iTRAQ‑based quantitative proteomic analysis and bioinformatics study of proteins in retinoblastoma

Cheng, Yong; Meng, Qingyu; Huang, Lvzhen; Shi, Xuan; Hou, Jing; Li, Xiaoxin; Liang, Jianhong

doi:10.3892/ol.2017.7221

Cited by 5 publications

(9 citation statements)

References 43 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…The samples that were cultivated under optimal conditions were used as a reference to identify the differential expression. We defined DEPs as those up-expressed > 1.2 or down-expressed < 0.8 with a p- value < 0.05 ( t -test, multiple testing correction) under each stress condition, which is the cutoff commonly used for iTRAQ-based proteomics analysis of both prokaryotes and eukaryotes ( Wang et al, 2016 , 2020 ; Cheng et al, 2017 ; Hou et al, 2019 ; Li et al, 2019 ). The details of the specific growth rates, maximum growth yields, and number of DEPs under each condition are presented in Table 1 .…”

Section: Resultsmentioning

confidence: 99%

Cross-Stress Adaptation in a Piezophilic and Hyperthermophilic Archaeon From Deep Sea Hydrothermal Vent

Zhao

Liu

et al. 2020

Front. Microbiol.

View full text Add to dashboard Cite

show abstract

Section: Resultsmentioning

confidence: 99%

Cross-Stress Adaptation in a Piezophilic and Hyperthermophilic Archaeon From Deep Sea Hydrothermal Vent

Zhao

Liu

et al. 2020

Front. Microbiol.

View full text Add to dashboard Cite

show abstract

“…One study examined levels of uric acid 44. Three studies analyzed proteins in AH, including protein concentrations25,31 and protein analysis 27. One study examined the cytokines, chemokines, matrix metalloproteinases, and acute-phase protein concentrations 45.…”

Section: Resultsmentioning

confidence: 99%

“…One study further assessed AH proteins by using the comparative proteomic technique of isobaric tags for relative and absolute quantitation coupled with offline two-dimensional liquid chromatography-tandem mass spectrometry 27. A total of 83 proteins that were expressed differently between the controls and patients' AH samples were identified using isobaric tags for relative and absolute quantitation analysis, including pigment epithelium-derived factor (PEDF) and retinoic acid 6 (STRA6) 27. The study revealed that the expression level of PEDF was lower in Rb than that in control samples.…”

Section: Discussionmentioning

confidence: 99%

“…Following that initial report, further studies explored the various clinicopathological correlations associated with LDH as an AH marker of ocular disease 22,23. Over the past few decades, numerous studies have explored AH in enucleated Rb eyes and have uncovered various markers that may demonstrate clinical value for diagnosis, clinicopathological associations,22,23 monitoring response to treatment,24–26 and possibly serve as targets for therapy 27. However, because all previous studies were from enucleated eyes, clinical correlations were difficult if impossible to make and the role of the AH in management of Rb remained limited.…”

Section: Introductionmentioning

confidence: 99%

See 1 more Smart Citation

Aqueous Humor Markers in Retinoblastoma, a Review

Ghiam

Berry

2019

Trans. Vis. Sci. Tech.

View full text Add to dashboard Cite

Purpose Retinoblastoma (Rb) is the most common primary intraocular cancer in children. Unlike with most solid tumors, direct biopsy is contraindicated due to risk of tumor dissemination. However, recent therapeutic techniques have allowed for the safe extraction of aqueous humor (AH) from eyes undergoing therapy, providing the unique opportunity to use AH as a liquid biopsy for Rb. Although the extraction of AH in Rb eyes undergoing therapy is new, the consideration of whether there are tumor biomarkers in the AH is not. The current manuscript is a systematic review of all studies that have examined biomarkers in the AH of Rb eyes. The authors hypothesized that AH sampling and analysis of tumor biomarkers may have new clinical relevance for the diagnosis, prognosis, and/or management of Rb. Methods A comprehensive database search (PubMed, Web of Science, Embase, and Cochrane Databases) was conducted in accordance with the Preferred Reporting Items for Systematic Reviews and Meta-Analyses statement to identify articles on AH markers in Rb eyes. Inclusion criteria included English language articles with original reports on AH markers in the eyes of patients with confirmed Rb. Data on marker type, number of eyes, marker means and ranges, and when available, control values and clinicopathological correlations were collected. Articles were stratified based on marker type, and assessed quantitatively and qualitatively. Results An initial database search produced 325 articles, and an additional 11 articles were identified through searching citations. After removing duplicates and applying the eligibility criteria, we selected 27 articles to be included in the current review. A total of 463 eyes with histologically confirmed Rb were included in this review. The various markers and their values, with comparison to controls and clinicopathological correlations, are discussed. Conclusions AH sampling and tumor biomarker analysis in eyes without undergoing enucleation have the potential to revolutionize the management of Rb. Translational Relevance Although previous studies evaluated markers in the AH only after enucleation and not at diagnosis or during therapy, the clinical relevance of these markers was limited. However, recent changes in the management of Rb have allowed for safe sampling of the aqueous during therapy and, thus, correlation of tumor biomarkers with disease course. Thus, the authors felt it important to revisit previous research to evaluate whether these markers may now be applicable for the diagnosis, prognosis, or management of Rb

