Efferocytosis-induced anti-inflammatory programme

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.

MODULE:efferocytosis_induced_anti_inflammatory_programmeDRAFTABSTRACTSignaling Pathwaymodules/efferocytosis_induced_anti_inflammatory_programme.yaml

negative regulation of inflammatory responseGO:0050728

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.

9Nodes

2Parts

1Variant Sets

6Variants

18Annotons

11Connections

Derived QC

Recommended-field compliance

42.9% recommended fields populated

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Module deep research

✗ none found

No MODULE:efferocytosis_induced_anti_inflammatory_programme deep-research report alongside the module YAML.

Leaf nodes lacking representative members

✓ representative grounding skipped for abstract module.

Template conformance

✓ every declared conforms_to bundle matches its template motif.

Function consistency and core coverage

8 gene-function check(s) reflected in core functions · 0 conflict(s) · 41 evidence or coverage gap(s) (52 comparison(s))

Retained noncore functions are reported separately; they do not require promotion to core functions. Support from representative genes does not establish conservation across the whole family. Missing reviews or identifiers leave a claim unverified.

Annoton	Participant	Function	Assessment
lxr_alpha	Nr1h3 (mouse) UniProtKB:Q9Z0Y9 Family Representative	nuclear receptor activity GO:0004879	Review Missing No ai-review exists for this protein; its function and core-function coverage cannot yet be checked.
lxr_alpha	NR1H3 (human) UniProtKB:Q13133 Family Representative	nuclear receptor activity GO:0004879	Review Missing No ai-review exists for this protein; its function and core-function coverage cannot yet be checked.
lxr_beta	Nr1h2 (mouse) UniProtKB:Q60644 Family Representative	nuclear receptor activity GO:0004879	Review Missing No ai-review exists for this protein; its function and core-function coverage cannot yet be checked.
lxr_beta	NR1H2 (human) UniProtKB:P55055 Family Representative	nuclear receptor activity GO:0004879	Review Missing No ai-review exists for this protein; its function and core-function coverage cannot yet be checked.
lxr_target_mertk	Mertk (mouse) UniProtKB:Q60805 Family Representative	transmembrane receptor protein tyrosine kinase activity GO:0004714	Review Missing No ai-review exists for this protein; its function and core-function coverage cannot yet be checked.
lxr_target_mertk	MERTK (human) UniProtKB:Q12866 Family Representative	transmembrane receptor protein tyrosine kinase activity GO:0004714	Review Missing No ai-review exists for this protein; its function and core-function coverage cannot yet be checked.
ppard_receptor	Ppard (mouse) UniProtKB:P35396 Family Representative	nuclear receptor activity GO:0004879	Review Missing No ai-review exists for this protein; its function and core-function coverage cannot yet be checked.
ppard_receptor	PPARD (human) UniProtKB:Q03181 Family Representative	nuclear receptor activity GO:0004879	Review Missing No ai-review exists for this protein; its function and core-function coverage cannot yet be checked.
risp_complex_iii	PROTEIN_COMPLEX Gene	quinol-cytochrome-c reductase activity GO:0008121	Participant Unchecked No direct UniProt participant to compare. Abstract selectors and complex-wide activities cannot be inferred from donor or subunit gene reviews.
sirt1_deacetylase	Sirt1 (mouse) UniProtKB:Q923E4 Family Representative	NAD-dependent protein lysine deacetylase activity GO:0034979	Review Missing No ai-review exists for this protein; its function and core-function coverage cannot yet be checked.
