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Identification of molecular targets of dietary grape-mediated chemoprevention of ultraviolet B skin carcinogenesis: a comparative quantitative proteomics analysis

ABSTRACT: Grape-supplemented SKH-1 tumor proteomics analysis. Two 10-plex TMT sample sets are included with each TMT sample set being comprised of 5 high pH fractions.

INSTRUMENT(S): LTQ Orbitrap Elite

ORGANISM(S): Mus Musculus (ncbitaxon:10090)

SUBMITTER: Nihal Ahmad

PROVIDER: MSV000084316 | MassIVE |

REPOSITORIES: MassIVE

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Identification of Molecular Targets of Dietary Grape-Mediated Chemoprevention of Ultraviolet B Skin Carcinogenesis: A Comparative Quantitative Proteomics Analysis.

Mintie Charlotte A CA Singh Chandra K CK Ndiaye Mary A MA Barrett-Wilt Gregory A GA Ahmad Nihal N

Journal of proteome research 20190923 10

We recently showed that dietary grape powder (GP) imparts considerable protection against ultraviolet B (UVB)-mediated skin carcinogenesis in SKH-1 mice. To determine molecular mechanisms of this response, we employed tandem mass tag (TMT) quantitative global proteomics approach on skin tumors from mice exposed to 180 mJ/cm<sup>2</sup> UVB twice per week and fed control or 5% GP diet. We found 2629 proteins modulated by GP feeding, with 34 identified using stringent cutoffs (false discovery rate ...[more]

PMID: 31487184

Similar Datasets

Identification of Molecular Targets of Dietary Grape-Mediated Chemoprevention of Ultraviolet B Skin Carcinogenesis: A Comparative Quantitative Proteomics Analysis.

Project description:We recently showed that dietary grape powder (GP) imparts considerable protection against ultraviolet B (UVB)-mediated skin carcinogenesis in SKH-1 mice. To determine molecular mechanisms of this response, we employed tandem mass tag (TMT) quantitative global proteomics approach on skin tumors from mice exposed to 180 mJ/cm2 UVB twice per week and fed control or 5% GP diet. We found 2629 proteins modulated by GP feeding, with 34 identified using stringent cutoffs (false discovery rate (FDR) q-value ≤ 0.1, fold change ≥ 1.2, p-value ≤ 0.05, ≥ 3 unique peptides). Ingenuity Pathway Analysis helped identify seven proteins involved in protein ubiquitination, including the deubiquitinase UCHL5 and 6 subunits of the 20S proteasome (PSMA1,3,4,6 and PSMB4,7). A second data set without the FDR q-value identified 239 modulated proteins, seven of which are involved in protein ubiquitination. Further, 14 proteins involved in acute phase response signaling were modulated >1.5-fold, including acute phase proteins APCS, FGA, FGB, HP, HPX, and RBP1. Evaluation of upstream regulators found inhibition of ERK1/2 phosphorylation and NF-κB p65, and an increase in IκBα in GP-treated tumors. Overall, our data suggested that GP consumption may mitigate tumorigenesis by enhancing protein ubiquitination and degradation caused by oxidative stress, and manipulates an otherwise tumor-promoting anti-inflammatory environment.

| S-EPMC7749711 | biostudies-literature

Isobaric peptide labeling on digital microfluidics for quantitative proteomics of low cell numbers is facilitated by low critical micellar concentration detergents

Project description:We developed protocols for isobaric TMT labeling on digital microfluidics (DMF) devices enabling the quantitative proteome analysis of approximately 25 mammalian cells per channel by subsequent bottom-up proteome analysis by LC-MS. This comprised identification of a compatible detergent for digestion, on-chip labeling, and LC-MS. Application of the method in a TMT 6-plex sample analysis enabled the relative quantification 648 proteins (2 unique peptides for quantification) from a total of 125 cell equivalents.

2022-02-28 | PXD023226 | Pride

Potential Photoprotective Effect of Dietary Corn Silk Extract on Ultraviolet B-Induced Skin Damage.

Project description:Ultraviolet B (UVB) irradiation causes adverse effects on the skin. Corn silk contains flavonoids and other bioactive compounds and antioxidants, which may prevent skin photoaging through antioxidant and anti-inflammatory effects. We aimed to investigate the potential photoprotective effects of dietary corn silk on UVB-induced skin damage in mice and the mechanisms behind these effects on human skin cells. Oral administration of corn silk water extract (CS) (2 or 4 g/kg/day) for 19 weeks decreased epidermal thickness, wrinkle formation, and positive staining for PCNA, Ki67, and 8-OHdG, and increased collagen staining in UVB-irradiated SKH-1 hairless mice compared with controls. The pro-inflammatory NF-κB target genes (IL-1β, iNOS, and COX-2) and MMP-9 expressions were lower in the CS groups, and TGF-β/Smad signaling increased. Low skin lipid peroxidation and blood DNA oxidation levels and high blood glutathione were detected. Antioxidant transcription factor Nrf2-related catalase and SOD1 proteins and glutaredoxin mRNA levels increased. The results of CS extract treatment and UVB irradiation in HaCaT cells showed the same results in Nrf2 and NF-κB target genes. An LC-MS/MS analysis showed that the CS extract contained potential antioxidants, which might have contributed to its anti-photoaging effects in tissues and cells. CS extract may reduce UVB-induced skin damage through antioxidant and anti-inflammatory mechanisms.

