id: MODULE:efferocytosis_induced_anti_inflammatory_programme title: Efferocytosis-induced anti-inflammatory programme description: 'A macrophage that has engulfed apoptotic cells suppresses inflammation and makes pro-resolving signals such as IL-10, TGF-beta1 and prostaglandin E2. Several parallel routes read components of the digested cell: sterols activate the liver X receptors, lipids activate PPAR-delta, fatty acids fuel mitochondrial oxidation that raises NAD+ and activates SIRT1 and PBX1, tryptophan feeds IDO1 and the aryl hydrocarbon receptor, DNA signals through TLR9 to the same receptor, and methionine supplies the methyl groups DNMT3A uses to keep ERK signalling on. Chloride sensing through SLC12A2 decides whether the corpse is read as anti-inflammatory. Each route has cargo-specificity controls: engulfing beads, necrotic cells or cargo-free phosphatidylserine beads does not trigger it.' status: DRAFT scope: ABSTRACT references: - id: PMID:19646905 title: Apoptotic cells promote their own clearance and immune tolerance through activation of the nuclear receptor LXR. reference_review: relevance: HIGH correctness: VERIFIED review_notes: PubMed-verified; full text cached and read in full. - id: PMID:19838202 title: PPAR-delta senses and orchestrates clearance of apoptotic cells to promote tolerance. reference_review: relevance: HIGH correctness: VERIFIED review_notes: PubMed-verified; full text cached and read in full. - id: PMID:30595481 title: Efferocytosis Fuels Requirements of Fatty Acid Oxidation and the Electron Transport Chain to Polarize Macrophages for Tissue Repair. reference_review: relevance: HIGH correctness: VERIFIED review_notes: PubMed-verified; full text cached and read in full. - id: PMID:39242914 title: Efferocytosis drives a tryptophan metabolism pathway in macrophages to promote tissue resolution. reference_review: relevance: HIGH correctness: VERIFIED review_notes: PubMed-verified; full text cached and read in full. - id: PMID:29760532 title: Apoptotic cell-induced AhR activity is required for immunological tolerance and suppression of systemic lupus erythematosus in mice and humans. reference_review: relevance: HIGH correctness: VERIFIED review_notes: PubMed-verified; full text cached and read in full. - id: PMID:35361955 title: Macrophages use apoptotic cell-derived methionine and DNMT3A during efferocytosis to promote tissue resolution. reference_review: relevance: HIGH correctness: VERIFIED review_notes: PubMed-verified; full text cached and read in full. - id: PMID:31792382 title: Interpreting an apoptotic corpse as anti-inflammatory involves a chloride sensing pathway. reference_review: relevance: HIGH correctness: VERIFIED review_notes: PubMed-verified; full text cached and read in full. notes: 'Boundary: this module starts with the digested cargo of an engulfed apoptotic cell and ends with suppressed inflammatory output and production of IL-10, TGF-beta1 and PGE2. Engulfment and digestion belong to the phagocytosis modules. IL-10, TGF-beta1 and the opsonin C1q are outputs or readouts and are not modelled as participants. The routes come mostly from separate laboratories and model systems. Two disagree: PMID:39242914 places IDO1 upstream of AhR, while PMID:29760532 found AhR activation intact without IDO1. They are modelled as independent routes rather than one chain. Some routes respond to engulfed cells in general, not only apoptotic ones (IgG-coated red cells also induce DNMT3A-dependent COX2 in PMID:35361955). Taxon scope: all shown in mouse, with some steps also in human macrophages. Whether any route operates outside mammals is not known.' module: id: efferocytosis_induced_anti_inflammatory_programme label: Efferocytosis-induced anti-inflammatory programme module_type: SIGNALING_PATHWAY concepts: - preferred_term: negative regulation of inflammatory response term: id: GO:0050728 label: negative regulation of inflammatory response notes: Shared output. GO has no term for this programme; "efferocytosis-induced interleukin-10 production" (is_a GO:0032613) has been proposed to GO in go-ontology#32748. context: taxa: - preferred_term: Mammalia term: id: NCBITaxon:40674 label: Mammalia notes: Mechanisms shown in mouse; SLC36A4, MAT2A, DNMT3A