sirt1_deacetylase	SIRT1 (human) UniProtKB:Q96EB6 Family Representative	NAD-dependent protein lysine deacetylase activity GO:0034979	Core Supported The GO molecular function is reflected in core_functions (exact term or a reviewed subclass).
pbx1_tf	Pbx1 (mouse) UniProtKB:P41778 Family Representative	DNA-binding transcription activator activity, RNA polymerase II-specific GO:0001228	Review Missing No ai-review exists for this protein; its function and core-function coverage cannot yet be checked.
pbx1_tf	PBX1 (human) UniProtKB:P40424 Family Representative	DNA-binding transcription activator activity, RNA polymerase II-specific GO:0001228	Review Missing No ai-review exists for this protein; its function and core-function coverage cannot yet be checked.
slc36a4_trp_export	Slc36a4 (mouse) UniProtKB:Q8CH36 Family Representative	L-tryptophan transmembrane transporter activity GO:0015196	Review Missing No ai-review exists for this protein; its function and core-function coverage cannot yet be checked.
slc36a4_trp_export	SLC36A4 (human) UniProtKB:Q6YBV0 Family Representative	L-tryptophan transmembrane transporter activity GO:0015196	Review Missing No ai-review exists for this protein; its function and core-function coverage cannot yet be checked.
ido1_dioxygenase	Ido1 (mouse) UniProtKB:P28776 Family Representative	indoleamine 2,3-dioxygenase activity GO:0033754	Review Missing No ai-review exists for this protein; its function and core-function coverage cannot yet be checked.
ido1_dioxygenase	IDO1 (human) UniProtKB:P14902 Family Representative	indoleamine 2,3-dioxygenase activity GO:0033754	Core Supported The GO molecular function is reflected in core_functions (exact term or a reviewed subclass).
ahr_trp_route	Ahr (mouse) UniProtKB:P30561 Family Representative	ligand-modulated transcription factor activity GO:0098531	Review Missing No ai-review exists for this protein; its function and core-function coverage cannot yet be checked.
ahr_trp_route	AHR (human) UniProtKB:P35869 Family Representative	ligand-modulated transcription factor activity GO:0098531	Core Supported The GO molecular function is reflected in core_functions (exact term or a reviewed subclass).
tlr9_dna_sensor	Tlr9 (mouse) UniProtKB:Q9EQU3 Family Representative	pattern recognition receptor activity GO:0038187	Review Missing No ai-review exists for this protein; its function and core-function coverage cannot yet be checked.
tlr9_dna_sensor	TLR9 (human) UniProtKB:Q9NR96 Family Representative	pattern recognition receptor activity GO:0038187	Core Supported The GO molecular function is reflected in core_functions (exact term or a reviewed subclass).
ahr_dna_route	Ahr (mouse) UniProtKB:P30561 Family Representative	ligand-modulated transcription factor activity GO:0098531	Review Missing No ai-review exists for this protein; its function and core-function coverage cannot yet be checked.
ahr_dna_route	AHR (human) UniProtKB:P35869 Family Representative	ligand-modulated transcription factor activity GO:0098531	Core Supported The GO molecular function is reflected in core_functions (exact term or a reviewed subclass).
mat2a_sam	Mat2a (mouse) UniProtKB:Q3THS6 Family Representative	methionine adenosyltransferase activity GO:0004478	Review Missing No ai-review exists for this protein; its function and core-function coverage cannot yet be checked.
mat2a_sam	MAT2A (human) UniProtKB:P31153 Family Representative	methionine adenosyltransferase activity GO:0004478	Review Missing No ai-review exists for this protein; its function and core-function coverage cannot yet be checked.
