Expertise: Not specified
Tools: Not specified
Related items
Public web page: Not specified
Organisms: Mus musculus, Rattus norvegicus, Homo sapiens, Macaca mulatta, Sus scrofa
Macroautophagy can regulate cell signalling and tumorigenesis via elusive molecular mechanisms. We establish a RAS mutant cancer cell model where the autophagy gene ATG5 is dispensable in A549 cells in vitro, yet promotes tumorigenesis in mice. ATG5 represses transcriptional activation by the TGFβ-SMAD gene regulatory pathway. However, autophagy does not terminate cytosolic signal transduction by TGFβ. Instead, we use proteomics to identify selective degradation of the signalling scaffold TRAF3. ...
Snapshots: No snapshots
The human lysosomal polypeptide ABC transporter TAPL (ABC subfamily B member 9, ABCB9) transports 6–59 amino-acids-long polypeptides from the cytosol into lysosomes. The subcellular localization of TAPL depends solely on its N-terminal transmembrane domain TMD0, which lacks conventional targeting sequences. However, the intracellular route and the molecular mechanisms that control TAPL localization remain unclear. Here, we delineated the route of TAPL to lysosomes and investigated the determinants ...
Submitter: Rainer Malik
Investigation: Proteomics
Assays: Affinity purification coupled with mass spectrometry proteomics
Snapshots: No snapshots
HEK293T cells stably expressing N-terminally HA-tagged BAG3 were employed to screen for novel BAG3 interacting proteins.
Submitter: Rainer Malik
Investigation: Proteomics
Assays: Affinity purification coupled with mass spectrometry proteomics
Snapshots: No snapshots
SILAC-based proximity proteomics of UAPEX2-tagged UBE2QL1 in differential LLOMe-treated HeLa cells
Submitter: Rainer Malik
Investigation: Proteomics
Assays: Affinity purification coupled with mass spectrometry proteomics
Snapshots: No snapshots
We selected GABARAPL2endoHA cells for a proof-of-principle immunoprecipitation (IP) followed by mass spectrometric (MS) analysis to identify new binding partner candidates of a hATG8 family member at endogenous levels. To distinguish between candidates that bind preferentially to PE-conjugated versus unconjugated GABARAPL2 we treated stable isotope labeling with amino acids in cell culture (SILAC)-labeled GABARAPL2endoHA cells with Torin1 and BafA1 (light) or ATG7 inhibitor (heavy).
Snapshots: No snapshots
Submitter: Rainer Malik
Assay type: Experimental Assay Type
Technology type: Technology Type
Investigation: Proteomics
Organisms: Homo sapiens
SOPs: No SOPs
Data files: Trafficking and interactions upon loss of TECPR2
Snapshots: No snapshots
Samples were lysed with lysis buffer (2% SDS, 50mM Tris-HCl pH 8.5, 10mM TCEP, 40mM chloroacetamide and protease inhibitor cocktail tablet [EDTA-free, Roche]). Samples were incubated for 5 minutes at 95°C before sonication with Sonic Vibra Cell at 1s ON/ 1s OFF pulse for 30s at a maximal amplitude of 30% to shear genomic DNA. After sonication, samples were incubated for 10min at 95°C. Proteins were precipitated using 3 volumes of ice-cold methanol, 1 volume Chloroform and 2.5 volumes ddH2O. After ...
Submitter: Rainer Malik
Assay type: Experimental Assay Type
Technology type: Technology Type
Investigation: Proteomics
Study: TBK1/ALS
Organisms: Mus musculus
SOPs: No SOPs
Data files: TBK1 p.E696K mutation causes autophagolysosomal...
Snapshots: No snapshots
Proximity labeling: Cells were supplemented with 500 µM biotin-phenol (IrisBiotech) for 30 min at 37°C before addition of 1 mM H2O2 at room temperature. Cells were then first washed with quencher solution (1 mM sodium azide, 10 mM sodium ascorbate and 5 mM Trolox in DPBS), then with DPBS, scraped and harvested. Proteinase K digest: All steps were carried out at 4°C unless stated otherwise. Cells were washed and suspended in homogenization buffer I (10 mM KCl, 1.5 mM MgCl2, 10 mM HEPES-KOH and 1 ...
Submitter: Rainer Malik
Assay type: Experimental Assay Type
Technology type: Technology Type
Investigation: Proteomics
Study: TBK1/ALS
Organisms: Homo sapiens
SOPs: No SOPs
Data files: Autophagosome content profiling in TBK1-E696K k...
Snapshots: No snapshots
BV2 cells were cultured in full medium in 10 cm cell culture dishes until they were confluent. MLN4924 (500 nM), CSN5i-3 (1 μM), or solvent control (0.01% DMSO) were added and the culturing continued for 6 h. After the incubation, cells were washed once with PBS, removed from the cell culture plate with a scraper, collected in tubes, and centrifuged in 1.5 ml Eppendorf tubes for 3 min to remove remaining PBS buffer, snap-frozen, and stored at -80 °C until further processing. Thereafter cells were ...
Submitter: Rainer Malik
Assay type: Experimental Assay Type
Technology type: Technology Type
Investigation: Proteomics
Organisms: Mus musculus
SOPs: No SOPs
Data files: The COP9 signalosome reduces neuroinflammation ...
