Reagents and tools table
| Reagent/resource | Reference or source | Identifier or catalog number |
|---|---|---|
| Experimental models | ||
| HEK 293T cell (H. sapiens) | ATCC | CRL-11268 |
| HaCat cells (H. sapiens) | Kind gift from Prof. Rajiv Khanna, Brisbane, Australia. | Generated in the laboratory of Prof. Norbert E. Fusenig (J. Cell Biol. 1998) |
| HeLa cells (H. sapiens) | ATCC | CCL-2 |
| LCL (Lymphoblastoid cell line (H. sapiens) | Generated in our laboratory using Healthy donor cells and Epstein Barr Virus supernatant | N/A |
| MP1-specific CD4+ T cell clone | Generated in the laboratory of Prof. Christian Münz, University of Zürich, Switzerland | |
| Ramos B cells | ATCC | CRL-1596 |
| C57BL/6 N Lrba −/− | Generated in the laboratory of Prof. Manfred Kilimann. Max-Planck Institute Göttingen, Germany |
C57BL/6N-Lrbatm1.1Kili/Ieg RRID:IMSR_EM:14924 |
| Naive B cells (M. musculus) | From C57BL/6 N WT and Lrba−/− mice | N/A |
| Recombinant DNA | ||
| pmCherry-GFP-LC3 |
Dr. Ian Gentle University of Freiburg, Germany |
N/A |
| pClneo FLAG | Promega | E1841 |
| Myc-DDK LRBA | Origene | RC17204 |
| pVitro-hygro-N-myc-hVps34/Vps15-C-V5-his | Addgene | 24296 |
| pEGFP-Atg14L | Addgene | 21635 |
| pEGFP-C1-hUVRAG | Addgene | 24296 |
| pClneo FLAG LRBA fragments |
Dr. Bernice Lo National Institute of Health, USA |
N/A |
| pGFP-FYCO1 |
Dr. Christian Behrends University of Frankfurt, Germany |
N/A |
| GFP-LC3 | Prof. Christian Münz, University of Zürich, Switzerland | N/A |
| MP1-LC3 | Prof. Christian Münz, University of Zürich, Switzerland | N/A |
| Antibodies | ||
| Rabbit anti-LC3 | Cell Signaling | E5Q2K |
| Mouse anti-Lamp1 | Invitrogen | MA1-205 |
| Mouse anti-WIPI2 | Abcam | ab105459 |
| Rabbit ZFYVE/DFCP1 | LS-bio | LS-B15646-50 |
| Rabbit anti-GAPDH | Cell Signalling | 2118 |
| Mouse anti-FLAG | Sigma-Aldrich | SAB4301135 |
| Mouse anti-GFP | Santa Cruz | SC-9996 |
| Mouse anti-AMPK total | Cell Signaling | 2793S |
| Rabbit anti-pAMPK (T172) | Cell Signaling | 2535S |
| Rabbit anti-LC3 | Novus | NB110-2220 |
| Rabbit anti-LRBA | Sigma-Aldrich | HPA023597 |
| Rabbit anti-Myc | Cell Signaling | 2278S |
| Mouse anti-PIK3R4 | Novus | H00030849-M02 |
| Rabbit anti-p62 | Enzo Lifescience | 5114S |
| Mouse anti-p62 AF647 | Abcam | ab194721 |
| Rabbit anti-p70S6K total | Cell Signaling | 2708S |
| Mouse anti-p-p70S6K (T389) | Cell Signaling | 9206S |
| Mouse anti-HLA-DR | Cell signaling | NB-100-7785 |
| Mouse anti-HLA-DM AF488 | Santa Cruz | sc-32248 AF488 |
| Rabbit anti-FYCO1 | Santa Cruz | 25730-1-AP |
| Rabbit anti-P6RP | Cell signaling | 4858 |
| Rabbit anti-VPS34 | Novus | NB110-87320SS |
| Mouse anti-HLA-DR FITC | Invitrogen | A16118 |
| Rabbit anti-pS6RP Pacific Blue | Cell signaling | 8520S |
| Anti-rabbit IgG-FITC | Invitrogen | A16118 |
| Anti-rabbit AF488 | Cell Signaling | 4412 |
| Anti-rabbit AF555 | Cell Signaling | 4413 |
| Anti-mouse AF647 | Cell Signaling | 4410 |
| HRP-linked anti-mouse | Santa Cruz | sc-516102 |
| HRP-linked anti-rabbit | Invitrogen | 31470 |
| HRP-linked anti-Tubulin | Prointech | HRP-66031 |
| PLA probe anti-mouse minus | Sigma-Aldrich | DU92004 |
| PLA probe anti-goat minus | Sigma-Aldrich | DU92006 |
| PLA probe anti-rabbit plus | Sigma-Aldrich | DUO92101 |
| Oligonucleotides and other sequence-based reagents | ||
| gRNA for CrispR | IDT | N.A. |
| shControl | Thermo Fisher | |
| shLRBA | Thermo Fisher | |
| Chemicals, enzymes and other reagents | ||
| 3’3-diaminobenzidine | Sigma-Aldrich | D12384 |
| ABC Elite Kit | BIOZOL | VEC-PK-6100 |
| Bafilomycin A1 | InvivoGen | tlrl-baf1 |
| B cell isolation kit, mouse | Miltenyi Biotec | 130-090-862 |
| BD Cytofix/Cytoperm solutionTM | BD | 554714 |
| BSA Albumin Bovine V | Serva | 11903.03 |