dnmt3a_methyltransferase	Dnmt3a (mouse) UniProtKB:O88508 Family Representative	DNA (cytosine-5-)-methyltransferase activity GO:0003886	Core Supported The GO molecular function is reflected in core_functions (exact term or a reviewed subclass).
dnmt3a_methyltransferase	DNMT3A (human) UniProtKB:Q9Y6K1 Family Representative	DNA (cytosine-5-)-methyltransferase activity GO:0003886	Core Supported The GO molecular function is reflected in core_functions (exact term or a reviewed subclass).
dusp4_phosphatase	Dusp4 (mouse) UniProtKB:Q8BFV3 Family Representative	MAP kinase tyrosine/serine/threonine phosphatase activity GO:0017017	Review Missing No ai-review exists for this protein; its function and core-function coverage cannot yet be checked.
dusp4_phosphatase	DUSP4 (human) UniProtKB:Q13115 Family Representative	MAP kinase tyrosine/serine/threonine phosphatase activity GO:0017017	Review Missing No ai-review exists for this protein; its function and core-function coverage cannot yet be checked.
ptgs2_cox2	Ptgs2 (mouse) UniProtKB:Q05769 Family Representative	prostaglandin-endoperoxide synthase activity GO:0004666	Review Missing No ai-review exists for this protein; its function and core-function coverage cannot yet be checked.
ptgs2_cox2	PTGS2 (human) UniProtKB:P35354 Family Representative	prostaglandin-endoperoxide synthase activity GO:0004666	Review Missing No ai-review exists for this protein; its function and core-function coverage cannot yet be checked.
slc12a2_chloride_import	Slc12a2 (mouse) UniProtKB:P55012 Family Representative	sodium:potassium:chloride symporter activity GO:0008511	Review Missing No ai-review exists for this protein; its function and core-function coverage cannot yet be checked.
slc12a2_chloride_import	SLC12A2 (human) UniProtKB:P55011 Family Representative	sodium:potassium:chloride symporter activity GO:0008511	Core Supported The GO molecular function is reflected in core_functions (exact term or a reviewed subclass).
wnk1_chloride_sensor	Wnk1 (mouse) UniProtKB:P83741 Family Representative	protein serine/threonine kinase activity GO:0004674	Review Missing No ai-review exists for this protein; its function and core-function coverage cannot yet be checked.
wnk1_chloride_sensor	WNK1 (human) UniProtKB:Q9H4A3 Family Representative	protein serine/threonine kinase activity GO:0004674	Review Missing No ai-review exists for this protein; its function and core-function coverage cannot yet be checked.
lxr_alpha	LXR-alpha PANTHER:PTHR24082:SF259 Family	nuclear receptor activity GO:0004879	Family Review Missing No supported structured family review is available for PANTHER:PTHR24082:SF259.
lxr_beta	LXR-beta PANTHER:PTHR24082:SF316 Family	nuclear receptor activity GO:0004879	Family Review Missing No supported structured family review is available for PANTHER:PTHR24082:SF316.
lxr_target_mertk	MERTK PANTHER:PTHR24416:SF257 Family	transmembrane receptor protein tyrosine kinase activity GO:0004714	Family Scope Restricted GO:0004714 requires member-level assessment of residue site kinase_catalytic_triad; a family identifier does not establish that condition. Within the DDR clade the activity follows the kinase catalytic triad, which is kept everywhere except the dipteran Ddr node PTN002400510: Drosophila Ddr (Ala789, Ser897, Ser910) and Anopheles DDR fail the site and are predicted pseudokinases (not assayed). The PTN001230349 node assessment records the matching IKR recommendation. RESIDUE_DETERMINED means the term is true wherever the triad is intact; it is not the most specific term for vertebrate DDR1 and DDR2, whose reviews refine it to GO:0038062.
