Refine
Year of publication
Language
- English (58)
Has Fulltext
- yes (58)
Is part of the Bibliography
- no (58)
Keywords
- Proteomics (3)
- complexome profiling (3)
- mitochondria (3)
- Aging (2)
- Calpain (2)
- Complex I (2)
- NADPH oxidase (2)
- Podospora anserina (2)
- Reactive oxygen species (2)
- aging (2)
- bioenergetics (2)
- long non-coding RNA (2)
- mitochondrial disease (2)
- A/D transition (1)
- AAA+ disaggregase (1)
- Activities of daily living (1)
- Adult neurogenesis (1)
- Alternative oxidase (1)
- Apoptosis (1)
- Ataxia (1)
- Autoimmune vasculopathy (1)
- Autophagy (1)
- BIAM switch assay (1)
- BIAM-switch (1)
- BPTF (1)
- Behavior (1)
- Biochemistry (1)
- Brain (1)
- Calcium calmodulin kinase (1)
- Cardiac infarction (1)
- Cardiology (1)
- Cardiomyopathy (1)
- Cell signalling (1)
- Chaperone (1)
- Chemical modification (1)
- Chemiluminescence (1)
- ClpB (1)
- Complex II (1)
- Complexome profiling (1)
- Conformational change (1)
- Cortex (1)
- DNA Damage (1)
- DNA methylation (1)
- Data visualization (1)
- Database (1)
- ERAL1 (1)
- Endothelial cell (EC) (1)
- Endothelial cells (1)
- Endothelial protein C receptor (1)
- FAIR (1)
- Flavin mononucleotide (1)
- G3BP1 (1)
- HARS2 (1)
- HSP (hereditary spastic paraplegia) (1)
- Heart (1)
- Heart transplantation (1)
- Hig1 (1)
- Hypoxia inducible factor (1)
- ICAM-1 (1)
- IL-1β (1)
- Innate immunity (1)
- IntelliCage (1)
- Isoforms (1)
- KLHL11 (1)
- LARS2 (1)
- Lactic acidosis (1)
- Leukodystrophy (1)
- LncRNA - long noncoding RNA (1)
- Long non-coding RNAs (1)
- Lucigenin (1)
- Lysosome (1)
- MEIS homeodomain protein (1)
- MTRNR1 (1)
- Mass spectrometry (1)
- Membrane assays (1)
- Microparticles (1)
- Mitochondria (1)
- Mitochondrial ROS (1)
- Mitochondrial amino acid tRNA synthetases (1)
- Mitochondrial complex I (1)
- Mitochondrial disease (1)
- Mitochondrial disorder (1)
- Mitochondrial dysfunction (1)
- N-hydroxysuccinimide (1)
- N471D strumpellin knock-in mice (1)
- NADH:ubiquinone oxidoreductase (1)
- NDUFA6 (1)
- NDUFAF8 (1)
- NURF (1)
- Neonatal (1)
- Neurodegeneration (1)
- Nitric oxide (1)
- Nox (1)
- Nox4 (1)
- OXPHOS (1)
- POLG (1)
- PRLTS3 (1)
- Parkinson’s disease (1)
- Perrault syndrome (1)
- Play (1)
- Pleasure (1)
- Post-translational modifications (1)
- Posttranslational modification (1)
- Prognosis (1)
- Progranulin (1)
- Protein complex (1)
- Protein tyrosine modification (1)
- RNA Biology (1)
- RNA turnover (1)
- RNA, long noncoding (1)
- Rapamycin (1)
- Rcf1 (1)
- Redox modification (1)
- Redoxin (1)
- Release of mtDNA and mtRNA (1)
- Respiratory chain (1)
- Reverse electron transfer (1)
- SDH (1)
- SPG8 (1)
- Senescence (1)
- Starvation (1)
- Stem cell (1)
- Stroke (1)
- Stroke genetics (1)
- Subventricular zone (1)
- Superoxide (1)
- TRIM25 (1)
- TWINKLE (1)
- TWNK (1)
- Tissue-specificity (1)
- Transcription factor (1)
- Treatment (1)
- Ubiquitin (1)
- Ubiquitin ligase (1)
- Vitamin (1)