show abstract

“…Cheng et al, on the other hand, analyzed aqueous humour samples from RB patients and compared them with aqueous humour samples from patients without intraocular cancer using the comparative proteomic technique of iTRAQ coupled with offline two-dimensional liquid chromatography-tandem mass spectrometry. A total of 83 proteins were identified to be differentially expressed, of which 44 were upregulated and 39 downregulated in the RB group (22). Assisted by the DAVID bioinformatics resource, protein expression in RB has been implicated in endopeptidase inhibitory activity, peptidase inhibitor, enzyme inhibitor, serine-type endopeptidase inhibitor, structural molecule, lipid binding and carbohydrate binding activities (22).…”

Section: Discussionmentioning

confidence: 99%

Protein profiling of WERI RB1 and etoposide resistant WERI ETOR reveals new insights into topoisomerase inhibitor resistance in retinoblastoma

Kakkassery

Gemoll

Kraemer

et al. 2022

Preprint

View full text Add to dashboard Cite

Chemotherapy resistance is one of the reasons for eye loss in patients with retinoblastoma (RB). RB chemotherapy resistance has been studied in different cell culture models such as WERI RB1. In addition, chemotherapy resistant RB subclones like the etoposide resistant WERI ETOR cell line have been established to improve the understanding of chemotherapy resistance in RB. The objective of this study was to characterize cell line models of an etoposide sensitive WERI RB1 and its etoposide resistant subclone WERI ETOR by proteomic analysis. Subsequently, quantitative proteomic data served for correlation analysis with known drug perturbation profiles. Methodically, WERI RB1 and WERI ETOR were cultured and prepared for quantitative mass spectrometry (MS). This was carried out in a data-independent acquisition (DIA) mode (Sequential Window Acquisition of All Theoretical Mass Spectra, SWATH-MS). The raw SWATH files were processed using neural networks in a library free mode along with machine learning algorithms. Pathway enrichment was performed using the REACTOME pathway resource and correlated to the Molecular Signature Database (MSigDB) hallmark gene set collections for functional annotation. Furthermore, a drug connectivity analysis using the L1000 database was used to correlate the mechanism-of-action (MOA) for different anticancer reagents to WERI RB1/WERI ETOR signatures. A total of 4,756 proteins were identified across all samples, showing a distinct clustering between the groups. Of these proteins, 64 were significantly altered (q < 0.05 & log2FC |>2|, 22% higher in WERI ETOR). Pathway analysis revealed an enriched metabolic pathway for retinoid metabolism and transport in WERI ETOR and for sphingolipid de novo biosynthesis in WERI RB1. In addition, this study revealed similar protein signatures of topoisomerase inhibitors in WERI ETOR as well as ATPase inhibitors, acetylcholine receptor antagonists and vascular endothelial growth factor receptor (VEGFR) inhibitors in WERI RB1. In this study, WERI RB1 and WERI ETOR were analyzed as a cell line model for chemotherapy resistance in RB using data-independent MS. The global proteome identified activation of sphingolipid de novo biosynthesis in WERI RB1 and revealed future potential treatment options for etoposide resistance in RB.

show abstract

iTRAQ‑based quantitative proteomic analysis and bioinformatics study of proteins in retinoblastoma

Cited by 5 publications

References 43 publications

Cross-Stress Adaptation in a Piezophilic and Hyperthermophilic Archaeon From Deep Sea Hydrothermal Vent

Cross-Stress Adaptation in a Piezophilic and Hyperthermophilic Archaeon From Deep Sea Hydrothermal Vent

Aqueous Humor Markers in Retinoblastoma, a Review

Protein profiling of WERI RB1 and etoposide resistant WERI ETOR reveals new insights into topoisomerase inhibitor resistance in retinoblastoma

Contact Info

Product

Resources

About