ppard_receptor	PPAR-delta PANTHER:PTHR24082:SF15 Family	nuclear receptor activity GO:0004879	Family Review Missing No supported structured family review is available for PANTHER:PTHR24082:SF15.
sirt1_deacetylase	SIRT1 PANTHER:PTHR11085:SF9 Family	NAD-dependent protein lysine deacetylase activity GO:0034979	Family Function Unreviewed The family review has no applicable adjudication supporting or excluding GO:0034979.
pbx1_tf	PBX1 PANTHER:PTHR11850:SF89 Family	DNA-binding transcription activator activity, RNA polymerase II-specific GO:0001228	Family Review Missing No supported structured family review is available for PANTHER:PTHR11850:SF89.
slc36a4_trp_export	SLC36A4 (PAT4) PANTHER:PTHR22950:SF190 Family	L-tryptophan transmembrane transporter activity GO:0015196	Family Review Missing No supported structured family review is available for PANTHER:PTHR22950:SF190.
ido1_dioxygenase	IDO1 PANTHER:PTHR28657:SF2 Family	indoleamine 2,3-dioxygenase activity GO:0033754	Family Supported Family review supports GO:0033754 FAMILY_WIDE. Asserted by nad_de_novo_and_salvage_fungal and kynurenine_nad_de_novo; accepted by IDO1 and kept as non-core by BNA2, whose core is the tryptophan-specific term.
ahr_trp_route	AhR PANTHER:PTHR10649:SF9 Family	ligand-modulated transcription factor activity GO:0098531	Family Review Missing No supported structured family review is available for PANTHER:PTHR10649:SF9.
tlr9_dna_sensor	TLR9 PANTHER:PTHR47410:SF3 Family	pattern recognition receptor activity GO:0038187	Family Review Missing No supported structured family review is available for PANTHER:PTHR47410:SF3.
ahr_dna_route	AhR PANTHER:PTHR10649:SF9 Family	ligand-modulated transcription factor activity GO:0098531	Family Review Missing No supported structured family review is available for PANTHER:PTHR10649:SF9.
mat2a_sam	MAT2A PANTHER:PTHR11964:SF73 Family	methionine adenosyltransferase activity GO:0004478	Family Supported Family review supports GO:0004478 FAMILY_WIDE. Asserted by methionine_cycle, sam_cycle and bacterial_methionine_cycle; accepted by SAM1, SAM2, sam1, MAT1A, P. putida MetK and the poplar SAMS paralogs.
dnmt3a_methyltransferase	DNMT3A PANTHER:PTHR23068:SF10 Family	DNA (cytosine-5-)-methyltransferase activity GO:0003886	Family Function Unreviewed Family review leaves GO:0003886 UNRESOLVED. DNMT3A in SF10 is a demonstrated catalytic DNA methyltransferase, while DNMT3L in SF13 is a catalytically inactive regulator. DNMT3B and active DRM proteins show that catalytic activity is not exclusive to the DNMT3A branch. The full boundary across DNMT3, DRM and other domain-related proteins has not been established, so no exhaustive allowed-subfamily set is asserted. This uncertainty concerns family-wide coverage; it does not weaken the established DNMT3A activity or the DNMT3L noncatalytic distinction.
dusp4_phosphatase	DUSP4 PANTHER:PTHR10159:SF111 Family	MAP kinase tyrosine/serine/threonine phosphatase activity GO:0017017	Family Review Missing No supported structured family review is available for PANTHER:PTHR10159:SF111.
ptgs2_cox2	PTGS2 (COX2) PANTHER:PTHR11903:SF8 Family	prostaglandin-endoperoxide synthase activity GO:0004666	Family Review Missing No supported structured family review is available for PANTHER:PTHR11903:SF8.
slc12a2_chloride_import	SLC12A2 (NKCC1) PANTHER:PTHR11827:SF58 Family	sodium:potassium:chloride symporter activity GO:0008511	Family Review Missing No supported structured family review is available for PANTHER:PTHR11827:SF58.
wnk1_chloride_sensor	WNK1 PANTHER:PTHR13902 Family	protein serine/threonine kinase activity GO:0004674	Family Review Missing No supported structured family review is available for PANTHER:PTHR13902.

