Development of barcode and proteome profiling of glioblastoma

Naryzhny, Stanislav N.; Ronzhina, N. L.; Mainskova, M. A.; Belyakova, N. V.; Пантина, Р. А.; Филатов, М. В.

doi:10.1134/s1990750814030111

Cited by 9 publications

(26 citation statements)

References 29 publications

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“…To prepare the cell samples for protein extraction, the cells were detached with 0.25% Trypsin‐EDTA solution, washed three times with PBS, and counted. Aliquots of the resulting cell suspension (each containing 10 million of cells) were centrifuged, the supernatant was removed, and cells were treated with lysis buffer (7 M urea, 2 M thiourea, 4% CHAPS, 1% DTT, 2% ampholytes, pH 3–10, protease inhibitor mixture) .…”

Section: Methodsmentioning

confidence: 99%

Combination of virtual and experimental 2DE together with ESI LC‐MS/MS gives a clearer view about proteomes of human cells and plasma

et al. 2015

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Virtual and experimental 2DE coupled with ESI LC-MS/MS was introduced to obtain better representation of the information about human proteome. The proteins from HEPG2 cells and human blood plasma were run by 2DE. After staining and protein spot identification by MALDI-TOF MS, the protein maps were generated. The experimental physicochemical parameters (pI/Mw) of the proteoforms further detected by ESI LC-MS/MS in these spots were obtained. Next, the theoretical pI and Mw of identified proteins were calculated using program Compute pI/Mw (http://web.expasy.org/compute_pi/pi_tool-doc.html). Accordingly, the relationship between theoretical and experimental parameters was analyzed, and the correlation plots were built. Additionally, virtual/experimental information about different protein species/proteoforms from the same genes was extracted. As it was revealed from the plots, the major proteoforms detected in HepG2 cell line have pI/Mw parameters similar to theoretical values. In opposite, the minor protein species have mainly very different from theoretical pI and Mw parameters. A similar situation was observed in plasma in much higher degree. It means that minor protein species are heavily modified in cell and even more in plasma proteome.

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Section: Methodsmentioning

confidence: 99%

Combination of virtual and experimental 2DE together with ESI LC‐MS/MS gives a clearer view about proteomes of human cells and plasma

et al. 2015

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“…Cofilin downregulation induced by CM16 might confer additional anti‐migratory properties to its cytostatic effects. Indeed, this actin filament assembly and disassembly regulator plays an important role in cell migration (Bernstein & Bamburg, ) and is overexpressed in glioblastoma (Naryzhny et al, ). The effects of CM16 on those five proteins seem thus promising when considering their roles in glioma biology as confirmed by the benefits obtained with their inhibition in glioma models, exemplified by the literature reported here.…”

Section: Discussionmentioning

confidence: 99%

A new potential anti‐cancer beta‐carboline derivative decreases the expression levels of key proteins involved in glioma aggressiveness: A proteomic investigation

Carvalho

Viaene

Vandenbussche

et al. 2019

Drug Development Research

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Gliomas remain highly fatal due to their high resistance to current therapies. Deregulation of protein synthesis contributes to cancer onset and progression and is a source of rising interest for new drugs. CM16, a harmine derivative with predicted high blood–brain barrier penetration, exerts antiproliferative effects partly through translation inhibition. We evaluated herein how CM16 alters the proteome of glioma cells. The analysis of the gel‐free LC/MS and auto‐MS/MS data showed that CM16 induces time‐ and concentration‐dependent significant changes in the total ion current chromatograms. In addition, we observed spontaneous clustering of the samples according to their treatment condition and their proper classification by unsupervised and supervised analyses, respectively. A two‐dimensional gel‐based approach analysis allowed us to identify that treatment with CM16 may downregulate four key proteins involved in glioma aggressiveness and associated with poor patient survival (HspB1, BTF3, PGAM1, and cofilin), while it may upregulate galectin‐1 and Ebp1. Consistently with the protein synthesis inhibition properties of CM16, HspB1, Ebp1, and BTF3 exert known roles in protein synthesis. In conclusion, the downregulation of HspB1, BTF3, PGAM1 and cofilin bring new insights in CM16 antiproliferative effects, further supporting CM16 as an interesting protein synthesis inhibitor to combat glioma.

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“…Therefore, the systems biology approaches, such as proteomics, transcriptomics, and metabolomics, based on the use of high throughput techniques are very promising. They could afford the developing of the detection of cancerous and precancerous states based on not just one but a group of markers [4,5].…”

Section: Introductionmentioning

confidence: 99%

“…Indeed, recently, genomic and proteomic high-throughput technologies have provided molecular profiling of human gliomas [4][5][6][7]. These studies have generated a number of candidate diagnostic, prognostic and prediction of response to therapy markers.…”

Section: Introductionmentioning

confidence: 99%

“…The list of these potential glioblastoma markers described in different publications is rather long. It indicates that the situation here is not very simple, even considering the publications, where possible molecular signatures associated with this tumor have been described [4,8,9]. Before adapting these biomarkers to the clinic, it is necessary to address many challenges hindering an in-depth, nonbiased profiling of the glioblastoma proteome [10].…”

Section: Introductionmentioning

confidence: 99%

See 1 more Smart Citation

Proteomic Profiling of High-grade Glioblastoma Using Virtual experimental 2DE

Naryzhny¹,

Maynskova²,

Zgoda³

et al. 2016

J Proteomics Bioinform

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Identification and quantitative analysis of different proteoforms (protein species) presented in a cell line generated from high grade glioblastoma was performed using two-dimensional electrophoresis (2DE), mass spectrometry (ESI LC-MS/MS), and immunodetection. A 2DE protein map containing an extensive data set comprising 937 spots with 1542 unique protein identifications (proteoforms) of 600 genes was obtained. Additionally, another set of experiments was performed where 16012 proteoforms coded by 4050 genes were identified by MS/MS according to their position in 96 gel sections (pixels). A special attention has been paid to the proteins that are the potential biomarkers of glioblastoma. The list of these biomarkers was compiled from literature. Next, we generated the graphs with theoretical and experimental information about proteoforms coded by the same gene. Such a virtualexperimental representation allowed better visualization of the state of these gene products. Many proteins, potential biomarkers of glioblastoma as well, are characterized by high numbers of protein species. We assume that these species could be a potential source of highly specific biomarkers of glioblastoma.

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Development of barcode and proteome profiling of glioblastoma

Cited by 9 publications

References 29 publications

Combination of virtual and experimental 2DE together with ESI LC‐MS/MS gives a clearer view about proteomes of human cells and plasma

Combination of virtual and experimental 2DE together with ESI LC‐MS/MS gives a clearer view about proteomes of human cells and plasma

A new potential anti‐cancer beta‐carboline derivative decreases the expression levels of key proteins involved in glioma aggressiveness: A proteomic investigation

Proteomic Profiling of High-grade Glioblastoma Using Virtual experimental 2DE

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