarkers for IBD, such as calprotectin and lactoferrin, but also revealed new fecal proteins from multiple pathways known to be dysregulated in IBD. These novel proteins could serve as potential noninvasive biomarkers to monitor specific aspects of IBD disease activity which could expedite clinical development of novel therapeutic targets.

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DIA Comparative Proteomic Analysis of Retro-oil Fluid and Vitreous Fluid From Retinal Detachment Patients

Cited by 8 publications

References 27 publications

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

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

Comprehensive Profiling of the Human Fecal Proteome from IBD Patients with DIA-MS Enables Evaluation of Disease-Relevant Proteins

Comprehensive profiling of the human fecal proteome from IBD patients with DIA‐MS enables evaluation of disease‐relevant proteins

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