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Global proteome of Atg5flox:Slc32a1-Cre:tdTomato FACS sorted WT and KO neurons

ABSTRACT: The experiment was performed to identify phosphorylation target proteins of cAMP-dependent kinase A (PKA) in mouse brain tissue. Therefore, coimmunoprecipitation analysis was performed using a PKA phosphorylation state-specific antibody (RRXS/T). Potential PKA target proteins were determined by LC-MS/MS.

INSTRUMENT(S): Q Exactive

ORGANISM(S): Mus Musculus (mouse)

SUBMITTER: Prerana Wagle

LAB HEAD: N.L. Kononenko

PROVIDER: PXD031553 | Pride | 2022-11-15

REPOSITORIES: pride

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			Action	DRS
	Q1_ColID_280_2671_01.raw	Raw
	Q1_ColID_280_2671_02.raw	Raw
	Q1_ColID_280_2671_03.raw	Raw
	Q1_ColID_280_2671_04.raw	Raw
	Q1_ColID_280_2671_05.raw	Raw

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Global proteome of Atg5flox:Slc32a1-Cre:tdTomato FACS sorted WT and KO neurons

Project description:The experiment was performed to identify autophagy targets in wildtype and autophagy-deficient forebrain inhibitory neurons. Therefore, neurons were isolated from the cortex, hippocampus and striatum of 2-3 weeks old Atg5flox/flox:Slc32a1-Cretg/wt:tdTomato+ (KO) and Atg5wt/wt:Slc332a1-Cretg/wt:tdTomato+ (WT) mice. Neurons in suspension were FACS sorted and inhibitory forebrain neurons expressing tdTomato were forwarded to global proteome analysis assessed by LC-MS/MS.

2022-11-15 | PXD031535 | Pride

Global proteome of Atg5flox:CamKIIα-Cre:tdTomato FACS sorted WT and KO neurons

Project description:The experiment was performed to identify autophagy targets in wildtype and autophagy-deficient forebrain excitatory neurons. Therefore, neurons were isolated from the cortex, hippocampus and striatum of 2-3 weeks old Atg5flox/flox:CamKIIα-Cretg/wt:tdTomato+ (KO) and Atg5wt/wt:CamKIIα-Cretg/wt:tdTomato+ (WT) mice. Neurons in suspension were FACS sorted and excitatory forebrain neurons expressing tdTomato were forwarded to global proteome analysis assessed by LC-MS/MS.

2022-11-15 | PXD031552 | Pride

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Project description:The experiment was performed to identify autophagy targets in wildtype and autophagy-deficient primary neurons. Therefore, cortico-hippocampal neurons were isolated from Atg5flox:CAG-CreTmx mice and treated with Tamoxifen (Tmx) to induce the knockout (KO) or EtOH for wildtype (WT) in-vitro. WT and KO Neurons were harvested at day in-vitro (DIV) 15-16, and global proteome analysis was measured by LC-MS/MS.

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Whole cell proteomics of NDUFAF8 knock-out cell line and NDUFAF5 knock-out cell line

Project description:Comparison of whole cell proteome of NDUFAF8 KO and NDUFAF5 KO to WT cell line

2023-05-08 | PXD040441 | Pride

Detection of putative PKA target phosphorylation sites in Atg5flox:CamKII-Cre wildtype and knockout mice brain tissue

Project description:The experiment was performed to identify PKA phosphorylation substrates in wildtype and autophagy-deficient brains. Therefore, hippocampus and cortex of wildtype and conditional knockout mice were isolated and sliced. The brain slices were incubated with DMSO or Forskolin, a cAMP elevating agent, to induce PKA activity. Samples were measured by LC-MS/MS and were used to quantify proteomic and phosphoproteomic changes.

2022-11-15 | PXD031106 | Pride

The choice of feed composition exerts a considerable influence on phenotypic, metabolic and proteomic outcome in BL/6 male mice

Project description:The multitude of obesogenic diets used in rodent studies is enormous and thus hardly manageable. Since standardization is missing and it is presumed that individual compositions provoke individual effects, the choice of quality, quantity and combination of diet ingredients seems to be crucial for the outcome and interpretation of obesity studies. Therefore, the present study was conducted to compare the effects of three commonly used obesogenic diets on selected parameters. Besides basic phenotypic and metabolic characterization, one main aspect was a comparative liver proteome analysis. As expected, the obtained results picture differentiated consequences mainly depending on fat source and/or fat- and sugar quantity. By confirming the general presumption that the choice of nutritional composition is a pivotal factor, the present findings demonstrate that a conscious selection is indispensable for obtaining reliable and sound results in obesity research.In conclusion, we strongly recommend a thorough selection of the appropriate obesogenic diet prior to an experiment and in consideration of the individual research question.

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Interactome of NDUFAF5-HA overexpressing cell line compared to mock

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2023-05-08 | PXD040453 | Pride

Interactome of NDUFAF8-HA overexpressing cell line compared to mock

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Stromal cells support the survival of human primary chronic lymphocytic leukemia (CLL) cells

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A compound-based therapy approach for epidermolysis bullosa simplex (EBS)

Project description:Keratin cytoskeletal proteins are crucial for the maintenance of skin integrity. Mutations in genes coding for K5 and K14 cause the human skin disorder epidermolysis bullosa simplex (EBS) leading to substantial alterations in keratin assembly and collapse of keratin filaments into cytoplasmic protein aggregates. The phenotypic consequences of K5 and K14 mutations comprise fragility of basal keratinocytes and skin blistering upon mild mechanical trauma. Treatment of EBS is only supportive and consists primarily of wound care and avoidance of mechanical stress. Besides symptomatic care, no efficient therapeutic treatment is available for EBS. In the present study, we used patient-derived keratinocytes carrying the most frequent K14.R125C mutation as a reproducible EBS model to understand EBS pathomechanisms and to develop a therapy approach aimed to restore a functional keratin network. Numerous post-translational modifications (PTMs) such as phosphorylation have been reported to occur on keratins, which affect the organization of keratin networks. Whether keratin mutations affect the occurrence of PTMs and thereby keratin aggregation in EBS is yet unknown. We find that the K14.R125C mutation alters keratin and keratin-associated protein PTMs in distinct ways and suggest that disease mutations and altered PTMs aggravate keratin aggregation. We reason that chemical compounds affecting the interplay of mutations and PTMs enable the reformation of a keratin cytoskeleton from aggregates are potential candidates for combating EBS.

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