- WASH complex subunit 5 (1)
- adaptive cardiac remodelling (1)
- alternative oxidase (1)
- alternative splicing (1)
- angiogenesis (1)
- aortic aneurysm (1)
- assembly (1)
- ataxia (1)
- atherosclerosis (1)
- cGAS-STING (1)
- cancer metastases (1)
- cardiac ischaemia‐reperfusion (1)
- cardiolipin (1)
- cardiovascular disease (1)
- caspase-2 (1)
- chemotherapy resistance (1)
- colon carcinoma cells (1)
- complex I (1)
- complex I deficiency (1)
- crista junction (1)
- cristae (1)
- cytochrome c oxidase (complex IV) (1)
- data repositories (1)
- diabetes mellitus (1)
- electron transport chain (1)
- epigenomics (1)
- gene expression (1)
- glioblastoma (1)
- hypertension, pulmonary (1)
- i-AAA protease (1)
- intrinsic apoptosis (1)
- ischemia (1)
- leukodystrophy (1)
- long non-coding RNAs (1)
- macrophage (1)
- mass spectrometry (1)
- matrix metalloproteinase (1)
- membrane protein complex (1)
- membrane structure (1)
- metabolomics (1)
- molecular diagnosis (1)
- mouse (1)
- neovascularization, physiologic (1)
- nonsense-mediated mRNA decay (1)
- polyunsaturated fatty acid (1)
- proliferation (1)
- protein complexes (1)
- protein quality control (1)
- protein–protein interaction (1)
- proteomics (1)
- reactive oxygen species (1)
- remodeling (1)
- smooth muscle cell (1)
- strumpellin (1)
- temperature (1)
- therapeutics (1)
- tight junctions (1)
- vascular disease (1)
- vascular integrity (1)
- vascular remodeling (1)
- yeast (1)
Institute
- Medizin (58) (remove)
Upregulations of neuronal nitric oxide synthase (nNOS/NOS1) in the mouse brain upon aging suggest a role in age-associated changes of protein homeostasis. We generated a cell model, in which constitutive expression of nNOS in SH-SY5Y cells at a level comparable to mouse brain replicates the aging phenotype i.e. slowing of cell proliferation, cell enlargement and expression of senescence markers. nNOS+ and MOCK cells were exposed to proteostasis stress by treatment with rapamycin or serum-free starvation. The proteomes were analyzed per SILAC or label-free using hybrid liquid chromatography/mass spectrometry (LC/MS). Full scan MS-data were acquired using Xcalibur, and raw mass spectra were analyzed using the proteomics software MaxQuant. The human reference proteome from uniprot was used as template to identify peptides and proteins and quantify protein expression. The DiB data file contains essential MaxQuant output tables and includes peptide and protein identification, accession numbers, protein and gene names, sequence coverage and quantification values of each sample. Differences in protein expression in MOCK versus nNOS+ SH-SY5Y cells and interpretation of results are presented in Valek et al. (2018). Raw mass spectra and MaxQuant output files have been deposited to the ProteomeXchange Consortium (Vizcaino et al., 2014) via the PRIDE partner repository with the dataset identifier PRIDE: PXD010538.
