KEY RESOURCES TABLE
| REAGENT or RESOURCE | SOURCE | IDENTIFIER |
|---|---|---|
| Antibodies—western blot and immunofluorescence | ||
| CD68 antibody, Abcam | Abcam | Cat# ab125212; RRID:AB_10975465 |
| UCP1 antibody, Abcam | Abcam | Cat# ab23841; RRID:AB_2213764 |
| 4 Hydroxynonenal antibody, Abcam | Abcam | Cat# ab46545; RRID:AB_722490 |
| Anti-CD36 antibody | Abcam | Cat# ab124515 |
| Recombinant Anti-iNOS antibody [EPR16630] | Abcam | Cat# ab205529 |
| Phospho-DRP1 (Ser637) Antibody, Cell Signaling TechnologySA | Cell Signaling Technology | Cat# 4867; RRID:AB_10622027 |
| Phospho-(Ser/Thr) PKA Substrate Antibody, Cell Signaling Technology | Cell Signaling Technology | Cat# 9621; RRID:AB_330304 |
| Pyruvate Dehydrogenase E1 beta subunit antibody, GeneTex | GeneTex | Cat# GTX119625; RRID:AB_11163683 |
| MDH2 antibody, GeneTex | GeneTex | Cat# GTX105870; RRID:AB_1950902 |
| ACAA2 antibody, GeneTex | GeneTex | Cat# GTX115417; RRID:AB_2885361 |
| Pyruvate Dehydrogenase E1 alpha antibody, GeneTex | GeneTex | Cat# GTX104015; RRID:AB_1951155 |
| Beta Tubulin antibody, Proteintech | Proteintech | Cat# 10094–1-AP; RRID:AB_2210695 |
| Beta Actin Polyclonal antibody | Proteintech | Cat# 20536-i-ap |
| PINK1 (38CT20.8.5) | Santa Cruz Biotechnology | Cat# sc-517353 |
| cytochrome c (A-8) antibody, Santa Cruz Biotechnology | Santa Cruz Biotechnology | Cat# sc-13156; RRID:AB_627385 |
| Tom20 (FL-145) Antibody, Santa Cruz Biotechnology | Santa Cruz Biotechnology | Cat# sc-11415; RRID:AB_2207533 |
| HSP 60 (H-300) Antibody, Santa Cruz Biotechnology | Santa Cruz Biotechnology | Cat# sc-13966; RRID:AB_2121457 |
| PCB (H-2) antibody, Santa Cruz Biotechnology | Santa Cruz Biotechnology | Cat# sc-271493; RRID:AB_10649369 |
| VDAC1 Antibody (B-6), Santa Cruz Biotechnology | Santa Cruz Biotechnology | Cat# sc-390996; RRID:AB_2750920 |
| Rabbit Anti-ACO2 Polyclonal Antibody, Unconjugated, Clone A-22, Santa Cruz Biotechnology | Santa Cruz Biotechnology | Cat# sc-130677; RRID:AB_2221514 |
| Mass-Cytometry antibodies | Table S4 | |
| Anti-CD63 Antibody, System Biosciences | System Biosciences | Cat# EXOAB-CD63A-1; RRID:AB_2561274 |
| Goat anti-Mouse IgG (H+L) Cross-Adsorbed Secondary Antibody, Alexa Fluor 555, Thermo Fisher Scientific | Thermo Fisher Scientific | Cat# A-21422; RRID:AB_2535844 |
| Goat anti-Mouse IgG (H+L) Cross-Adsorbed Secondary Antibody, Alexa Fluor 488, Thermo Fisher Scientific | Thermo Fisher Scientific | Cat# A-11001; RRID:AB_2534069 |
| Goat anti-Rabbit IgG (H+L) Cross-Adsorbed Secondary Antibody, Alexa Fluor 488, Thermo Fisher Scientific | Thermo Fisher Scientific | Cat# A-11008; RRID:AB_143165 |
| Goat anti-Rabbit IgG (H+L) Cross-Adsorbed Secondary Antibody, Alexa Fluor 555, Thermo Fisher Scientific | Thermo Fisher Scientific | Cat# A-21428; RRID:AB_2535849 |
