2016 update of the PRIDE database and its related tools

Vizcaíno, Juan Antonio; Csordás, Attila; del-Toro, Noemi; Dianes, José A.; Griss, Johannes; Lavidas, Ilias; Mayer, Gerhard; Perez‐Riverol, Yasset; Reisinger, Florian; Ternent, Tobias; Xu, Qingwei; Wang, Rui; Hermjakob, Henning

doi:10.1093/nar/gkw880

Cited by 1,055 publications

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“…Only proteins identified in both runs with ≥2 peptides were reported. The mass spectrometry proteomics data have been deposited to the ProteomeXchange Consortium via the PRIDE 34 partner repository with the dataset identifier PXD006049. The proteins captured by different AC-NPs formulations were compared and the overall P value was calculated by one-way analysis of variance (ANOVA) with Tukey post-test using the GraphPad Prism 5.0.…”

Section: Methodsmentioning

confidence: 99%

Antigen-capturing nanoparticles improve the abscopal effect and cancer immunotherapy

et al. 2017

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Immunotherapy holds tremendous promise for improving cancer treatment1. Administering radiotherapy with immunotherapy has been shown to improve immune responses and can elicit an “abscopal effect”2. Unfortunately, response rates for this strategy remain low3. Herein, we report an improved cancer immunotherapy approach that utilizes antigen-capturing nanoparticles (AC-NPs). We engineered several AC-NPs formulations and demonstrated that the set of protein antigens captured by each AC-NP formulation is dependent upon NP surface properties. We showed that AC-NPs deliver tumor specific proteins to antigen-presenting cells and significantly improve the efficacy of αPD-1 treatment using the B16F10 melanoma model, generating up to 20% cure rate as compared to 0% without AC-NPs. Mechanistic studies revealed that AC-NPs induced an expansion of CD8+ cytotoxic T cells and increased both CD4+/Treg and CD8+/Treg ratios. Our work presents a novel strategy for improving cancer immunotherapy with nanotechnology.

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Section: Methodsmentioning

confidence: 99%

Antigen-capturing nanoparticles improve the abscopal effect and cancer immunotherapy

et al. 2017

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“…The mass spectrometry proteomics data have been deposited to the ProteomeXchange Consortium via the PRIDE partner repository with the dataset identifier PXD009870 (http://www.ebi.ac.uk/pride/archive/) [80]. By partial least squares discriminant analysis, participants with MI who later presented with adjudicated heart failure hospitalization showed a distinct separation of the sexes based on the lack of ellipse overlap (Fig.…”

Section: Resultsmentioning

confidence: 99%

LXR/RXR signaling and neutrophil phenotype following myocardial infarction classify sex differences in remodeling

et al. 2018

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Sex differences in heart failure development following myocardial infarction (MI) are not fully understood. We hypothesized that differential MI signaling could explain variations in outcomes. Analysis of the mouse heart attack research tool 1.0 (422 mice; young = 5.4 ± 0.1; old = 23.3 ± 0.1 months of age) was used to dissect MI signaling pathways, which was validated in a new cohort of mice (4.8 ± 0.2 months of age); and substantiated in humans. Plasma collected at visit 2 from the MI subset of the Jackson Heart Study (JHS; a community-based study consisting of middle aged and older adults of African ancestry) underwent glycoproteomics grouped by outcome: (1) heart failure hospitalization after visit 2 (n = 3 men/12 women) and (2) without hospitalization through 2012 (n = 24 men/21 women). Compared to young male mice, the infarct region of young females had fewer, but more efficient tissue clearing neutrophils with reduced pro-inflammatory gene expression. Apolipoprotein (Apo) F, which acts upstream of the liver X receptors/retinoid X receptor (LXR/RXR) pathway, was elevated in the day 7 infarcts of old mice compared to young controls and was increased in both men and women with heart failure. In vitro, Apo F stimulated CD36 and peroxisome proliferator-activated receptor (PPAR)γ activation in male neutrophils to turn off NF-κB activation and stimulate LXR/RXR signaling to initiate resolution. Female neutrophils were desensitized to Apo F and instead relied on thrombospondin-1 stimulation of CD36 to upregulate AMP-activated protein kinase, resulting in an overall better wound healing strategy. With age, female mice were desensitized to LXR/RXR signaling, resulting in enhanced interleukin-6 activation, a finding replicated in the JHS community cohort. This is the first report to uncover sex differences in post-MI neutrophil signaling that yielded better outcomes in young females and worse outcomes with age.Electronic supplementary materialThe online version of this article (10.1007/s00395-018-0699-5) contains supplementary material, which is available to authorized users.

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“…The results were filtered with following parameters: only high confident peptides with a global FDR < 1% based on a target-decoy approach and first ranked peptides were included in the results. The mass spectrometry proteomics data have been deposited to the ProteomeXchange Consortium via the PRIDE partner repository with the dataset identifier PXD009709 [37]. …”

Section: Methodsmentioning

confidence: 99%

Ultrafiltration and size exclusion chromatography combined with asymmetrical‐flow field‐flow fractionation for the isolation and characterisation of extracellular vesicles from urine

Oeyen

Mol²,

Baggerman

et al. 2018

J of Extracellular Vesicle

106

107

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Extracellular vesicles (EVs) have a great potential in clinical applications. However, their isolation from different bodily fluids and their characterisation are currently not optimal or standardised. Here, we report the results of examining the performance of ultrafiltration combined with size exclusion chromatography (UF-SEC) to isolate EVs from urine. The results reveal that UF-SEC is an efficient method and provides high purity. Furthermore, we introduce asymmetrical-flow field-flow fractionation coupled with a UV detector and multi-angle light-scattering detector (AF4/UV-MALS) as a characterisation method and compare it with current methods. We demonstrate that AF4/UV-MALS is a straightforward and reproducible method for determining size, amount and purity of isolated urinary EVs.

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2016 update of the PRIDE database and its related tools

Cited by 1,055 publications

References 0 publications

Antigen-capturing nanoparticles improve the abscopal effect and cancer immunotherapy

Antigen-capturing nanoparticles improve the abscopal effect and cancer immunotherapy

LXR/RXR signaling and neutrophil phenotype following myocardial infarction classify sex differences in remodeling

Ultrafiltration and size exclusion chromatography combined with asymmetrical‐flow field‐flow fractionation for the isolation and characterisation of extracellular vesicles from urine

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