Identification of differentially expressed proteins in retinoblastoma tumors using mass spectrometry-based comparative proteomic approach

2017 ◽  
Vol 159 ◽  
pp. 77-91 ◽  
Author(s):  
Jasmine Naru ◽  
Ritu Aggarwal ◽  
Ashok Kumar Mohanty ◽  
Usha Singh ◽  
Deepak Bansal ◽  
...  
Keyword(s):  
Mass Spectrometry ◽  
Differentially Expressed ◽  
Differentially Expressed Proteins ◽  
Proteomic Approach

Quantitative Proteomic Studies of gamma-Secretase Inhibition in Hodgkin Lymphoma Cells Reveal Novel Insights into Notch Signaling.

Blood ◽  
2005 ◽  
Vol 106 (11) ◽  
pp. 963-963
Author(s):  
Jeremy C. Wallentine ◽  
David K. Crockett ◽  
Kojo S.J. Elenitoba-Johnson ◽  
Megan S. Lim
Keyword(s):  
Mass Spectrometry ◽  
Notch Signaling ◽  
Hodgkin Lymphoma ◽  
Butyl Ester ◽  
Proteolytic Cleavage ◽  
Notch Receptor ◽  
Differentially Expressed ◽  
Gamma Secretase ◽  
Differentially Expressed Proteins ◽  
Proteomic Approach

Abstract Notch signaling has been implicated in the regulation of Hodgkin lymphoma (HL) survival via NF-kappaB. Notch signaling is dependent on the interaction of ligands with the transmembrane notch receptor. Ligand binding triggers proteolytic cleavage of the intracellular notch domain with subsequent translocation to the nucleus and activation of transcription factors. Gamma-secretase which catalyzes the proteolytic cleavage and release of the notch intracellular domain is critical in the mediation of notch signaling. Inhibition of gamma-secretase using 7{N-[N-(3,5-difluorophenyl)-L-alanyl]-s-phenyl-glycine t-butyl ester} (DAPT) in rat fetal thymocytes significantly reduces the expression of notch target genes. We identified proteins released by HL-derived cells into conditioned media including multiple upstream and downstream components of the notch signaling cascade, specifically: notch1, notch2, jagged1, jagged2, HES2, Hes4, GATA2 and GATA5. A proteomic analysis of the differentially expressed proteins among DAPT treated and untreated cells will reveal potential novel downstream mediators of notch signaling, increasing our understanding of HL pathogenesis. We sought to identify the proteomic consequences of notch signaling inhibition in L428 HL cells using a mass spectrometry-based proteomic approach. Treatment of L428 HL cells with DAPT (50μM) resulted in decreased cell proliferation as measured by the MTT assay which was associated with induction of p27Kip1. We utilized an endoproteinase catalyzed O16/O18 differential isotopic strategy to quantitatively determine the global proteomic changes following inhibition of the notch signaling pathway using DAPT. Proteins were collected from the cell lysate of treated and non-treated L428 cells, subjected to O16/O18 labeling and then analyzed by reverse-phase liquid chromatography coupled with electrospray ionization tandem mass spectrometry. A total of 156 proteins with 2 or more unique peptides were identified as being differentially expressed between treated and non-treated L428 cells. Proteins of diverse location and function were identified. Importantly a large number of proteins involved in transcription (12%; RelB, TRRAP, RB-associated protein, NCOR1), and located in the nucleus (27%; H2AO, FUSE binding protein 1, ANC5, SMYD1) were identified. Other important functional categories of the identified proteins included signaling activity (28%), and catalytic activity (41%). Several known proteins regulated by notch and involved with the regulation of notch activity such as (Histone acetyltransferase PCAF, RelB, N-COR1) were identified and found to be under expressed in treated cells. In addition, novel proteins with transcriptional and cell signaling activities have been identified, representing unique pathways that may be directly or indirectly affected by notch signaling. Our study represents the first comprehensive analysis of differentially expressed proteins following the inhibition of notch signaling. These results provide novel insights into our understanding of the pathogenesis and the role of notch signaling in HL

Proteomic analysis of the effects of lutein on mammary gland metabolism in dairy cows

2018 ◽  
Vol 85 (2) ◽  
pp. 152-156
Author(s):  
Caihong Wang ◽  
Chong Wang ◽  
Jianxin Liu ◽  
Hongyun Liu
Keyword(s):  
Blood Flow ◽  
Mammary Gland ◽  
Fatty Acid ◽  
Dairy Cows ◽  
Control Diet ◽  
Differentially Expressed ◽  
Acid Oxidation ◽  
Differentially Expressed Proteins ◽  
Proteomic Approach ◽  
Increased Blood Flow

The aim of the research reported in this Research Communication was to identify differentially expressed proteins in dairy cows with normal and lutein diet and to elucidate the mechanisms of lutein-induced effects on bovine mammary gland metabolism using a comparative proteomic approach. Thirty-three differentially expressed proteins were identified from mammary gland of control diet-fed and lutein diet-fed dairy cows. Among these proteins, 15 were upregulated and 18 were downregulated in the lutein group. Functional analysis of the differentially expressed proteins showed that increased blood flow, depressed glycolysis, enhanced lactose anabolism, decreased fatty acid oxidation and up-regulated beta lactoglobulin expression were connected with lutein addition. These results suggested that the increased blood flow, reduced glucose catabolism, enhanced capacity for milk lactose synthesis, depressed fatty acid catabolism and increased expression of antioxidantion related protein may be the prime factors contributing to the increased milk production and enhanced immune status in lutein-fed dairy cows. This study provides molecular mechanism of dietary lutein in regulating lactation of dairy cows.