| Vinculin Monoclonal Antibody (VLN01), Thermo Fisher Scientific | Thermo Fisher Scientific | Cat# MA5–11690; RRID:AB_10976821 |
|
Antibodies—flow cytometry | ||
| Rat Anti-CD45 Monoclonal Antibody, PerCP-Cy5.5 Conjugated, Clone 30-F11, BD Biosciences | BD Biosciences | Cat# 550994; RRID:AB_394003 |
| CD195 (CCR5) antibody, BD Biosciences | BD Biosciences | Cat# 743697; RRID:AB_2741679 |
| APC anti-mouse CD11c antibody, BioLegend | Biolegend | Cat# 117309; RRID:AB_313778 |
| PE anti-mouse/human CD11b antibody, BioLegend | BioLegend | Cat# 101207; RRID:AB_312790 |
| FITC anti-mouse Ly-6C antibody, BioLegend | BioLegend | Cat# 128005; RRID:AB_1186134 |
| Purified anti-mouse CD64 (FcgammaRI) antibody, BioLegend | BioLegend | Cat# 139301; RRID:AB_10612757 |
| Purified anti-mouse F4/80 antibody, BioLegend | BioLegend | Cat# 123101; RRID:AB_893504 |
| Alexa Fluor(R) 647 anti-mouse Tim-4 antibody, BioLegend | BioLegend | Cat# 130007; RRID:AB_2201842 |
| FITC anti-mouse/human CD11b antibody, BioLegend | BioLegend | Cat# 101206; RRID:AB_312789 |
| PE/Cyanine7 anti-mouse/human CD11b antibody, BioLegend | BioLegend | Cat# 101216; RRID:AB_312799 |
| PerCP/Cyanine5.5 anti-mouse CD36 antibody, BioLegend | BioLegend | Cat# 102619; RRID:AB_2750187 |
| Brilliant Violet 510(TM) anti-mouse CD45 antibody, BioLegend | BioLegend | Cat# 103138; RRID:AB_2563061 |
| CD62L BV650 | BioLegend | Cat# 1122265 |
| Brilliant Violet 711(TM) anti-mouse CD64 (FcgammaRI) antibody, BioLegend | BioLegend | Cat# 139311; RRID:AB_2563846 |
| FITC anti-mouse CD80 antibody, BioLegend | BioLegend | Cat# 104705; RRID:AB_313126 |
| PE anti-mouse CD115 (CSF-1R) antibody, BioLegend | BioLegend | Cat# 135505; RRID:AB_1937254 |
| PerCP/Cyanine5.5 anti-mouse CD169 (Siglec-1) antibody, BioLegend | BioLegend | Cat# 142409; RRID:AB_2563908 |
| PE/Cyanine7 anti-mouse CD206 (MMR) antibody, BioLegend | BioLegend | Cat# 141720; RRID:AB_2562248 |
| FITC anti-mouse CD192 (CCR2) antibody, BioLegend | BioLegend | Cat# 150608; RRID:AB_2616980 |
| Brilliant Violet 421(TM) anti-mouse CX3CR1 antibody, BioLegend | BioLegend | Cat# 149023; RRID:AB_2565706 |
| APC anti-mouse F4/80 antibody, BioLegend | BioLegend | Cat# 123116; RRID:AB_893481 |
| APC/Cyanine7 anti-mouse F4/80 antibody, BioLegend | BioLegend | Cat# 123117; RRID:AB_893489 |
| PE/Cyanine7 anti-mouse Ly-6C antibody, BioLegend | BioLegend | Cat# 128018; RRID:AB_1732082 |
| PE/Dazzle(TM) 594 anti-mouse Ly-6G antibody, BioLegend | BioLegend | Cat# 127648; RRID:AB_2566319 |
| Brilliant Violet 650(TM) anti-mouse CD62L antibody, BioLegend | BioLegend | Cat# 104453; RRID:AB_2800559 |
| CD11b MicroBeads, human and mouse | Miltenyi Biotec | Cat#130–049-601 |