Leigh syndrome is one of the most common neurological phenotypes observed in pediatric mitochondrial disease presentations. It is characterized by symmetrical lesions found on neuroimaging in the basal ganglia, thalamus, and brainstem and by a loss of motor skills and delayed developmental milestones. Genetic diagnosis of Leigh syndrome is complicated on account of the vast genetic heterogeneity with >75 candidate disease-associated genes having been reported to date. Candidate genes are still emerging, being identified when “omics” tools (genomics, proteomics, and transcriptomics) are applied to manipulated cell lines and cohorts of clinically characterized individuals who lack a genetic diagnosis. NDUFAF8 is one such protein; it has been found to interact with the well-characterized complex I (CI) assembly factor NDUFAF5 in a large-scale protein-protein interaction screen. Diagnostic next-generation sequencing has identified three unrelated pediatric subjects, each with a clinical diagnosis of Leigh syndrome, who harbor bi-allelic pathogenic variants in NDUFAF8. These variants include a recurrent splicing variant that was initially overlooked due to its deep-intronic location. Subject fibroblasts were found to express a complex I deficiency, and lentiviral transduction with wild-type NDUFAF8-cDNA ameliorated both the assembly defect and the biochemical deficiency. Complexome profiling of subject fibroblasts demonstrated a complex I assembly defect, and the stalled assembly intermediates corroborate the role of NDUFAF8 in early complex I assembly. This report serves to expand the genetic heterogeneity associated with Leigh syndrome and to validate the clinical utility of orphan protein characterization. We also highlight the importance of evaluating intronic sequence when a single, definitively pathogenic variant is identified during diagnostic testing.
Colorectal cancer (CRC) is one of the most common cancers that is characterized by a high mortality due to the strong metastatic potential of the primary tumor and the high rate of therapy resistance. Hereby, evasion of apoptosis is the primary underlying cause of reduced sensitivity of tumor cells to chemo- and radiotherapy. Using RNA affinity chromatography, we identified the tripartite motif-containing protein 25 (TRIM25) as a bona fide caspase-2 mRNA-binding protein in colon carcinoma cells. Loss-of-function and gain-of-function approaches revealed that TRIM25 attenuates the protein levels of caspase-2 without significantly affecting caspase-2 mRNA levels. In addition, experiments with cycloheximide revealed that TRIM25 does not affect the protein stability of caspase-2. Furthermore, silencing of TRIM25 induced a significant redistribution of caspase-2 transcripts from RNP particles to translational active polysomes, indicating that TRIM25 negatively interferes with caspase-2 translation. Functionally, the elevation in caspase-2 upon TRIM25 depletion significantly increased the sensitivity of colorectal cells to drug-induced intrinsic apoptosis as implicated by increased caspase-3 cleavage and cytochrome c release. Importantly, the apoptosis-sensitizing effects by transient TRIM25 knockdown were rescued by concomitant silencing of caspase-2, demonstrating a critical role of caspase-2. Inhibition of caspase-2 by TRIM25 implies a survival mechanism that critically contributes to chemotherapeutic drug resistance in CRC.
BIAM switch assay coupled to mass spectrometry identifies novel redox targets of NADPH oxidase 4
(2019)
Aim: NADPH oxidase (Nox) -derived reactive oxygen species have been implicated in redox signaling via cysteine oxidation in target proteins. Although the importance of oxidation of target proteins is well known, the specificity of such events is often debated. Only a limited number of Nox-oxidized proteins have been identified thus far; especially little is known concerning redox-targets of the constitutively active NADPH oxidase Nox4.
In this study, HEK293 cells with tetracycline-inducible Nox4 overexpression (HEK-tet-Nox4), as well as podocytes of WT and Nox4-/- mice, were utilized to identify Nox4-dependent redox-modified proteins.
Results: TGFβ1 induced an elevation in Nox4 expression in podocytes from WT but not Nox4-/- mice. Using BIAM based redox switch assay in combination with mass spectrometry and western blot analysis, 142 proteins were identified as differentially oxidized in podocytes from wild type vs. Nox4-/- mice and 131 proteins were differentially oxidized in HEK-tet-Nox4 cells upon Nox4 overexpression. A predominant overlap was found for peroxiredoxins and thioredoxins, as expected. More interestingly, the GRB2-associated-binding protein 1 (Gab1) was identified as being differentially oxidized in both approaches. Further analysis using mass spectrometry-coupled BIAM switch assay and site directed mutagenesis, revealed Cys374 and Cys405 as the major Nox4 targeted oxidation sites in Gab1.
