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Defining the cellular proteolytic landscape cross time points

ABSTRACT: Mass spectrometry analysis of cellular targets of protein degradation

INSTRUMENT(S): Q Exactive

ORGANISM(S): Homo Sapiens (human)

TISSUE(S): Epithelial Cell, Cell Culture

SUBMITTER: Assaf Kacen

LAB HEAD: Yifat Merbl

PROVIDER: PXD007263 | Pride | 2018-10-11

REPOSITORIES: Pride

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			Action	DRS
	QEP2_5583_YMER_667_1_260717.raw	Raw
	QEP2_5583_YMER_668_1_260717.raw	Raw
	QEP2_5583_YMER_669_1_260717.raw	Raw
	QEP2_5583_YMER_670_1_260717.raw	Raw
	QEP2_5583_YMER_673_1_260717.raw	Raw

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Revealing the cellular degradome by mass spectrometry analysis of proteasome-cleaved peptides.

Wolf-Levy Hila H Javitt Aaron A Eisenberg-Lerner Avital A Kacen Assaf A Ulman Adi A Sheban Daoud D Dassa Bareket B Fishbain-Yoskovitz Vered V Carmona-Rivera Carmelo C Kramer Matthias P MP Nudel Neta N Regev Ifat I Zahavi Liron L Elinger Dalia D Kaplan Mariana J MJ Morgenstern David D Levin Yishai Y Merbl Yifat Y

Nature biotechnology 20181022

Cellular function is critically regulated through degradation of substrates by the proteasome. To enable direct analysis of naturally cleaved proteasomal peptides under physiological conditions, we developed mass spectrometry analysis of proteolytic peptides (MAPP), a method for proteasomal footprinting that allows for capture, isolation and analysis of proteasome-cleaved peptides. Application of MAPP to cancer cell lines as well as primary immune cells revealed dynamic modulation of the cellula ...[more]

PMID: 30346940

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Defining the cellular proteolytic landscape

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Defining the cellular proteolytic landscape in systemic lupus erythematosus – nonspecific digest

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Defining the cellular proteolytic landscape cross time points, part 2

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Defining the cellular proteolytic landscape with different controls

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Defining the proteolytic landscape during enterovirus infection.

Project description:Viruses cleave cellular proteins to remodel the host proteome. The study of these cleavages has revealed mechanisms of immune evasion, resource exploitation, and pathogenesis. However, the full extent of virus-induced proteolysis in infected cells is unknown, mainly because until recently the technology for a global view of proteolysis within cells was lacking. Here, we report the first comprehensive catalog of proteins cleaved upon enterovirus infection and identify the sites within proteins where the cleavages occur. We employed multiple strategies to confirm protein cleavages and assigned them to one of the two enteroviral proteases. Detailed characterization of one substrate, LSM14A, a p body protein with a role in antiviral immunity, showed that cleavage of this protein disrupts its antiviral function. This study yields a new depth of information about the host interface with a group of viruses that are both important biological tools and significant agents of disease.

| S-EPMC7549765 | biostudies-literature

Defining the cellular proteolytic landscape

Project description:Mass spectrometry analysis of cellular targets of protein degradation

2018-10-11 | PXD009360 | Pride

Defining the cellular proteolytic landscape in systemic lupus erythematosus

Project description:Mass spectrometry analysis of cellular targets of protein degradation in PBMCs of healthy individuals and systemic lupus

2018-10-11 | PXD009112 | Pride

Relative kinetic expressions defining cleavage synchronicity are better predictors of blastocyst formation and quality than absolute time points.