| Anti-F4/80 MicroBeads UltraPure, mouse antibody, Miltenyi Biotec | Miltenyi Biotec | Cat# 130–110-443; RRID:AB_2858241 |
| CD11b Antibody, anti-human/mouse, APC-Vio® 770, Miltenyi Biotec | Miltenyi Biotec | Cat# 130–113-232; RRID:AB_2726043 |
| CD11c-APC, mouse antibody, Miltenyi Biotec | Miltenyi Biotec | Cat# 130–102-800; RRID:AB_2660155 |
| CD68 Antibody, anti-mouse, PE, Miltenyi Biotec | Miltenyi Biotec | Cat# 130–102-923; RRID:AB_2659048 |
| CD86 Antibody, anti-mouse, FITC, Miltenyi Biotec | Miltenyi Biotec | Cat# 130–123-672; RRID:AB_2889633 |
| CD200R Antibody, anti-mouse, PE, REAfinity™, Miltenyi Biotec | Miltenyi Biotec | Cat# 130–112-458; RRID:AB_2725830 |
| MHC Class II (I-Ak) Antibody, anti-mouse, APC, REAfinity™, Miltenyi Biotec | Miltenyi Biotec | Cat# 130–109-273; RRID:AB_2652875 |
| Mouse CCR2 PE-conjugated Antibody | R&D Systems | Cat# FAB5538P |
|
Antibodies—magnetic cells sorting | ||
| Miltenyi Biotec, Inc. CD45 MICROBEADS | Miltenyi Biotec | Cat#130–052-301;RRID:AB_2877061 |
|
Antibodies—mass cytometry | ||
| CD3e | Fluidigm | Cat# 3152004b |
| CD4 | Fluidigm | Cat# 3145002b |
| CD8a | Fluidigm | Cat# 3153012b |
| CD11b | Fluidigm | Cat# 3148003b |
| CD11c | Fluidigm | Cat# 3142003b |
| CD19 | Fluidigm | Cat# 3149002b |
| CD25 | Fluidigm | Cat# 3150002b |
| CD45 | Fluidigm | Cat# 3147003b |
| CD69 | Fluidigm | Cat# 3143004b |
| CD80 | Fluidigm | Cat# 3171008b |
| CD86 | Fluidigm | Cat# 3172016b |
| CD90 | Fluidigm | Cat# 3156006b |
| CD117 | Fluidigm | Cat# 3166004b |
| CD161 | Fluidigm | Cat# 3170002b |
| CD184 | Fluidigm | Cat# 3159030b |
| CD197 | Fluidigm | Cat# 3164013a |
| CD206 | Fluidigm | Cat# 3169021b |
| CD335 | Fluidigm | Cat# 3167008b |
| F4/80 | Fluidigm | Cat# 3146008b |
| FceR1a | Fluidigm | Cat# 3176006b |
| Ly6c | Fluidigm | Cat# 3162014b |
| Ly6g | Fluidigm | Cat# 3141008b |
|
Bacterial and virus strains | ||
| Pdhb (NM_024221) Mouse Tagged ORF Clone Lentiviral Particle | OriGene Technologies | Cat# MR205484L3V |
| Sod2 (BC066063) Mouse Tagged ORF Clone Lentiviral Particle | OriGene Technologies | Cat# MR201642L2V |
| Lenti ORF control particles of pLenti-C-mGFP-P2A-Puro | OriGene Technologies | Cat# PS100093V |
| PINK1 shRNA (m) Lentiviral particles | Santa Cruz Biotechnologies | Cat# sc-44599-V |
|
Chemicals, peptides, and recombinant proteins | ||
| Recombinant Mouse MCSF (Animal-Free) | Cell Guidance Systems | Cat# GMF8AF |
| Clophosome anionic liposomal clodronate for macrophage depletion | FormuMax Scientific | Cat# F70101C-A |
| Placebo control liposomes for Clophosome-A (anionic) | FormuMax Scientific | Cat# F70101-A |
| Puromycin | Invivogen | Cat# ant-pr-1 |
| Chloroquine diphosphate salt | Sigma Aldrich | # C6628 |
| DNase I | Sigma Aldrich | Cat# 10104159001 |