| Chloroquine | Sigma-Aldrich | C6628 |
| DAPI | Sigma-Aldrich | D9542 |
| DMEM high glucose | Life Technologies GmbH | 31966047 |
| DPBS | Sigma-Aldrich | D8537 |
| Duolink In Situ Mounting Medium with DAPI | Merck | DEU82040 |
| Duolink PLA Kit | Sigma-Aldrich | DUO92008 |
| Durcupan resin | Sigma-Aldrich | 44611 |
| Dynabeads protein G | Thermo Fisher Scientific | 10004D |
| EBSS | Thermo Fisher | 14155063 |
| EDTA-free protease inhibitor cocktail | Roche | 5,893E + 09 |
| Ethanol | VWR | 20.821.310 |
| Ethylenediaminetetraacetic acid solution (EDTA) | Sigma-Aldrich | E8008 |
| Fetal bovine serum (FBS) | Thermo Fisher | F7524 |
| Glutraldehyde | Sigma-Aldrich | 354400 |
| Goat serum | Sigma-Aldrich | G9023 |
| HEPES | Sigma-Aldrich | H0887 |
| Hydrochloric acid (HCl) | AppliChem | 182883.12 |
| IFN-γ ELISA Kit | MABTECH | 3420-1H-6 |
| IL-6 ELISA Kit | MABTECH | 3460-1HP-1 |
| Lead(II) acetate trihydrate | Merck Millipore | 107375 |
| Lipofectamine™ 2000 | Invitrogen | 11668-027 |
| LPS from E. coli 055 | Sigma-Aldrich | L2654 |
| Lysotracker Red | Invitrogen | L12492 |
| Methanol | Honeywell | 32213 |
| MG132 | InvivoGen | tlrl-mg132-2 |
| Milk powder | Roth | T145.1/.3 |
| MIP-1β ELISA Kit | Thermo Fisher | 88-7034-22 |
| NP-40 | Calbiochem | 492018 |
| Opti-MEM™ - Reduced Serum Medium | Thermo Fisher | 31985070 |
| Optiprep | Sigma-Aldrich | D1556 |
| Osimum tetroxide (OsO4) | Sigma-Aldrich | 201030 |
| Paraformaldehyde | Sigma-Aldrich | 158127 |
| Penicillin-Streptomycin (10 000U/ml) | Thermo Fisher | 15140122 |
| Perm/Wash BufferTM | BD | 554723 |
| PI(3)P Mass ELISA kit | Echelon | K-3300 |
| PierceTM BCA Protein Assay Kit | Thermo Fisher | 23225 |
| Potassium hydroxide (KOH) | Sigma-Aldrich | 6103 |
| Propylene oxide | Sigma-Aldrich | 75-56-9 |
| Proteinase K | Zymo Research | D3001-2 |
| PVDF membrane | Bio-Rad Laboratories GmbH | 1620177 |
| Rapamycin | InvivoGen | tlrl-rap |
| Recombinant human IFN-γ | Peprotech | 300-02 |
| RPMI 1640 + L-Glutamine | Sigma-Aldrich | 21875091 |
| Saponin | Sigma-Aldrich | 47036 |
| Signal Fire/Plus chemiluminescent substrates | Cell Signaling | 12630S |
| Silver enhancement HQ-Silver kit | Nanoprobe | 2012 |
| Sodium chloride (NaCl) | Roth | 9265.1 |
| Sodium deoxycholate | Sigma-Aldrich | 89904 |
| Sodium dodecyl sulfate (SDS) | Sigma-Aldrich | 436143 |
| Sodium pyruvate | Sigma-Aldrich | P5280 |
| Sucrose | Sigma-Aldrich | 84097 |
| Sulfuric acid (H2SO4) | Sigma-Aldrich | 339741 |
| TMB substrate | MABTECH | 3652-F10 |
| TNF-α ELISA Kit | MABTECH | 3512-1HP-1 |
| Torin1 | InVivoGen | inh-tor1 |
| Trichloroacetic acid (TCA) | Sigma-Aldrich | 8.223.420.250 |
| Tris | Applichem GmbH | A1379 |
| Triton X-100 | Sigma-Aldrich | 93443 |
| Trypsin-EDTA (0.05%), phenol red | Thermo Fischer | 25300-054 |
| Tween 20 | Sigma-Aldrich | P9416 |
| Uranyl acetate | Polysciences | 21447-25 |
| Viability Dye eFluor780 | Invitrogen | 65-0865-14 |
| VPS34-In1 | Selleckchem | S7980 |
| Wortmannin | InVivogen | tlrl-wtm |
| Software | ||
| Affinity designer 2 | Serif | N/A |
| Duolink Image Tool | Sigma-Aldrich | |
| FlowJo | Treestar Inc | |
| FUNCBase database | ||
| GraphPad Prism 10 | ||
| High Ambiguity Driven Biomolecular DOCKing, version 2.2 | ||
| Homology modelling software Prime | Schrödinger Suite 2018-1, LLC | |
| ImageJ/FiJi | ||
| ImageSP | ||
| Imaris9.7 | Oxford Instrument | |
| STRING database | ||
| Zeiss blue/black | Zeiss | |
| Other | ||
| BD FACS canto II | Beckton Dickinson | |
| Dounce homogenizer | WHEATON® Dounce Tissue Grinder | |
| Fusion SL device | Peqlab | |
| SP8 | Leica | |
| Zeiss LSM 710 | Zeiss | |
| Zeiss LSM 880 | Zeiss | |
| Zeiss LEO 906 transmission electron microscope | Zeiss | |