Feedback loops (advisory, prose-driven: a regulator counts as "feedback" when its own description says so)

✓ every negative regulator described as feedback has an upstream edge closing the loop.

dnmt3a_methyltransferase ⊣ dusp4_phosphatase [closed]
dnmt3a_methyltransferase is regulated by mat2a_sam: feedback loop closed
dusp4_phosphatase ⊣ ptgs2_cox2 [input]
dusp4_phosphatase is a negative regulator with no upstream edge (not described as feedback)

Gene-review completeness (8/34 grounded genes reviewed)

4 complete review(s) · 5 with deep research · 26 missing review · 3 reviewed but lacking deep research

Gene	Review	Complete	Deep research
AHR P35869	✓	✓	✓
Dnmt3a O88508	✓	117/121	✗
DNMT3A Q9Y6K1	✓	88/89	✓
IDO1 P14902	✓	✓	✗
Ido1 (mouse) P28776	✗	—	—
Ahr (mouse) P30561	✗	—	—
MAT2A (human) P31153	✗	—	—
PTGS2 (human) P35354	✗	—	—
Ppard (mouse) P35396	✗	—	—
PBX1 (human) P40424	✗	—	—
Pbx1 (mouse) P41778	✗	—	—
Slc12a2 (mouse) P55012	✗	—	—
NR1H2 (human) P55055	✗	—	—
Wnk1 (mouse) P83741	✗	—	—
PPARD (human) Q03181	✗	—	—
Ptgs2 (mouse) Q05769	✗	—	—
MERTK (human) Q12866	✗	—	—
DUSP4 (human) Q13115	✗	—	—
NR1H3 (human) Q13133	✗	—	—
Mat2a (mouse) Q3THS6	✗	—	—
Nr1h2 (mouse) Q60644	✗	—	—
Mertk (mouse) Q60805	✗	—	—
SLC36A4 (human) Q6YBV0	✗	—	—
Dusp4 (mouse) Q8BFV3	✗	—	—
Slc36a4 (mouse) Q8CH36	✗	—	—
Sirt1 (mouse) Q923E4	✗	—	—
Uqcrfs1 (mouse) Q9CR68	✗	—	—
Tlr9 (mouse) Q9EQU3	✗	—	—
WNK1 (human) Q9H4A3	✗	—	—
Nr1h3 (mouse) Q9Z0Y9	✗	—	—
SIRT1 Q96EB6	✓	364/380	✓
SLC12A2 P55011	✓	✓	✗
TLR9 Q9NR96	✓	135/136	✓
UQCRFS1 P47985	✓	✓	✓

Tree

Efferocytosis-induced anti-inflammatory programmeSignaling Pathwayefferocytosis_induced_anti_inflammatory_programme

Parts
1. 1. cargo-derived signal routes
2. Cargo-derived signal routesSignaling Pathwaycargo_signal_routes
  
  Variants
  1. Cargo component sensed by component of the engulfed cell that supplies the signal (One Or More)
    
    Sterol route: LXRSignaling Pathwaysterol_lxr_route
    
    Annotons
    
    LXR-alpha sterol-activated receptor Family: LXR-alpha
    
    LXR-beta sterol-activated receptor Family: LXR-beta
    
    MERTK induced by LXR Family: MERTK
    
    Lipid route: PPAR-deltaSignaling Pathwaylipid_ppard_route
    
    Annotons
    
    PPAR-delta lipid-sensing receptor Family: PPAR-delta
    
    Fatty acid oxidation route: NAD+, SIRT1 and PBX1Signaling Pathwayfatty_acid_oxidation_route
    
    Annotons
    
    Complex III (Rieske subunit deleted) Protein Complex: respiratory chain complex III
    
    SIRT1 NAD-dependent deacetylase Family: SIRT1
    
    PBX1 at the IL-10 promoter Family: PBX1
    
    Tryptophan route: SLC36A4, IDO1 and AhRSignaling Pathwaytryptophan_ahr_route
    
    Annotons
    
    SLC36A4 exports tryptophan from the phagolysosome Family: SLC36A4 (PAT4)
    
    IDO1 converts cargo tryptophan Family: IDO1
    
    AhR activated by kynurenine Family: AhR
    
    DNA route: TLR9 and AhRSignaling Pathwaydna_tlr9_ahr_route
    
    Annotons
    
    TLR9 senses apoptotic-cell DNA Family: TLR9
    
    AhR binds the Il10 promoter Family: AhR
    
    Methionine route: DNMT3A, ERK and prostaglandin E2Signaling Pathwaymethionine_dnmt3a_route
    
    Annotons
    
    MAT2A makes SAM from cargo methionine Family: MAT2A
    
    DNMT3A silences Dusp4 Family: DNMT3A
    
    DUSP4 ERK phosphatase (silenced) Family: DUSP4
    
    PTGS2 makes prostaglandin H2 for PGE2 Family: PTGS2 (COX2)
3. 2. interpretation gate optional
4. Chloride sensing sets the anti-inflammatory readingRegulatory Stepchloride_sensing_gate
  
  Annotons
  - SLC12A2 chloride importer Family: SLC12A2 (NKCC1)
  - WNK1 chloride-sensing kinase Family: WNK1

Details

Context

MammaliaNCBITaxon:40674

macrophageCL:0000235

Efferocytosis-induced anti-inflammatory programmeSignaling Pathwayefferocytosis_induced_anti_inflammatory_programme

negative regulation of inflammatory responseGO:0050728

Context

MammaliaNCBITaxon:40674

macrophageCL:0000235

Connections

lxr_alpha -> lxr_target_mertk Positively Regulates

LXR binds an LXR response element in the Mertk promoter.

