SEEK ID: http://localhost:3000/projects/2
Public web page: Not specified
Organisms: Mus musculus, Rattus norvegicus, Homo sapiens, Macaca mulatta, Sus scrofa
FAIRDOM PALs: No PALs for this Project
Project created: 29th May 2024
Related items
- People (31)
- Institutions (7)
- Investigations (3)
- Studies (60)
- Assays (64)
- Data files (86)
- Publications (52)
- Sample types (0+1)
Projects: SyNergy - published datasets
Institutions: DZNE
Projects: SyNergy - published datasets
Institutions: Klinikum der Universität München
Projects: SyNergy - published datasets
Institutions: DZNE
Projects: SyNergy - published datasets
Institutions: Klinikum der Universität München
Projects: SyNergy - published datasets
Institutions: DZNE
Submitter: Rainer Malik
Studies: A genome-wide in vivo CRISPR screen identifies essential regulators of T..., Correlation spatial transcriptomics/EM, Direct neuronal reprogramming of NDUFS4 patient cells identifies the unf..., Early adaptive immune activation detected in monozygotic twins with prod..., Histone Deacetylase 9 Activates IKK to Regulate Atherosclerotic Plaque V..., Innate immune memory after brain injury drives inflammatory cardiac dysf..., Microglia in white matter aging, Myelin degeneration in leucodystrophies, Oligodendrocytes in AD models, Oligodendrocytes in white matter aging, Phagocyte-mediated synapse removal in cortical neuroinflammation is prom..., Skin and gut imprinted helper T cell subsets exhibit distinct functional..., T cells modulate the microglial response to brain ischemia
Assays: Bulk RNA-seq, Expression profiling by high throughput sequencing, Expression profiling by high throughput sequencing, Expression profiling by high throughput sequencing, Expression profiling by high throughput sequencing, Expression profiling by high throughput sequencing, Expression profiling by high throughput sequencing, Expression profiling by high throughput sequencing, Expression profiling by high throughput sequencing, Expression profiling by high throughput sequencing, Expression profiling by high throughput sequencing, Single cell RNA sequencing experiment, scRNA-seq 5 day, scRNA-seq day 20
Snapshots: No snapshots
Submitter: Rainer Malik
Studies: GIGASTROKE, MEGASTROKE
Snapshots: No snapshots
Submitter: Rainer Malik
Studies: ACSL3/GABARAPL2 interactor, ADAM10-Mediated Ectodomain Shedding Is an Essential Driver of Podocyte D..., AMPK/Lysosomal Damage/Galectins, An optimized quantitative proteomics method establishes the cell type-re..., Autophagosome content profiling, Autophagy cargo/CD4+ T cell proliferation, BAG3-mediated autophagy, Basic Fibroblast Growth Factor 2-Induced Proteome Changes Endorse Lewy B..., Beneficial Effect of ACI-24 Vaccination on Aβ Plaque Pathology and Micro..., C9orf72/UBR5/Quality control, CCNF/ALS, CNN2/Lysosome damage, COP9 signalosome/Ischemic stroke, Cell-type-specific profiling of brain mitochondria reveals functional an..., Deciphering sources of PET signals in the tumor microenvironment of glio..., Endothelial Aging, Experimental evidence for temporal uncoupling of brain Aβ deposition and..., Fibrillar Aβ triggers microglial proteome alterations and dysfunction in..., Loss of NPC1 enhances phagocytic uptake and impairs lipid trafficking in..., Lysosomal targeting of TAPL, NDP52 interactome, Neuronal differentiation of LUHMES cells is accompanied by substantial c..., NrCAM is a marker for substrate-selective activation of ADAM10 in Alzhei..., Pro-inflammatory activation following demyelination is required for myel..., Protein content of autophagic vesicles, Proteolysis enhanced proximity proteomics, Proteomic and lipidomic profiling of demyelinating lesions identifies fa..., Proteomic profiling in cerebral amyloid angiopathy reveals an overlap wi..., Proteomics of inflammasome activation for rapid immune responses, Proteomics of mouse brain endothelium uncovers dysregulation of vesicula..., Reactivated endogenous retroviruses promote protein aggregate spreading, Signal peptide peptidase-like 2c impairs vesicular transport and cleaves..., Signatures of glial activity can be detected in the CSF proteome, Spatial proteomics in three-dimensional intact specimens, Spatial proteomics reveals secretory pathway disturbances caused by neur..., TBK1/ALS, TECPR2/secretory pathway, Targeting the TCA cycle can ameliorate widespread axonal energy deficien..., The Alzheimer's disease-linked protease BACE1 modulates neuronal IL-6 si..., The Alzheimer's disease-linked protease BACE2 cleaves VEGFR3 and modulat..., The intramembrane protease SPPL2c promotes male germ cell development by..., The pseudoprotease iRhom1 controls ectodomain shedding of membrane prote..., The tetraspanin Tspan15 is an essential subunit of an ADAM10 scissor com..., UBE2QL1/Lysosome damage, UBQLN2/ALS