| 3,3′,5-Triiodo-L-thyronine sodium salt powder, BioReagent, suitable for cell culture 3,3′,5-Triiodo-L-thyronine sodium salt | Sigma Aldrich | Cat# T6397 |
| Rosiglitazone,≥98% (HPLC) | Sigma Aldrich | Cat# R2408 |
| Insulin solution human | Sigma Aldrich | Cat# I9278 |
| 3-Isobutyl-1-methylxanthine,BioUltra, ≥99% | Sigma Aldrich | Cat# I7018 |
| Indomethacin | Sigma Aldrich | Cat# I7378 |
| Cl 316,243 hydrate, ≥98% (HPLC), powder | Sigma Aldrich | Cat# C5976 |
| Carbonyl cyanide 4-(trifluoromethoxy)pheny lhydrazone ≥98% (TLC), powder Carbonyl cyanide 4-(trifluoromethoxy)pheny lhydrazone | Sigma Aldrich | Cat# C2920 |
| N-Acetyl-L-cysteine, cell culture tested, BioReagent, CAS 616–91-1, Sigma-Aldrich | Sigma Aldrich | Cat# A9165 |
| Doxycycline hyclate, ≥98% (HPLC) | Sigma Aldrich | Cat# D9891 |
| (R)-(—)-Isoproterenol crystalline (R)-(—)-Isoproterenol | Sigma Aldrich | Cat# I6379 |
| AMPK Inhibitor, Compound C – CAS 866405–64-3 – Calbiochem | Sigma Aldrich | Cat# 171260 |
| Antimycin a from Streptomyces sp. | Sigma Aldrich | Cat# A8674 |
| Lipopolysaccharides from Escherichia coli O111:B4,gamma-irradiated, BioXtra | Sigma Aldrich | Cat# L4391 |
| Sulfo-N-succinimidyl Oleate sodium | Sigma Aldrich | Cat# SML2148 |
| Rotenone | Sigma Aldrich | Cat# R8875 |
| Oligomycin A | Sigma Aldrich | Cat# 75351 |
| Collagenase, Type I, powder | Thermo Fisher Scientific | Cat# 17100017 |
| Collagenase, Type II, powder | Thermo Fisher Scientific | Cat# 17101015 |
| eBioscience™ 1X RBC Lysis Buffer | Thermo Fisher Scientific | Cat# 00–4333-57 |
|
Critical commercial assays | ||
| Seahorse XFe96 FluxPak | Agilent Technologies | Cat# 102416–100 |
| Seahorse XF DMEM assay medium pack, pH 7.4 | Agilent Technologies | Cat# 103680–100 |
| Zombie UV™ Fixable Viability Kit | Biolegend | Cat# 423107 |
| Zombie NIR™ Fixable Viability Kit | Biolegend | Cat# 423105 |
| Maxpar 10X Barcode Perm Buffer | Fluidigm | Cat# 201057 |
| Cell-ID™ 20-Plex Pd Barcoding Kit | Fluidigm | Cat# 201060 |
| Maxpar® Cell Staining Buffer | Fluidigm | Cat# 201068 |
| Cell-ID™ Intercalator-Ir | Fluidigm | Cat# 201192A |
| EQ Four Element Calibration Beads | Fluidigm | Cat# 201078 |
| OctoMACS™ Starting Kit | Miltenyi Biotec | Cat# 130–042-108 |
| QuadroMACS™ Starting Kit (LS) | Miltenyi Biotec | Cat# 130–091-051 |
| MS Columns | Miltenyi Biotec | Cat# 130–042-201 |
| LS Columns | Miltenyi Biotec | Cat# 130–042-401 |
| Pre-Separation Filters (30 μm) | Miltenyi Biotec | Cat# 130–041-407 |
| Mitochondria Isolation Kit, mouse tissue | Miltenyi Biotec | Cat# 130–096-946 |
| RNeasy Lipid Tissue Mini Kit | Qiagen | Cat# 74804 |
| Mito Tracker Green | Thermo Fisher Scientific | Cat# M7514 |
| Lipofectamine™ 2000 Transfection Reagent | Thermo Fisher Scientific | Cat# 11668019 |