Snapshots: No snapshots
All samples were reconstituted in 0.1% formic acid and separated using an Easy-nLC1200 liquid chromatograph (Thermo Scientific) followed by peptide detection on a Q Exactive HF mass spectrometer (Thermo Scientific). Samples were separated on a 75 µm x 15 cm custom-made fused silica capillary packed with C18AQ resin (Reprosil-PUR 120, 1.9 µm, Dr. Maisch), flow rates and gradients were adjusted according to the experiment. Except for plasma membranome analysis, peptide mixtures were separated on a ...
Submitter: Rainer Malik
Assay type: Experimental Assay Type
Technology type: Technology Type
Investigation: Proteomics
Study: TECPR2/secretory pathway
Organisms: Homo sapiens
SOPs: No SOPs
Data files: Trafficking and interactions upon loss of TECPR2
Snapshots: No snapshots
Creators: Rainer Malik, Christian Behrends
Submitter: Rainer Malik
The human lysosomal polypeptide ABC transporter TAPL (ABC subfamily B member 9, ABCB9) transports 6–59 amino-acids-long polypeptides from the cytosol into lysosomes. The subcellular localization of TAPL depends solely on its N-terminal transmembrane domain TMD0, which lacks conventional targeting sequences. However, the intracellular route and the molecular mechanisms that control TAPL localization remain unclear. Here, we delineated the route of TAPL to lysosomes and investigated the determinants ...
Creators: Rainer Malik, Christian Behrends
Submitter: Rainer Malik
Investigations: Proteomics
Studies: Lysosomal targeting of TAPL
HEK293T cells stably expressing N-terminally HA-tagged BAG3 were employed to screen for novel BAG3 interacting proteins.
Creators: Rainer Malik, Christian Behrends
Submitter: Rainer Malik
Investigations: Proteomics
Studies: BAG3-mediated autophagy
SILAC-based proximity proteomics of UAPEX2-tagged UBE2QL1 in differential LLOMe-treated HeLa cells
Creators: Rainer Malik, Christian Behrends
Submitter: Rainer Malik
Investigations: Proteomics
Studies: UBE2QL1/Lysosome damage
We selected GABARAPL2endoHA cells for a proof-of-principle immunoprecipitation (IP) followed by mass spectrometric (MS) analysis to identify new binding partner candidates of a hATG8 family member at endogenous levels. To distinguish between candidates that bind preferentially to PE-conjugated versus unconjugated GABARAPL2 we treated stable isotope labeling with amino acids in cell culture (SILAC)-labeled GABARAPL2endoHA cells with Torin1 and BafA1 (light) or ATG7 inhibitor (heavy).
Creators: Rainer Malik, Christian Behrends
Submitter: Rainer Malik
Abstract (Expand)
Authors: D. Brenner, K. Sieverding, J. Srinidhi, S. Zellner, C. Secker, R. Yilmaz, J. Dyckow, S. Amr, A. Ponomarenko, E. Tunaboylu, Y. Douahem, J. S. Schlag, L. Rodriguez Martinez, G. Kislinger, C. Niemann, K. Nalbach, W. P. Ruf, J. Uhl, J. Hollenbeck, L. Schirmer, A. Catanese, C. S. Lobsiger, K. M. Danzer, D. Yilmazer-Hanke, C. Munch, P. Koch, A. Freischmidt, M. Fetting, C. Behrends, R. Parlato, J. H. Weishaupt
Date Published: 6th May 2024
Publication Type: Journal
PubMed ID: 38517332
Citation: J Exp Med. 2024 May 6;221(5):e20221190. doi: 10.1084/jem.20221190. Epub 2024 Mar 22.
Abstract (Expand)
Authors: Y. Tian, J. Milic, L. S. Monasor, R. Chakraborty, S. Wang, Y. Yuan, Y. Asare, C. Behrends, S. Tahirovic, J. Bernhagen
Date Published: 19th Aug 2023
Publication Type: Journal
PubMed ID: 37597109
Citation: Cell Mol Life Sci. 2023 Aug 19;80(9):262. doi: 10.1007/s00018-023-04911-8.
Abstract (Expand)
Authors: J. Julg, D. Edbauer, C. Behrends
Date Published: 3rd Aug 2023
Publication Type: Journal
PubMed ID: 37317656
Citation: EMBO Rep. 2023 Aug 3;24(8):e55895. doi: 10.15252/embr.202255895. Epub 2023 Jun 15.
Abstract (Expand)
Authors: K. Nalbach, M. Schifferer, D. Bhattacharya, H. Ho-Xuan, W. C. Tseng, L. A. Williams, A. Stolz, S. F. Lichtenthaler, Z. Elazar, C. Behrends
Date Published: 16th Feb 2023
Publication Type: Journal
PubMed ID: 36797266
Citation: Nat Commun. 2023 Feb 16;14(1):870. doi: 10.1038/s41467-023-36553-6.
Abstract (Expand)
Authors: D. Schmitt, S. Bozkurt, P. Henning-Domres, H. Huesmann, S. Eimer, L. Bindila, C. Behrends, E. Boyle, F. Wilfling, G. Tascher, C. Munch, C. Behl, A. Kern
Date Published: 6th Dec 2022
Publication Type: Journal
PubMed ID: 36215690
Citation: EMBO Rep. 2022 Dec 6;23(12):e53065. doi: 10.15252/embr.202153065. Epub 2022 Oct 10.