and PTGS2 steps also in human macrophages. cell_types: - preferred_term: macrophage term: id: CL:0000235 label: macrophage parts: - order: 1 role: cargo-derived signal routes node: id: cargo_signal_routes label: Cargo-derived signal routes module_type: SIGNALING_PATHWAY description: 'Each route reads a different component of the digested cell. The routes are additive alternatives: losing one blunts the response but does not abolish all of it, and several converge on IL-10 or TGF-beta1.' variant_sets: - id: cargo_component label: Cargo component sensed axis: component of the engulfed cell that supplies the signal selection: ONE_OR_MORE variants: - id: sterol_lxr_route label: 'Sterol route: LXR' module_type: SIGNALING_PATHWAY description: Sterols from the engulfed cell activate the liver X receptors. LXR induces the engulfment receptor MERTK, which speeds further clearance, and is needed for induction of IL-10 and TGF-beta and for repression of inflammatory genes. Depleting sterols from the corpses blunts LXR target induction. concepts: - preferred_term: oxysterol receptor signaling pathway term: id: GO:0141209 label: oxysterol receptor signaling pathway annotons: - id: lxr_alpha label: LXR-alpha sterol-activated receptor participant: selector_type: FAMILY family: preferred_term: LXR-alpha term: id: PANTHER:PTHR24082:SF259 label: OXYSTEROLS RECEPTOR LXR-ALPHA representative_members: - preferred_term: Nr1h3 (mouse) term: id: UniProtKB:Q9Z0Y9 label: Oxysterols receptor LXR-alpha - preferred_term: NR1H3 (human) term: id: UniProtKB:Q13133 label: Oxysterols receptor LXR-alpha function: preferred_term: nuclear receptor activity term: id: GO:0004879 label: nuclear receptor activity processes: - preferred_term: oxysterol receptor signaling pathway term: id: GO:0141209 label: oxysterol receptor signaling pathway locations: &id001 - preferred_term: nucleus term: id: GO:0005634 label: nucleus role_description: 'Sterol-activated transcription factor. Redundant with LXR-beta: only the double knockout loses Mertk induction by agonists and the response to apoptotic cells.' evidence: - source_id: PMID:19646905 title: Apoptotic cells promote their own clearance and immune tolerance through activation of the nuclear receptor LXR. statement: LXR agonists induce Mertk unless both LXRs are absent. supporting_text: Expression of Mer was induced by LXR and RXR agonists in WT, Lxrα-/- and Lxrβ-/- but not in Lxrαβ-/- primary macrophages - source_id: PMID:19646905 title: Apoptotic cells promote their own clearance and immune tolerance through activation of the nuclear receptor LXR. statement: 'The trigger is sterol cargo: sterol-depleted corpses induce LXR targets less.' supporting_text: depletion of sterols from AT by means of methyl beta-cyclodextran treatment reduced their ability to induce LXR target gene expression (Mer, Abca1) following ingestion by macrophages - id: lxr_beta label: LXR-beta sterol-activated receptor participant: selector_type: FAMILY family: preferred_term: LXR-beta term: id: PANTHER:PTHR24082:SF316 label: OXYSTEROLS RECEPTOR LXR-BETA representative_members: - preferred_term: Nr1h2 (mouse) term: id: UniProtKB:Q60644 label: Oxysterols receptor LXR-beta - preferred_term: NR1H2 (human) term: id: UniProtKB:P55055 label: Oxysterols receptor LXR-beta function: preferred_term: nuclear receptor activity term: id: GO:0004879 label: nuclear receptor activity processes: - preferred_term: oxysterol receptor signaling pathway term: id: GO:0141209 label: oxysterol receptor signaling pathway locations: *id001 role_description: Acts redundantly with LXR-alpha in this programme. evidence: - source_id: PMID:19646905 title: Apoptotic cells promote their own clearance and immune tolerance through activation of the nuclear receptor LXR. statement: LXRs are needed for the IL-10 and TGF-beta response to apoptotic cells. supporting_text: AT promoted the expression of immunosuppressive mediators such as Tgf-β and Il-10 in WT macrophages (Fig. 4A,B). However, induction of these genes was impaired in macrophages lacking LXRs. - id: lxr_target_mertk label: MERTK induced by LXR participant: selector_type: FAMILY family: preferred_term: MERTK term: id: PANTHER:PTHR24416:SF257 label: TYROSINE-PROTEIN KINASE MER representative_members: - preferred_term: Mertk (mouse) term: id: UniProtKB:Q60805 label: Tyrosine-protein kinase Mer - preferred_term: MERTK (human) term: id: UniProtKB:Q12866 label: Tyrosine-protein kinase Mer function: preferred_term: transmembrane receptor protein tyrosine kinase activity term: id: GO:0004714 label: transmembrane receptor protein tyrosine kinase activity processes: - preferred_term: positive regulation of apoptotic cell clearance term: id: GO:2000427 label: positive regulation of apoptotic cell clearance locations: - preferred_term: plasma membrane term: id: GO:0005886 label: plasma membrane role_description: Direct LXR target. Its induction feeds back to raise clearance of further apoptotic cells. - id: lipid_ppard_route label: 'Lipid route: PPAR-delta' module_type: SIGNALING_PATHWAY description: Engulfment of apoptotic cells, but not of beads, necrotic cells or opsonised red cells, induces and activates PPAR-delta. PPAR-delta directly induces the opsonin C1qb and is needed for the switch to IL-10 production. concepts: - preferred_term: peroxisome proliferator activated receptor signaling pathway term: id: GO:0035357 label: peroxisome proliferator activated receptor signaling pathway annotons: - id: ppard_receptor label: PPAR-delta lipid-sensing receptor participant: selector_type: FAMILY family: preferred_term: PPAR-delta term: id: PANTHER:PTHR24082:SF15 label: PEROXISOME PROLIFERATOR-ACTIVATED RECEPTOR DELTA representative_members: - preferred_term: Ppard (mouse) term: id: UniProtKB:P35396 label: Peroxisome proliferator-activated receptor delta - preferred_term: PPARD (human) term: id: UniProtKB:Q03181 label: Peroxisome proliferator-activated receptor delta function: preferred_term: nuclear receptor activity term: id: GO:0004879 label: nuclear receptor activity processes: - preferred_term: peroxisome proliferator activated receptor signaling pathway term: id: GO:0035357 label: peroxisome proliferator activated receptor signaling pathway locations: *id001 role_description: Transcriptional sensor of engulfed apoptotic cells. Global and macrophage-specific (LysM-Cre) knockouts lose opsonin expression and the anti-inflammatory cytokine switch and develop lupus-like disease. evidence: - source_id: PMID:19838202 title: PPAR-delta senses and orchestrates clearance of apoptotic cells to promote tolerance. statement: PPAR-delta is activated by apoptotic cells but not by other engulfed particles. supporting_text: this transcriptional activation of PPAR-δ by apoptotic cells was specific, because necrotic cells and opsonized sRBCs failed to activate PPAR-δ - source_id: PMID:19838202 title: PPAR-delta senses and orchestrates clearance of apoptotic cells to promote tolerance. statement: PPAR-delta/RXR directly controls C1qb. supporting_text: Deletion analysis of the mouse promoter affirmed that PPAR-δ/RXR heterodimers directly regulate C1qb gene expression - id: fatty_acid_oxidation_route label: 'Fatty acid oxidation route: NAD+, SIRT1 and PBX1' module_type: SIGNALING_PATHWAY description: Fatty acids from the engulfed cell are oxidised in the macrophage's mitochondria. Electron transport through complex III raises NAD+, which activates SIRT1, and SIRT1 is needed for the transcription factor PBX1 to occupy the IL-10 promoter. Beads and live cells do not raise respiration. concepts: - preferred_term: positive regulation of interleukin-10 production term: id: GO:0032733 label: positive regulation of interleukin-10 production annotons: - id: risp_complex_iii label: Complex III (Rieske subunit deleted) participant: selector_type: PROTEIN_COMPLEX protein_complex: preferred_term: respiratory chain complex III term: id: GO:0045275 label: respiratory chain complex III active_units: - label: Rieske iron-sulfur subunit (RISP) participant: selector_type: FAMILY family: preferred_term: UQCRFS1 (RISP) term: id: PANTHER:PTHR10134 label: CYTOCHROME B-C1 COMPLEX SUBUNIT RIESKE, MITOCHONDRIAL representative_members: - preferred_term: Uqcrfs1 (mouse) term: id: UniProtKB:Q9CR68 label: Cytochrome b-c1 complex subunit Rieske, mitochondrial - preferred_term: UQCRFS1 (human) term: id: UniProtKB:P47985 label: Cytochrome b-c1 complex subunit Rieske, mitochondrial