| S-EPMC6680388 | biostudies-literature

29-Plex Tandem Mass Tag Mass Spectrometry Enabling Accurate Quantification by Interference Correction

Project description:Tandem mass tag (TMT) mass spectrometry is a mainstream isobaric chemical labeling strategy for profiling proteomes. Here we present a 29-plex TMT method to combine the 11-plex and 18-plex labeling strategies. The 29-plex method was examined with a pooled sample composed of 1x, 3x and 10x E. coli peptides with 100x human background peptides, which generated two E. coli datasets (TMT11 and TMT18), displaying the distorted ratios of 1.0:1.7:4.2 and 1.0:1.8:4.9, respectively. This ratio compression from the expected 1:3:10 ratios was caused by co-isolated TMT-labeled ions (i.e., noise). Interestingly, the mixture of two TMT sets produced MS/MS spectra with unique features for the noise detection: (i) in TMT11-labeled spectra, TMT18-specific reporter ions (e.g., 135N) were shown as the noise; (ii) in TMT18-labeled spectra, the TMT11/TMT18-shared reporter ions (e.g., 131C) typically exhibited higher intensities than TMT18-specific reporter ions, due to contaminated TMT11-labeled ions in these shared channels. We further estimated the noise levels contributed by both TMT11- and TMT18-labeled peptides, and corrected reporter ion intensities in every spectrum. Finally, the anticipated 1:3:10 ratios were largely restored. This strategy was also validated using another 29-plex sample with 1:5 ratios. Thus the 29-plex method expands the TMT throughput and enhances the quantitative accuracy.

2023-03-10 | PXD033865 | Pride

YTHDF1 links hypoxia adaptation and non-small cell lung cancer progression

Project description:10plex TMT labelling quantification expriments were performed to access the knockdown effect of YTHDF1 in cells.3 shGFPs control samples, 3 YTHDF1 shRNA-2 knockdown samples , 3 YTHDF1 shRNA-3 knockdown samples and 1 mixture sample were labelled by TMT 10-plex reagents.

2019-09-27 | PXD015182 | Pride

Comparative Analysis of murine tritosomal fractions after different starvation times

Project description:Lysosomal fractions were isolated following Triton WR1339 injection. Additionally, Mice weresubjected to food deprivation of 6 or 24 hours prior to sacrifice. Tritosome were labelled with TMT 10-plex

2024-11-18 | PXD047158 | Pride

Expression Analysis of Trimethyltin Chlorides (TMT) Impact on Embryonic Development

Project description:Investigation of whole genome expression pattern of 60 and 72 hours post fertilization Danio Rerio embryos exposed to TMT and vehicle control Embryos were exposed to 10uM TMT or control from 48hpf to 60 or 72 hpf. Three replicates were collected for each time point. 40 embryos were pooled to comprise a replicate.

2011-03-23 | E-GEOD-28131 | biostudies-arrayexpress

Microarray analysis of the effects of a Î³-tocopherol-rich mixture of tocopherols on global gene expression in the prostates of TRAMP mice

Project description:We used whole mouse genome microarrays to the effects of Î³-TmT on global gene expression in the prostate TRAMP and age-matched C57BL/6 mice were administered either 600 mg/kg of Î³-TmT or a control vehicle via oral gavage. Twelve hours after dosing, prostate tissues were collected for RNA extraction.

2014-09-16 | E-GEOD-61416 | biostudies-arrayexpress

Microarray expression analysis of Drosophila DrosDel deficiency lines

Project description:Microarray data of DrosDel deficiency (Df/+) and parental strain diploid flies along with spike-in controls was performed on the Nimblegen 12-plex array platform. Samples are named in this dataset according to the following sample naming scheme: tissue_genotype shorthand_sex_biological replicate #.

2012-04-03 | GSE31386 | GEO

NanoTPOT: Enhanced Sample Preparation for Quantitative Nanoproteomic Analysis

Project description:In this study, we developed and optimized a nanoproteomic workflow that we termed Nanogram TMT Processing in One Tube (NanoTPOT). Through the assessment of proteolytic digestion, tandem mass tag (TMT) labeling, online and offline frac-tionation strategies, our optimized workflow effectively eliminated the need for sample desalting and enabled compatible sample processing for MS analysis. We further applied the NanoTPOT workflow to examine cellular response to stress caused by dithiothreitol in Hela cells, where we identified and quantified 6935 proteins in a TMT 10-plex experiment with one microgram of starting material in each channel.

2021-01-11 | PXD016960 | Pride

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