| Annexin V Conjugates for Apoptosis Detection | Thermo Fisher Scientific | Cat# A35111 |
| Exosome Spin Columns (MW 3000) (DISCONTINUED PRODUCT) | Thermo Fisher Scientific | Cat# 4484449 |
| MitoTracker™ Red CMXRos | Thermo Fisher Scientific | Cat# M7512 |
| MitoSOX™ Red Mitochondrial Superoxide Indicator, for live-cell imaging | Thermo Fisher Scientific | Cat# M36008 |
| LysoTracker™ Deep Red | Thermo Fisher Scientific | Cat# L12492 |
| Alexa Fluor™ 488 Phalloidin | Thermo Fisher Scientific | Cat# A12379 |
|
Deposited data | ||
| RNA-seq data | This paper | ArrayExpress: E-MTAB-10655 |
| Proteomics data | This paper | ProteomeXchange: PXD026080 |
|
Experimental models: Cell lines | ||
| iBPA_m | (Liu et al., 2019) | N/A |
| iBPA_h | (Liu et al., 2019) | N/A |
| RAW 264.7 cell line, ATCC | ATCC | Cat# TIB-71, RRID:CVCL_0493 |
| T37i murine preadipocytes | Professor Marc Lombes (INSERM U1185, Paris, France) | |
|
Oligonucleotides | ||
| mtDendra2 | (Brestoff et al., 2021) | N/A |
| CD45.1 | (Brestoff et al., 2021) | N/A |
| Adipoq Cre +/− | (Brestoff et al., 2021) | N/A |
| MitoFat | (Brestoff et al., 2021) | N/A |
| CD45.2 WT | (Brestoff et al., 2021) | N/A |
| CD45.2 DENDRA2 | (Brestoff et al., 2021) | N/A |
| CD169 MICE | (Chow et al., 2011) | N/A |
| See Real-time qPCR section for qPCR primers | N/A | N/A |
| Smpd3 (Mouse) - 3 unique 27mer siRNA duplexes - 2 nmol each | OriGene Technologies | Cat# SR427338 |
| PINK1 siRNA (human) | OriGene Technologies | CAT#: SR324912 |
| C57BL/6J | The Jackson Laboratory | #000664; RRID: IMSR_JAX:000664 |
|
Software and algorithms | ||
| Trimmomatic version 0.36 | (Bolger et al., 2014) | N/A |
| JACoP plugin | (Bolte and Cordeliè res, 2006) | N/A |
| HISAT2 version 2.1.0 | (Kim et al., 2015) | N/A |
| Cytobank software platform | (Kotecha et al., 2010) | N/A |
| StringTie version 1.3.4d | (Pertea et al., 2015) | N/A |
| Desktop Wave Software | Agilent Technologies | N/A |
| Debarcoder software | Fluidigm | N/A |
| Babelomics 5 online software | http://babelomics.bioinfo.cipf.es | N/A |
| AnnotationDbi R library | http://bioconductor.org | N/A |
| FunRich version 3.1.3 | http://www.funrich.org | N/A |
| EnrichR | https://amp.pharm.mssm.edu/Enrichr | N/A |
| MultiQuant™ software version 3.0.2 | https://download.sciex.com/MultiQuant_302_Software_Release_Notes.pdf | N/A |
| Fiji Image J | https://imagej.net/software/fiji/downloads | N/A |
| FastQC version 0.11.5 | https://www.bioinformatics.babraham.ac.uk/projects/fastqc | N/A |
| Gene Expression Omnibus database | https://www.ncbi.nlm.nih.gov | N/A |
| Olympus ITEM software | OLYMPUS | N/A |
|
Other | ||
| Mini Rectal Probe Type T, 0.1°C (RET-3) | ThermoWorks | Cat# RET-3 |