function: preferred_term: quinol-cytochrome-c reductase activity term: id: GO:0008121 label: quinol-cytochrome-c reductase activity locations: - preferred_term: mitochondrial inner membrane term: id: GO:0005743 label: mitochondrial inner membrane role_description: Couples oxidation of cargo fatty acids to NAD+ regeneration. Myeloid Risp deletion abolishes IL-10 after efferocytosis, and an NAD+ precursor rescues it. evidence: - source_id: PMID:30595481 title: Efferocytosis Fuels Requirements of Fatty Acid Oxidation and the Electron Transport Chain to Polarize Macrophages for Tissue Repair. statement: An NAD+ precursor rescues IL-10 in Risp-deficient macrophages, placing NAD+ downstream of complex III. supporting_text: we added NAD+ precursor NMN to Rispfl/fl LysMcre macrophages during efferocytosis and found that NMN was sufficient to rescue IL-10 production - id: sirt1_deacetylase label: SIRT1 NAD-dependent deacetylase participant: selector_type: FAMILY family: preferred_term: SIRT1 term: id: PANTHER:PTHR11085:SF9 label: NAD-DEPENDENT PROTEIN DEACETYLASE SIRTUIN-1 representative_members: - preferred_term: Sirt1 (mouse) term: id: UniProtKB:Q923E4 label: NAD-dependent protein deacetylase sirtuin-1 - preferred_term: SIRT1 (human) term: id: UniProtKB:Q96EB6 label: NAD-dependent protein deacetylase sirtuin-1 function: preferred_term: NAD-dependent protein lysine deacetylase activity term: id: GO:0034979 label: NAD-dependent protein lysine deacetylase activity processes: - preferred_term: positive regulation of interleukin-10 production term: id: GO:0032733 label: positive regulation of interleukin-10 production locations: *id001 role_description: Reads the NAD+ rise. siRNA only. Its substrate in this programme is not known; it is needed for PBX1 binding at the IL-10 promoter. evidence: - source_id: PMID:30595481 title: Efferocytosis Fuels Requirements of Fatty Acid Oxidation and the Electron Transport Chain to Polarize Macrophages for Tissue Repair. statement: SIRT1 is needed for PBX1 occupancy of the IL-10 promoter. supporting_text: Sirt1 deficiency reduced PBX-1 binding to the apoptotic cell response element of the IL-10 promoter (Figure 6F) - id: pbx1_tf label: PBX1 at the IL-10 promoter participant: selector_type: FAMILY family: preferred_term: PBX1 term: id: PANTHER:PTHR11850:SF89 label: PRE-B-CELL LEUKEMIA TRANSCRIPTION FACTOR 1 representative_members: - preferred_term: Pbx1 (mouse) term: id: UniProtKB:P41778 label: Pre-B-cell leukemia transcription factor 1 - preferred_term: PBX1 (human) term: id: UniProtKB:P40424 label: Pre-B-cell leukemia transcription factor 1 function: preferred_term: DNA-binding transcription activator activity, RNA polymerase II-specific term: id: GO:0001228 label: DNA-binding transcription activator activity, RNA polymerase II-specific processes: - preferred_term: positive regulation of interleukin-10 production term: id: GO:0032733 label: positive regulation of interleukin-10 production locations: *id001 role_description: Transcription factor that drives Il10 after efferocytosis. siRNA only. - id: tryptophan_ahr_route label: 'Tryptophan route: SLC36A4, IDO1 and AhR' module_type: SIGNALING_PATHWAY description: Tryptophan released by digestion of the engulfed cell's proteins leaves the phagolysosome through SLC36A4. IDO1 converts it toward kynurenine, which activates AhR, and AhR induces IL-10 and TGF-beta1 and supports continued efferocytosis. Phosphatidylserine-coated beads, which engage the same receptors but carry no cargo, do not trigger it. concepts: - preferred_term: L-tryptophan catabolic process term: id: GO:0006569 label: L-tryptophan catabolic process annotons: - id: slc36a4_trp_export label: SLC36A4 exports tryptophan from the phagolysosome participant: selector_type: FAMILY family: preferred_term: SLC36A4 (PAT4) term: id: PANTHER:PTHR22950:SF190 label: NEUTRAL AMINO ACID UNIPORTER 4 representative_members: - preferred_term: Slc36a4 (mouse) term: id: UniProtKB:Q8CH36 label: Neutral amino acid uniporter 4 - preferred_term: SLC36A4 (human) term: id: UniProtKB:Q6YBV0 label: Neutral amino acid uniporter 4 function: preferred_term: L-tryptophan transmembrane transporter activity term: id: GO:0015196 label: L-tryptophan transmembrane