Innovation & conclusion: BIAM switch assay coupled to mass spectrometry is a powerful and versatile tool to identify differentially oxidized proteins in a global untargeted way. Nox4, as a source of hydrogen peroxide, changes the redox-state of numerous proteins. Of those, we identified Gab1 as a novel redox target of Nox4.
High-resolution cryo-EM structures of respiratory complex I: Mechanism, assembly, and disease
(2019)
Respiratory complex I is a redox-driven proton pump, accounting for a large part of the electrochemical gradient that powers mitochondrial adenosine triphosphate synthesis. Complex I dysfunction is associated with severe human diseases. Assembly of the one-megadalton complex I in the inner mitochondrial membrane requires assembly factors and chaperones. We have determined the structure of complex I from the aerobic yeast Yarrowia lipolytica by electron cryo-microscopy at 3.2-Å resolution. A ubiquinone molecule was identified in the access path to the active site. The electron cryo-microscopy structure indicated an unusual lipid-protein arrangement at the junction of membrane and matrix arms that was confirmed by molecular simulations. The structure of a complex I mutant and an assembly intermediate provide detailed molecular insights into the cause of a hereditary complex I-linked disease and complex I assembly in the inner mitochondrial membrane.
Myeloid-specific deletion of the AMPK2 subunit alters monocyte protein expression and atherogenesis
(2019)
The AMP-activated protein kinase (AMPK) is an energy sensing kinase that is activated by a drop in cellular ATP levels. Although several studies have addressed the role of the AMPKα1 subunit in monocytes and macrophages, little is known about the α2 subunit. The aim of this study was to assess the consequences of AMPKα2 deletion on protein expression in monocytes/macrophages, as well as on atherogenesis. A proteomics approach was applied to bone marrow derived monocytes from wild-type mice versus mice specifically lacking AMPKα2 in myeloid cells (AMPKα2∆MC mice). This revealed differentially expressed proteins, including methyltransferases. Indeed, AMPKα2 deletion in macrophages increased the ratio of S-adenosyl methionine to S-adenosyl homocysteine and increased global DNA cytosine methylation. Also, methylation of the vascular endothelial growth factor and matrix metalloproteinase-9 (MMP9) genes was increased in macrophages from AMPKα2∆MC mice, and correlated with their decreased expression. To link these findings with an in vivo phenotype, AMPKα2∆MC mice were crossed onto the ApoE-/- background and fed a western diet. ApoExAMPKα2∆MC mice developed smaller atherosclerotic plaques than their ApoExα2fl/fl littermates, that contained fewer macrophages and less MMP9 than plaques from ApoExα2fl/fl littermates. These results indicate that the AMPKα2 subunit in myeloid cells influences DNA methylation and thus protein expression and contributes to the development of atherosclerotic plaques.
Complexome profiling is an emerging ‘omics approach that systematically interrogates the composition of protein complexes (the complexome) of a sample, by combining biochemical separation of native protein complexes with mass-spectrometry based quantitation proteomics. The resulting fractionation profiles hold comprehensive information on the abundance and composition of the complexome, and have a high potential for reuse by experimental and computational researchers. However, the lack of a central resource that provides access to these data, reported with adequate descriptions and an analysis tool, has limited their reuse. Therefore, we established the ComplexomE profiling DAta Resource (CEDAR, www3.cmbi.umcn.nl/cedar/), an openly accessible database for depositing and exploring mass spectrometry data from complexome profiling studies. Compatibility and reusability of the data is ensured by a standardized data and reporting format containing the “minimum information required for a complexome profiling experiment” (MIACE). The data can be accessed through a user-friendly web interface, as well as programmatically using the REST API portal. Additionally, all complexome profiles available on CEDAR can be inspected directly on the website with the profile viewer tool that allows the detection of correlated profiles and inference of potential complexes. In conclusion, CEDAR is a unique, growing and invaluable resource for the study of protein complex composition and dynamics across biological systems.
