Integrating SWATH‐MS proteomics and transcriptome analysis to preliminarily identify three DEGs as biomarkers for proliferative diabetic retinopathy

Wu, Haijian; Wang, Dongguo; Zheng, Qianyin; Zhiwei, Xu

doi:10.1002/prca.202100016

Cited by 7 publications

(3 citation statements)

References 39 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…In the study by Wu et al, FCGR3A was identified as a potential biomarker for patients with PDR. FCGR3A is a member of the FCGR family of plasma proteins 51 . MAPK-related pathways are currently a hot topic in DR research.…”

Section: Discussionmentioning

confidence: 99%

Exploration of potential novel drug targets for diabetic retinopathy by plasma proteome screening

Yuan,

Xu,

et al. 2024

Sci Rep

View full text Add to dashboard Cite

The aim of this study is to identify novel potential drug targets for diabetic retinopathy (DR). A bidirectional two-sample Mendelian randomization (MR) analysis was performed using protein quantitative trait loci (pQTL) of 734 plasma proteins as the exposures and clinically diagnosed DR as the outcome. Genetic instruments for 734 plasma proteins were obtained from recently published genome-wide association studies (GWAS), and external plasma proteome data was retrieved from the Icelandic Decoding Genetics Study and UK Biobank Pharma Proteomics Project. Summary-level data of GWAS for DR were obtained from the Finngen Consortium, comprising 14,584 cases and 202,082 population controls. Steiger filtering, Bayesian co-localization, and phenotype scanning were used to further verify the causal relationships calculated by MR. Three significant (p < 6.81 × 10−5) plasma protein-DR pairs were identified during the primary MR analysis, including CFH (OR = 0.8; 95% CI 0.75–0.86; p = 1.29 × 10−9), B3GNT8 (OR = 1.09; 95% CI 1.05–1.12; p = 5.9 × 10−6) and CFHR4 (OR = 1.11; 95% CI 1.06–1.16; p = 1.95 × 10−6). None of the three proteins showed reverse causation. According to Bayesian colocalization analysis, CFH (coloc.abf-PPH4 = 0.534) and B3GNT8 (coloc.abf-PPH4 = 0.638) in plasma shared the same variant with DR. All three identified proteins were validated in external replication cohorts. Our research shows a cause-and-effect connection between genetically determined levels of CFH, B3GNT8 and CFHR4 plasma proteins and DR. The discovery implies that these proteins hold potential as drug target in the process of developing drugs to treat DR.

show abstract

Section: Discussionmentioning

confidence: 99%

Exploration of potential novel drug targets for diabetic retinopathy by plasma proteome screening

Yuan,

Xu,

et al. 2024

Sci Rep

View full text Add to dashboard Cite

show abstract

“…The early detection of PDR is a challenge that has not yet been overcome in clinical work, and this is due to there being a lack of a simple, rapid, and specific molecular markers to detect the progression of PDR. In the plasma of PDR patients, a total of 23 upregulated and 13 downregulated proteins were found, with FCGR3A, DPEP2, and ADGRF5 identified as potential protein markers in the plasma [ 93 ]. Wang et al [ 85 ] used RP-HPLC and ESI-MS/MS to detect 96 differentially expressed proteins, 37 upregulated proteins, and 59 downregulated proteins in the vitreous of PDR patients.…”

Section: Application Of Proteomics In Optic Nerve Injury Diseasesmentioning

confidence: 99%

Application of Proteomics Analysis and Animal Models in Optic Nerve Injury Diseases

et al. 2023

View full text Add to dashboard Cite

Optic nerve damage is a common cause of blindness. Optic nerve injury is often accompanied by fundus vascular disease, retinal ganglion cell apoptosis, and changes in retinal thickness. These changes can cause alterations in protein expression within neurons in the retina. Proteomics analysis offers conclusive evidence to decode a biological system. Furthermore, animal models of optic nerve injury made it possible to gain insight into pathological mechanisms, therapeutic targets, and effective treatment of such injuries. Proteomics takes the proteome as the research object and studies protein changes in cells and tissues. At present, a variety of proteomic analysis methods have been widely used in the research of optic nerve injury diseases. This review summarizes the application of proteomic research in optic nerve injury diseases and animal models of optic nerve injury. Additionally, differentially expressed proteins are summarized and analyzed. Various optic nerve injuries, including those associated with different etiologies, are discussed along with their potential therapeutic targets and future directions.

show abstract

“…Previous reports suggest that DPEP2 acts as an inflammatory regulator of macrophages and may have a protective effect against CVB3-induced viral myocarditis [ 12 ]. DPEP2 has also been identified as a potential biomarker for diabetic retinopathy [ 13 ]. In respiratory diseases, DPEP2 has been implicated in chronic rhinitis, sinusitis, and asthma [ 14 ].…”

Section: Introductionmentioning

confidence: 99%

Integrated Single-Cell and Transcriptome Sequencing Analyses Identify Dipeptidase 2 as an Immune-Associated Prognostic Biomarker for Lung Adenocarcinoma

Zhang

Gao

et al. 2023

Pharmaceuticals

View full text Add to dashboard Cite

Dipeptidase 2 (DPEP2) is a dipeptidyl peptidase that plays an important role in the hydrolysis of leukotriene D4 (LTD4) to leukotriene E4 (LTE4). Previous studies have suggested that LTD4 promotes tumor progression and survival in non-small cell lung cancer (NSCLC). Therefore, we hypothesized that DPEP2 may play a pivotal role in this tumor. Given that lung adenocarcinoma (LUAD) is the most common subtype of NSCLC, our study aimed to examine the expression and function of DPEP2 in LUAD. Based on bioinformatics and the analysis of clinical samples, our findings revealed that DPEP2 is highly expressed in normal lung tissues, but downregulated in LUAD tissues, and its expression levels were significantly associated with clinical indicators of tumor grade and prognosis. Pathway enrichment analysis showed that DPEP2 is involved in biological processes such as chemokine signaling pathways, leukocyte trans-endothelial migration, and humoral immune responses in LUAD. In addition, DPEP2 expression was significantly associated with various immune cells, especially monocytes–macrophages. Single-cell transcriptome data further confirmed the expression of DPEP2 dominantly in macrophages from normal lung tissues. Analysis of the TCIA database revealed that high DPEP2 expression is associated with a stronger response to immune checkpoint inhibitors such as CTLA4 and PD1, and determines sensitivity to LUAD therapeutic agents. Furthermore, we found that DPEP2 inhibits the migration and invasion of LUAD cells. Therefore, DPEP2 may serve as a potential immune biomarker and therapeutic target for LUAD, providing novel therapeutic approaches for this disease.

show abstract

Integrating SWATH‐MS proteomics and transcriptome analysis to preliminarily identify three DEGs as biomarkers for proliferative diabetic retinopathy

Abstract: Purpose:We intended to preliminarily find differentially expressed proteins that play crucial roles in proliferative diabetic retinopathy (PDR), and lay the foundation for subsequent further research on the mechanism.

Cited by 7 publications

References 39 publications

Exploration of potential novel drug targets for diabetic retinopathy by plasma proteome screening

Exploration of potential novel drug targets for diabetic retinopathy by plasma proteome screening

Application of Proteomics Analysis and Animal Models in Optic Nerve Injury Diseases

Integrated Single-Cell and Transcriptome Sequencing Analyses Identify Dipeptidase 2 as an Immune-Associated Prognostic Biomarker for Lung Adenocarcinoma

Contact Info

Product

Resources

About