transporter activity locations: - preferred_term: phagolysosome membrane term: id: GO:0061474 label: phagolysosome membrane role_description: Rises on phagolysosomes containing apoptotic cells. Knockdown in mouse and human macrophages blocks the downstream response but not engulfment. evidence: - source_id: PMID:39242914 title: Efferocytosis drives a tryptophan metabolism pathway in macrophages to promote tissue resolution. statement: Cargo-free beads do not induce SLC36A4. supporting_text: upregulation of SLC36A4 was not seen in macrophages incubated with phosphatidylserine (PS)-coated beads, which bind to and are internalized by efferocytosis receptors but have no cellular cargo - id: ido1_dioxygenase label: IDO1 converts cargo tryptophan participant: selector_type: FAMILY family: preferred_term: IDO1 term: id: PANTHER:PTHR28657:SF2 label: INDOLEAMINE 2,3-DIOXYGENASE 1 representative_members: - preferred_term: Ido1 (mouse) term: id: UniProtKB:P28776 label: Indoleamine 2,3-dioxygenase 1 - preferred_term: IDO1 (human) term: id: UniProtKB:P14902 label: Indoleamine 2,3-dioxygenase 1 function: preferred_term: indoleamine 2,3-dioxygenase activity term: id: GO:0033754 label: indoleamine 2,3-dioxygenase activity processes: - preferred_term: L-tryptophan catabolic process term: id: GO:0006569 label: L-tryptophan catabolic process locations: - preferred_term: cytosol term: id: GO:0005829 label: cytosol role_description: First step from tryptophan to kynurenine. Knockout, myeloid and inducible macrophage knockouts and an inhibitor added after the first engulfment all block the response; kynurenine partly rescues it. evidence: - source_id: PMID:39242914 title: Efferocytosis drives a tryptophan metabolism pathway in macrophages to promote tissue resolution. statement: IDO1 is needed for IL-10 and TGF-beta1 induction in efferocytosing macrophages. supporting_text: We found that both siIdo1 and epacadostat markedly blocked the increases in levels of Tgfb1 and Il10 mRNAs in efferocytosing macrophages - id: ahr_trp_route label: AhR activated by kynurenine participant: selector_type: FAMILY family: preferred_term: AhR term: id: PANTHER:PTHR10649:SF9 label: ARYL HYDROCARBON RECEPTOR representative_members: - preferred_term: Ahr (mouse) term: id: UniProtKB:P30561 label: Aryl hydrocarbon receptor - preferred_term: AHR (human) term: id: UniProtKB:P35869 label: Aryl hydrocarbon receptor function: preferred_term: ligand-modulated transcription factor activity term: id: GO:0098531 label: ligand-modulated transcription factor activity processes: - preferred_term: positive regulation of interleukin-10 production term: id: GO:0032733 label: positive regulation of interleukin-10 production locations: *id001 role_description: Ligand-activated transcription factor that induces Il10 and Tgfb1. Knockout, myeloid knockout and an antagonist block the response. evidence: - source_id: PMID:39242914 title: Efferocytosis drives a tryptophan metabolism pathway in macrophages to promote tissue resolution. statement: Kynurenine plus cargo-free engulfment reconstitutes AhR activation; neither alone does. supporting_text: neither Kyn alone nor PS beads alone could activate AhR or induce Ido1, Il10, or Tgfb1 mRNA expression, the combination of Kyn and PS beads was able to activate these downstream mediators - id: dna_tlr9_ahr_route label: 'DNA route: TLR9 and AhR' module_type: SIGNALING_PATHWAY description: DNA in the engulfed apoptotic cell signals through endolysosomal TLR9 to activate AhR, which binds the Il10 promoter. Engulfment, not contact alone, is needed, and DNase-treated corpses fail to activate AhR. In this study AhR activation did not need IDO1, so this route is independent of the tryptophan route. concepts: - preferred_term: toll-like receptor 9 signaling pathway term: id: GO:0034162 label: toll-like receptor 9 signaling pathway annotons: - id: tlr9_dna_sensor label: TLR9 senses apoptotic-cell DNA participant: selector_type: FAMILY family: preferred_term: TLR9 term: id: PANTHER:PTHR47410:SF3 label: TOLL-LIKE RECEPTOR 9 representative_members: - preferred_term: Tlr9 (mouse) term: id: UniProtKB:Q9EQU3 label: Toll-like receptor 9 - preferred_term: TLR9 (human) term: id: UniProtKB:Q9NR96 label: Toll-like receptor 9 function: preferred_term: pattern recognition receptor activity term: id: GO:0038187 label: pattern recognition receptor activity processes: - preferred_term: toll-like receptor 9 signaling pathway term: id: GO:0034162 label: toll-like receptor 9 signaling pathway locations: - preferred_term: endolysosome membrane term: id: GO:0036020 label: endolysosome membrane role_description: Needed for AhR activation after efferocytosis. An AhR agonist rescues Tlr9-/- cells, placing TLR9 upstream. evidence: - source_id: PMID:29760532 title: Apoptotic cell-induced AhR activity is required for immunological tolerance and suppression of systemic lupus erythematosus in mice and humans. statement: AhR does not enter the nucleus after efferocytosis without TLR9. supporting_text: Tlr9−/− BMDMs did not show nuclear accumulation of AhR after efferocytosis (Fig. 3d) - id: ahr_dna_route label: AhR binds the Il10 promoter participant: selector_type: FAMILY family: preferred_term: AhR term: id: PANTHER:PTHR10649:SF9 label: ARYL HYDROCARBON RECEPTOR representative_members: - preferred_term: Ahr (mouse) term: id: UniProtKB:P30561 label: Aryl hydrocarbon receptor - preferred_term: AHR (human) term: id: UniProtKB:P35869 label: Aryl hydrocarbon receptor function: preferred_term: ligand-modulated transcription factor activity term: id: GO:0098531 label: ligand-modulated transcription factor activity processes: - preferred_term: positive regulation of interleukin-10 production term: id: GO:0032733 label: positive regulation of interleukin-10 production locations: *id001 role_description: Myeloid AhR deletion causes autoimmunity; AhR binds the Il10 promoter after efferocytosis. The ligand in this route is not identified. evidence: - source_id: PMID:29760532 title: Apoptotic cell-induced AhR activity is required for immunological tolerance and suppression of systemic lupus erythematosus in mice and humans. statement: AhR occupies the Il10 promoter after efferocytosis. supporting_text: AhR association with the AhRE was enriched 13-fold in the Cyp1a1 promoter and 7 fold in the Il10 promoter in Ap-BMDMs compared to resting BMDMs - id: methionine_dnmt3a_route label: 'Methionine route: DNMT3A, ERK and prostaglandin E2' module_type: SIGNALING_PATHWAY description: Methionine from the digested cell is made into S-adenosylmethionine by MAT2A. DNMT3A uses it to methylate and silence Dusp4, so ERK1/2 stays active after the initial receptor signal. Sustained ERK induces PTGS2, and the PGE2 it makes induces TGF-beta1. Responses to LPS, IFN-gamma and IL-4 are normal without DNMT3A. concepts: - preferred_term: positive regulation of transforming growth factor beta1 production term: id: GO:0032914 label: positive regulation of transforming growth factor beta1 production annotons: - id: mat2a_sam label: MAT2A makes SAM from cargo methionine participant: selector_type: FAMILY family: preferred_term: MAT2A term: id: PANTHER:PTHR11964:SF73 label: S-ADENOSYLMETHIONINE SYNTHASE ISOFORM TYPE-2 representative_members: - preferred_term: Mat2a (mouse) term: id: UniProtKB:Q3THS6 label: S-adenosylmethionine synthase isoform type-2 - preferred_term: MAT2A (human) term: id: UniProtKB:P31153 label: S-adenosylmethionine synthase isoform type-2 function: preferred_term: methionine adenosyltransferase activity term: id: GO:0004478 label: methionine adenosyltransferase activity processes: - preferred_term: S-adenosylmethionine biosynthetic process term: id: GO:0006556 label: S-adenosylmethionine biosynthetic process role_description: Inhibitor and siRNA block the response; added SAM bypasses it. Labelled methionine from corpses becomes SAM only in macrophages that engulfed them. evidence: - source_id: PMID:35361955 title: Macrophages use apoptotic cell-derived methionine and DNMT3A during efferocytosis to promote tissue resolution. statement: SAM made from cargo methionine needs phagolysosomal digestion. supporting_text: 13C515N-SAM was found only in AC+ macrophages and, importantly, this was markedly inhibited when phagolysosomal hydrolysis was blocked by bafilomycin - id: dnmt3a_methyltransferase label: DNMT3A silences Dusp4 participant: selector_type: FAMILY family: preferred_term: DNMT3A term: id: PANTHER:PTHR23068:SF10 