Project description:PurposeMorphology alone is not enough for the selection of the embryo (s) with the highest implantation potential and time-lapse imaging has added embryo development kinetics as another selection criterion. Therefore, a combination of morphology with kinetics has inspired a new field termed "morphokinetics", providing a new way of evaluating and selecting embryos. The aim of the study was to identify a criterion solely based on morphokinetic data and available up to the 8-cell stage (t8) to predict blastocyst formation and quality.MethodsThe study included 3,354 embryos, with annotations up to t8, and cultured until day 5 from 626 infertile patients. A total of 17 kinetic expressions, either absolute cleavage timings and time intervals or time ratios were tested retrospectively for the prediction of blastocyst formation and quality.ResultsRelative timings (t8-t5, the cleavage synchronicity from 4 to 8 cells and from 2 to 8 cells) were found to be better indicators of blastocyst formation and quality when compared to absolute time-points. Especially, the cleavage synchronicity from 2 to 8 cells (CS2-8) = ((t3-t2) + (t5-t4))/(t8-t2)) was found to be the best predictor available on day 3 for blastocyst formation and quality (AUC:0.786; sensitivity: 83.43; specificity: 62.46).ConclusionsTime intervals and relative ratios based on selected cleavage cycles defining synchronicity allowed a specific analysis providing high predictivity of blastocyst formation and quality.

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Defining obesity cut-off points for migrant South Asians.

Project description:BACKGROUND:Body mass index (BMI) and waist circumference (WC) are used to define cardiovascular and type 2 diabetes risk. We aimed to derive appropriate BMI and WC obesity cut-off points in a migrant South Asian population. METHODS:4688 White Europeans and 1333 South Asians resident in the UK aged 40-75 years inclusive were screened for type 2 diabetes. Principal components analysis was used to derive a glycaemia, lipid, and a blood pressure factor. Regression models for each factor, adjusted for age and stratified by sex, were used to identify BMI and WC cut-off points in South Asians that correspond to those defined for White Europeans. FINDINGS:For South Asian males, derived BMI obesity cut-off points equivalent to 30.0 kg/m(2) in White Europeans were 22.6 kg/m(2) (95% Confidence Interval (95% CI) 20.7 kg/m(2) to 24.5 kg/m(2)) for the glycaemia factor, 26.0 kg/m(2) (95% CI 24.7 kg/m(2) to 27.3 kg/m(2)) for the lipid factor, and 28.4 kg/m(2) (95% CI 26.5 kg/m(2) to 30.4 kg/m(2)) for the blood pressure factor. For WC, derived cut-off points for South Asian males equivalent to 102 cm in White Europeans were 83.8 cm (95% CI 79.3 cm to 88.2 cm) for the glycaemia factor, 91.4 cm (95% CI 86.9 cm to 95.8 cm) for the lipid factor, and 99.3 cm (95% CI 93.3 cm to 105.2 cm) for the blood pressure factor. Lower ethnicity cut-off points were seen for females for both BMI and WC. CONCLUSIONS:Substantially lower obesity cut-off points are needed in South Asians to detect an equivalent level of dysglycemia and dyslipidemia as observed in White Europeans. South Asian ethnicity could be considered as a similar level of risk as obesity (in White Europeans) for the development of type 2 diabetes.

| S-EPMC3198431 | biostudies-literature

Myelin basic protein fragmentation by engineered human proteasomes with different catalytic phenotypes revealed direct peptide ligands of MS-associated and protective HLA class I molecules

Project description:Proteasomes exist in mammalian cells in multiple combinatorial variants due to the broadly diversified regulatory particles and catalytic subunits exchange. Here, using biotin carboxyl carrier domain of transcarboxylase from Propionibacterium shermanii fused with different proteasome subunits of catalytic and regulatory particles, we report comprehensive characterization of highly homogenous one-step purified human constitutive and immune 20S and 26S/30S proteasomes. Hydrolysis of multiple sclerosis (MS) autoantigen, myelin basic protein (MBP), by engineered human proteasomes with different catalytic phenotypes revealed peptides, which may be directly loaded on the HLA class I. Prediction of affinity of HLA class I to these peptides demonstrated that protective HLA I alleles are high affinity binders, whereas MS-associated alleles tend to have moderate-to-low affinity. Core peptide QDENPVVHFF, originated from the encephalitogenic MBP part, and its deaminated form was shown to be high affinity ligand for the protective HLA A*44, -B*40 and -B*35 alleles, demonstrating complexity of the autoimmune neurodegeneration.

2023-01-13 | PXD038387 | Pride

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