Assays: Affinity purification coupled with mass spectrometry proteomics, Affinity purification coupled with mass spectrometry proteomics, Affinity purification coupled with mass spectrometry proteomics, Affinity purification coupled with mass spectrometry proteomics, Affinity purification coupled with mass spectrometry proteomics, Affinity purification coupled with mass spectrometry proteomics, Affinity purification coupled with mass spectrometry proteomics, Bottom-up proteomics, Gel-based experiment, Proteomics analysis of brain endothelial cells, Proteomics of Inflammasome, SWATH MS, Shotgun Proteomics, Shotgun proteomics, Shotgun proteomics, Shotgun proteomics, Shotgun proteomics, Shotgun proteomics, Shotgun proteomics, Shotgun proteomics, Shotgun proteomics, Shotgun proteomics, Shotgun proteomics, Shotgun proteomics, Shotgun proteomics, Shotgun proteomics, Shotgun proteomics, Shotgun proteomics, Shotgun proteomics, Shotgun proteomics, Shotgun proteomics, Shotgun proteomics, Shotgun proteomics, Shotgun proteomics, Shotgun proteomics, Shotgun proteomics, Shotgun proteomics, Shotgun proteomics, Shotgun proteomics, Shotgun proteomics, Shotgun proteomics, Shotgun proteomics, Shotgun proteomics, Shotgun proteomics, Shotgun proteomics, Shotgun proteomics, Shotgun proteomics, Shotgun proteomics
Snapshots: Snapshot 1
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: Proteomics
Technology type: Mass Spectrometry
Investigation: Proteomics
Study: Endothelial Aging
Organisms: No organisms
SOPs: No SOPs
Data files: LC-MS/MS analysis of AAV-treated ARF6-KO vs WT ..., LC-MS/MS analysis of isolated murine brain endo..., LC-MS/MS analysis of isolated murine brain endo...
Snapshots: No snapshots
Submitter: Rainer Malik
Assay type: Proteomics
Technology type: Mass Spectrometry
Investigation: Proteomics
Organisms: No organisms
SOPs: No SOPs
Data files: IKKβ binds NLRP3 providing a shortcut to inflam...
Snapshots: No snapshots
Submitter: Rainer Malik
Assay type: Transcriptomics
Technology type: Technology Type
Investigation: Transcriptomics
Organisms: No organisms
SOPs: No SOPs
Data files: Histone deacetylase 9 promotes vascular inflamm...
Snapshots: No snapshots
Submitter: Rainer Malik
Biological problem addressed: Genome Scale
Investigation: Genetics
Study: MEGASTROKE
Organisms: No organisms
Models: No Models
SOPs: No SOPs
Data files: MEGASTROKE IS EUR
Snapshots: No snapshots
Submitter: Rainer Malik
Assay type: Experimental Assay Type
Technology type: Technology Type
Investigation: Transcriptomics
Organisms: No organisms
SOPs: No SOPs
Data files: White matter aging drives microglial diversity, White matter aging drives microglial diversity
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: A. Schmidt, B. Hrupka, F. van Bebber, S. Sunil Kumar, X. Feng, S. K. Tschirner, M. Assfalg, S. A. Muller, L. S. Hilger, L. I. Hofmann, M. Pigoni, G. Jocher, I. Voytyuk, E. L. Self, M. Ito, K. Hyakkoku, A. Yoshimura, N. Horiguchi, R. Feederle, B. De Strooper, S. Schulte-Merker, E. Lammert, D. Moechars, B. Schmid, S. F. Lichtenthaler
Date Published: 18th Jun 2024
Publication Type: Journal
PubMed ID: 38888964
Citation: J Clin Invest. 2024 Jun 18:e170550. doi: 10.1172/JCI170550.
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: K. Todorov-Volgyi, J. Gonzalez-Gallego, S. A. Muller, N. Beaufort, R. Malik, M. Schifferer, M. I. Todorov, D. Crusius, S. Robinson, A. Schmidt, J. Korbelin, F. Bareyre, A. Erturk, C. Haass, M. Simons, D. Paquet, S. F. Lichtenthaler, M. Dichgans
Date Published: 22nd Apr 2024
Publication Type: Journal
PubMed ID: 38519806
Citation: Nat Aging. 2024 Apr;4(4):595-612. doi: 10.1038/s43587-024-00598-z. Epub 2024 Mar 22.
Abstract (Expand)
Authors: G. Sonsalla, A. B. Malpartida, T. Riedemann, M. Gusic, E. Rusha, G. Bulli, S. Najas, A. Janjic, B. A. Hersbach, P. Smialowski, M. Drukker, W. Enard, J. H. M. Prehn, H. Prokisch, M. Gotz, G. Masserdotti
Date Published: 3rd Apr 2024
Publication Type: Journal
PubMed ID: 38266647
Citation: Neuron. 2024 Apr 3;112(7):1117-1132.e9. doi: 10.1016/j.neuron.2023.12.020. Epub 2024 Jan 23.
Abstract (Expand)
Authors: J. Groh, T. Abdelwahab, Y. Kattimani, M. Horner, S. Loserth, V. Gudi, R. Adalbert, F. Imdahl, A. E. Saliba, M. Coleman, M. Stangel, M. Simons, R. Martini
Date Published: 30th Oct 2023
Publication Type: Journal
PubMed ID: 37903797
Citation: Nat Commun. 2023 Oct 30;14(1):6911. doi: 10.1038/s41467-023-42570-2.