Long non-coding RNAs (lncRNAs) contribute to cardiac (patho)physiology. Aging is the major risk factor for cardiovascular disease with cardiomyocyte apoptosis as one underlying cause. Here, we report the identification of the aging-regulated lncRNA Sarrah (ENSMUST00000140003) that is anti-apoptotic in cardiomyocytes. Importantly, loss of SARRAH (OXCT1-AS1) in human engineered heart tissue results in impaired contractile force development. SARRAH directly binds to the promoters of genes downregulated after SARRAH silencing via RNA-DNA triple helix formation and cardiomyocytes lacking the triple helix forming domain of Sarrah show an increase in apoptosis. One of the direct SARRAH targets is NRF2, and restoration of NRF2 levels after SARRAH silencing partially rescues the reduction in cell viability. Overexpression of Sarrah in mice shows better recovery of cardiac contractile function after AMI compared to control mice. In summary, we identified the anti-apoptotic evolutionary conserved lncRNA Sarrah, which is downregulated by aging, as a regulator of cardiomyocyte survival.
Respiratory chain signalling is essential for adaptive remodelling following cardiac ischaemia
(2020)
Cardiac ischaemia‐reperfusion (I/R) injury has been attributed to stress signals arising from an impaired mitochondrial electron transport chain (ETC), which include redox imbalance, metabolic stalling and excessive production of reactive oxygen species (ROS). The alternative oxidase (AOX) is a respiratory enzyme, absent in mammals, that accepts electrons from a reduced quinone pool to reduce oxygen to water, thereby restoring electron flux when impaired and, in the process, blunting ROS production. Hence, AOX represents a natural rescue mechanism from respiratory stress. This study aimed to determine how respiratory restoration through xenotopically expressed AOX affects the re‐perfused post‐ischaemic mouse heart. As expected, AOX supports ETC function and attenuates the ROS load in post‐anoxic heart mitochondria. However, post‐ischaemic cardiac remodelling over 3 and 9 weeks was not improved. AOX blunted transcript levels of factors known to be up‐regulated upon I/R such as the atrial natriuretic peptide (Anp) whilst expression of pro‐fibrotic and pro‐apoptotic transcripts were increased. Ex vivo analysis revealed contractile failure at nine but not 3 weeks after ischaemia whilst label‐free quantitative proteomics identified an increase in proteins promoting adverse extracellular matrix remodelling. Together, this indicates an essential role for ETC‐derived signals during cardiac adaptive remodelling and identified ROS as a possible effector.
Human RNF213, which encodes the protein mysterin, is a known susceptibility gene for moyamoya disease (MMD), a cerebrovascular condition with occlusive lesions and compensatory angiogenesis. Mysterin mutations, together with exposure to environmental trigger factors, lead to an elevated stroke risk since childhood. Mysterin is induced during cell stress, to function as cytosolic AAA+ ATPase and ubiquitylation enzyme. Little knowledge exists, in which context mysterin is needed. Here, we found that genetic ablation of several mitochondrial matrix factors, such as the peptidase ClpP, the transcription factor Tfam, as well as the peptidase and AAA+ ATPase Lonp1, potently induces Rnf213 transcript expression in various organs, in parallel with other components of the innate immune system. Mostly in mouse fibroblasts and human endothelial cells, the Rnf213 levels showed prominent upregulation upon Poly(I:C)-triggered TLR3-mediated responses to dsRNA toxicity, as well as upon interferon gamma treatment. Only partial suppression of Rnf213 induction was achieved by C16 as an antagonist of PKR (dsRNA-dependent protein kinase). Since dysfunctional mitochondria were recently reported to release immune-stimulatory dsRNA into the cytosol, our results suggest that mysterin becomes relevant when mitochondrial dysfunction or infections have triggered RNA-dependent inflammation. Thus, MMD has similarities with vasculopathies that involve altered nucleotide processing, such as Aicardi-Goutières syndrome or systemic lupus erythematosus. Furthermore, in MMD, the low penetrance of RNF213 mutations might be modified by dysfunctions in mitochondria or the TLR3 pathway.