scholarly journals Bayesian identification of protein differential expression in multi-group isobaric labelled mass spectrometry data

2014 ◽  
Vol 13 (5) ◽  
Author(s):  
Howsun Jow ◽  
Richard J. Boys ◽  
Darren J. Wilkinson
Keyword(s):  
Mass Spectrometry ◽  
Simulated Data ◽  
Differentially Expressed ◽  
Mass Spectrometry Data ◽  
Control Group ◽  
Differentially Expressed Proteins ◽  
Statistical Methodology ◽  
Proteomic Data ◽  
Bayesian Identification ◽  
Multiple Groups

AbstractIn this paper we develop a Bayesian statistical inference approach to the unified analysis of isobaric labelled MS/MS proteomic data across multiple experiments. An explicit probabilistic model of the log-intensity of the isobaric labels’ reporter ions across multiple pre-defined groups and experiments is developed. This is then used to develop a full Bayesian statistical methodology for the identification of differentially expressed proteins, with respect to a control group, across multiple groups and experiments. This methodology is implemented and then evaluated on simulated data and on two model experimental datasets (for which the differentially expressed proteins are known) that use a TMT labelling protocol.

scholarly journals Nitrogen Fertilizer Induced Alterations in The Root Proteome of Two Rice Cultivars

2019 ◽  
Vol 20 (15) ◽  
pp. 3674 ◽  
Author(s):  
Tang ◽  
Sun ◽  
Chen ◽  
Damaris ◽  
Lu ◽  
...  
Keyword(s):  
Crop Production ◽  
Oryza Sativa L ◽  
N Fertilizer ◽  
Differentially Expressed ◽  
Growth And Yield ◽  
Limiting Factor ◽  
Fertilizer Treatment ◽  
Rice Cultivars ◽  
Differentially Expressed Proteins ◽  
Proteomic Approach

Nitrogen (N) is an essential nutrient for plants and a key limiting factor of crop production. However, excessive application of N fertilizers and the low nitrogen use efficiency (NUE) have brought in severe damage to the environment. Therefore, improving NUE is urgent and critical for the reductions of N fertilizer pollution and production cost. In the present study, we investigated the effects of N nutrition on the growth and yield of the two rice (Oryza sativa L.) cultivars, conventional rice Huanghuazhan and indica hybrid rice Quanliangyou 681, which were grown at three levels of N fertilizer (including 135, 180 and 225 kg/hm2, labeled as N9, N12, N15, respectively). Then, a proteomic approach was employed in the roots of the two rice cultivars treated with N fertilizer at the level of N15. A total of 6728 proteins were identified, among which 6093 proteins were quantified, and 511 differentially expressed proteins were found in the two rice cultivars after N fertilizer treatment. These differentially expressed proteins were mainly involved in ammonium assimilation, amino acid metabolism, carbohydrate metabolism, lipid metabolism, signal transduction, energy production/regulation, material transport, and stress/defense response. Together, this study provides new insights into the regulatory mechanism of nitrogen fertilization in cereal crops.

scholarly journals iTRAQ Quantitative Analysis of Multidrug Resistance Mechanisms in Human Gastric Cancer Cells

2010 ◽  
Vol 2010 ◽  
pp. 1-11 ◽  
Author(s):  
Huai-Dong Hu ◽  
Feng Ye ◽  
Da-Zhi Zhang ◽  
Peng Hu ◽  
Hong Ren ◽  
...  
Keyword(s):  
Gastric Cancer ◽  
Multidrug Resistance ◽  
Cell Line ◽  
Molecular Mechanisms ◽  
Absolute Quantification ◽  
Differentially Expressed ◽  
Human Gastric Cancer ◽  
Differentially Expressed Proteins ◽  
Gastric Cancer Cells ◽  
Proteomic Approach

Multidrug resistance (MDR) is a major obstacle towards a successful treatment of gastric cancer. However, the mechanisms of MDR are intricate and have not been fully understood. To elucidate the molecular mechanisms of MDR in gastric cancer, we employed the proteomic approach of isobaric tags for relative and absolute quantification (iTRAQ), followed by LC-MS/MS, using the vincristine-resistant SGC7901/VCR cell line and its parental SGC7901 cell line as a model. In total, 820 unique proteins were identified and 91 proteins showed to be differentially expressed in SGC7901/VCR compared with SGC7901. Several differentially expressed proteins were further validated by western blot analysis. Furthermore, the association of MVP, one of the highly expressed proteins in SGC7901/VCR, with MDR was verified. Our study is the first application of iTRAQ technology for MDR mechanisms analysis in gastric cancer, and many of the differentially expressed proteins identified have not been linked to MDR in gastric cancer before, which showed the value of this technology in identifying differentially expressed proteins in cancer.

Identification of Differentially Expressed Proteins in Triple-Negative Breast Carcinomas Using DIGE and Mass Spectrometry

2009 ◽  
Vol 8 (7) ◽  
pp. 3430-3438 ◽  
Author(s):  
Daniela M. Schulz ◽  
Claudia Böllner ◽  
Gerry Thomas ◽  
Mike Atkinson ◽  
Irene Esposito ◽  
...  
Keyword(s):  
Mass Spectrometry ◽  
Triple Negative ◽  
Differentially Expressed ◽  
Differentially Expressed Proteins ◽  
Breast Carcinomas
Sign in / Sign up

Export Citation Format

Share Document