label: DNA (CYTOSINE-5)-METHYLTRANSFERASE 3A representative_members: - preferred_term: Dnmt3a (mouse) term: id: UniProtKB:O88508 label: DNA (cytosine-5)-methyltransferase 3A - preferred_term: DNMT3A (human) term: id: UniProtKB:Q9Y6K1 label: DNA (cytosine-5)-methyltransferase 3A function: preferred_term: DNA (cytosine-5-)-methyltransferase activity term: id: GO:0003886 label: DNA (cytosine-5-)-methyltransferase activity processes: - preferred_term: negative regulation of gene expression via chromosomal CpG island methylation term: id: GO:0044027 label: negative regulation of gene expression via chromosomal CpG island methylation locations: *id001 role_description: Hematopoietic deletion blocks COX2, PGE2, TGF-beta1 and resolution in three in vivo models. Knockdown of Dusp4 rescues the DNMT3A defect. evidence: - source_id: PMID:35361955 title: Macrophages use apoptotic cell-derived methionine and DNMT3A during efferocytosis to promote tissue resolution. statement: DNMT3A methylates the Dusp4 promoter after efferocytosis. supporting_text: the CpG-rich promoter region of the Dusp4 gene was methylated in response to ACs in wild-type but not DNMT3A-deficient macrophages - source_id: PMID:35361955 title: Macrophages use apoptotic cell-derived methionine and DNMT3A during efferocytosis to promote tissue resolution. statement: DNMT3A loss does not affect other macrophage activation pathways. supporting_text: control and DNMT3A-KO macrophages, or macrophages treated with scrambled RNA or siDnmt3a, responded similarly to LPS - id: dusp4_phosphatase label: DUSP4 ERK phosphatase (silenced) participant: selector_type: FAMILY family: preferred_term: DUSP4 term: id: PANTHER:PTHR10159:SF111 label: DUAL SPECIFICITY PROTEIN PHOSPHATASE 4 representative_members: - preferred_term: Dusp4 (mouse) term: id: UniProtKB:Q8BFV3 label: Dual specificity protein phosphatase 4 - preferred_term: DUSP4 (human) term: id: UniProtKB:Q13115 label: Dual specificity protein phosphatase 4 function: preferred_term: MAP kinase tyrosine/serine/threonine phosphatase activity term: id: GO:0017017 label: MAP kinase tyrosine/serine/threonine phosphatase activity locations: *id001 role_description: Limits ERK activity. Its silencing lets ERK stay active; its knockdown rescues DNMT3A loss. - id: ptgs2_cox2 label: PTGS2 makes prostaglandin H2 for PGE2 participant: selector_type: FAMILY family: preferred_term: PTGS2 (COX2) term: id: PANTHER:PTHR11903:SF8 label: PROSTAGLANDIN G_H SYNTHASE 2 representative_members: - preferred_term: Ptgs2 (mouse) term: id: UniProtKB:Q05769 label: Prostaglandin G/H synthase 2 - preferred_term: PTGS2 (human) term: id: UniProtKB:P35354 label: Prostaglandin G/H synthase 2 function: preferred_term: prostaglandin-endoperoxide synthase activity term: id: GO:0004666 label: prostaglandin-endoperoxide synthase activity processes: - preferred_term: prostaglandin biosynthetic process term: id: GO:0001516 label: prostaglandin biosynthetic process locations: - preferred_term: endoplasmic reticulum membrane term: id: GO:0005789 label: endoplasmic reticulum membrane role_description: Induced by sustained ERK. Its knockdown or inhibition blocks TGF-beta1 induction; added PGE2 restores it. - order: 2 role: interpretation gate optional: true node: id: chloride_sensing_gate label: Chloride sensing sets the anti-inflammatory reading module_type: REGULATORY_STEP description: Corpse uptake lowers cytosolic chloride. The WNK1-OSR1/SPAK kinases activate the chloride importer SLC12A2, and chloride influx limits further uptake and is needed for the corpse to be read as anti-inflammatory. Without SLC12A2, phagocytes switch to a pro-inflammatory programme even though they eat more; phagocytes made to eat more by TIM4 overexpression do not switch. annotons: - id: slc12a2_chloride_import label: SLC12A2 chloride importer participant: selector_type: FAMILY family: preferred_term: SLC12A2 (NKCC1) term: id: PANTHER:PTHR11827:SF58 label: SOLUTE CARRIER FAMILY 12 MEMBER 2 representative_members: - preferred_term: Slc12a2 (mouse) term: id: UniProtKB:P55012 label: Solute carrier family 12 member 2 - preferred_term: SLC12A2 (human) term: id: UniProtKB:P55011 label: Solute carrier family 12 member 2 function: preferred_term: sodium:potassium:chloride symporter activity term: id: GO:0008511 label: sodium:potassium:chloride symporter activity locations: - preferred_term: plasma membrane term: id: GO:0005886 label: plasma membrane role_description: Gate on the anti-inflammatory reading. Deletion or knockdown increases uptake and flips the response to pro-inflammatory; re-expression reverses this. evidence: - source_id: PMID:31792382 title: Interpreting an apoptotic corpse as anti-inflammatory involves a chloride sensing pathway. statement: Loss of SLC12A2 increases corpse uptake. supporting_text: targeted deletion of Slc12a2 via CRISPR/Cas9 or siRNA-mediated knockdown in LR73 phagocytes resulted in significantly enhanced uptake of apoptotic corpses - source_id: PMID:31792382 title: Interpreting an apoptotic corpse as anti-inflammatory involves a chloride sensing pathway. statement: The pro-inflammatory flip is not caused by eating more. supporting_text: Despite eating more corpses, the TIM4-overexpressing phagocytes did not show upregulation of pro-inflammatory signature genes, contrasting with Slc12a2-deficient phagocytes notes: Most mechanism is in hamster LR73 fibroblasts; macrophage evidence is mostly uptake phenotypes and inhibitors. - id: wnk1_chloride_sensor label: WNK1 chloride-sensing kinase participant: selector_type: FAMILY family: preferred_term: WNK1 term: id: PANTHER:PTHR13902 label: SERINE/THREONINE-PROTEIN KINASE WNK WITH NO LYSINE -RELATED representative_members: - preferred_term: Wnk1 (mouse) term: id: UniProtKB:P83741 label: Serine/threonine-protein kinase WNK1 - preferred_term: WNK1 (human) term: id: UniProtKB:Q9H4A3 label: Serine/threonine-protein kinase WNK1 function: preferred_term: protein serine/threonine kinase activity term: id: GO:0004674 label: protein serine/threonine kinase activity role_description: Upstream kinase of OSR1/SPAK and SLC12A2. Gene deletion only in LR73 cells; in macrophages only a pan-WNK inhibitor. notes: Treat as provisional in macrophages. connections: - source: lxr_alpha target: lxr_target_mertk connection_type: POSITIVELY_REGULATES description: LXR binds an LXR response element in the Mertk promoter. - source: lxr_beta target: lxr_target_mertk connection_type: POSITIVELY_REGULATES - source: risp_complex_iii target: sirt1_deacetylase connection_type: POSITIVELY_REGULATES description: Complex III activity raises NAD+, which SIRT1 uses. - source: sirt1_deacetylase target: pbx1_tf connection_type: POSITIVELY_REGULATES description: Needed for PBX1 occupancy of the IL-10 promoter; direct deacetylation of PBX1 is not shown. - source: slc36a4_trp_export target: ido1_dioxygenase connection_type: PROVIDES_INPUT_FOR description: Exported tryptophan is the IDO1 substrate. - source: ido1_dioxygenase target: ahr_trp_route connection_type: POSITIVELY_REGULATES description: Kynurenine activates AhR. - source: tlr9_dna_sensor target: ahr_dna_route connection_type: POSITIVELY_REGULATES - source: mat2a_sam target: dnmt3a_methyltransferase connection_type: PROVIDES_INPUT_FOR description: SAM is the methyl donor. - source: dnmt3a_methyltransferase target: dusp4_phosphatase connection_type: NEGATIVELY_REGULATES description: Promoter methylation silences Dusp4. - source: dusp4_phosphatase target: ptgs2_cox2 connection_type: NEGATIVELY_REGULATES description: DUSP4 ends ERK signalling that induces Ptgs2. - source: wnk1_chloride_sensor target: slc12a2_chloride_import connection_type: POSITIVELY_REGULATES description: Through OSR1 and SPAK. knowledge_gaps: - gap_statement: The AhR ligand produced downstream of TLR9 after efferocytosis is unknown. boundary: TLR9 and corpse DNA are needed for AhR activation, but DNA is not an AhR ligand and the IDO1-kynurenine route was not needed in this system. gap_kind: - BIOLOGY dark_aspect: MF_DARK status: OPEN significance: The DNA route has no defined chemical link between TLR9 and AhR. resolution: Metabolite profiling of TLR9-dependent AhR ligands in efferocytosing Ido1-/- macrophages, with AhR binding assays. provenance: - reference_id: PMID:29760532 supporting_text: we could observe Cyp1a1 mRNA induction by sqPCR analysis in Ap-BMDMs treated with the IDO inhibitor 1MT (Supplementary Fig. 3c) or in Ido1−/− Ap-BMDMs