lxr_beta -> lxr_target_mertk Positively Regulates

risp_complex_iii -> sirt1_deacetylase Positively Regulates

Complex III activity raises NAD+, which SIRT1 uses.

sirt1_deacetylase -> pbx1_tf Positively Regulates

Needed for PBX1 occupancy of the IL-10 promoter; direct deacetylation of PBX1 is not shown.

slc36a4_trp_export -> ido1_dioxygenase Provides Input For

Exported tryptophan is the IDO1 substrate.

ido1_dioxygenase -> ahr_trp_route Positively Regulates

Kynurenine activates AhR.

tlr9_dna_sensor -> ahr_dna_route Positively Regulates

mat2a_sam -> dnmt3a_methyltransferase Provides Input For

SAM is the methyl donor.

dnmt3a_methyltransferase -> dusp4_phosphatase Negatively Regulates

Promoter methylation silences Dusp4.

dusp4_phosphatase -> ptgs2_cox2 Negatively Regulates

DUSP4 ends ERK signalling that induces Ptgs2.

wnk1_chloride_sensor -> slc12a2_chloride_import Positively Regulates

Through OSR1 and SPAK.

Part 1: cargo-derived signal routes

Cargo-derived signal routesSignaling Pathwaycargo_signal_routes

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 set: Cargo component sensed by component of the engulfed cell that supplies the signal (One Or More)

Sterol route: LXRSignaling Pathwaysterol_lxr_route

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.

oxysterol receptor signaling pathwayGO:0141209

Annotons

LXR-alpha sterol-activated receptor

lxr_alpha

Participant: Family: LXR-alpha

Family:

LXR-alphaPANTHER:PTHR24082:SF259

Representative Members: Nr1h3 (mouse)UniProtKB:Q9Z0Y9 NR1H3 (human)UniProtKB:Q13133

Function

nuclear receptor activityGO:0004879

Processes

oxysterol receptor signaling pathwayGO:0141209

Locations

nucleusGO:0005634

Sterol-activated transcription factor. Redundant with LXR-beta: only the double knockout loses Mertk induction by agonists and the response to apoptotic cells.

PMID:19646905

Apoptotic cells promote their own clearance and immune tolerance through activation of the nuclear receptor LXR.

LXR agonists induce Mertk unless both LXRs are absent.

Expression of Mer was induced by LXR and RXR agonists in WT, Lxrα-/- and Lxrβ-/- but not in Lxrαβ-/- primary macrophages

PMID:19646905

Apoptotic cells promote their own clearance and immune tolerance through activation of the nuclear receptor LXR.

The trigger is sterol cargo: sterol-depleted corpses induce LXR targets less.

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

LXR-beta sterol-activated receptor

lxr_beta

Participant: Family: LXR-beta

Family:

LXR-betaPANTHER:PTHR24082:SF316

Representative Members: Nr1h2 (mouse)UniProtKB:Q60644 NR1H2 (human)UniProtKB:P55055

Function

nuclear receptor activityGO:0004879

Processes

oxysterol receptor signaling pathwayGO:0141209

Locations

nucleusGO:0005634

Acts redundantly with LXR-alpha in this programme.

PMID:19646905

Apoptotic cells promote their own clearance and immune tolerance through activation of the nuclear receptor LXR.

LXRs are needed for the IL-10 and TGF-beta response to apoptotic cells.

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.

MERTK induced by LXR

lxr_target_mertk

Participant: Family: MERTK

Family:

MERTKPANTHER:PTHR24416:SF257

Representative Members: Mertk (mouse)UniProtKB:Q60805 MERTK (human)UniProtKB:Q12866

Function

transmembrane receptor protein tyrosine kinase activityGO:0004714

Processes

positive regulation of apoptotic cell clearanceGO:2000427

Locations

plasma membraneGO:0005886

Direct LXR target. Its induction feeds back to raise clearance of further apoptotic cells.

Lipid route: PPAR-deltaSignaling Pathwaylipid_ppard_route

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.

peroxisome proliferator activated receptor signaling pathwayGO:0035357

Annotons

PPAR-delta lipid-sensing receptor

ppard_receptor

Participant: Family: PPAR-delta

Family:

PPAR-deltaPANTHER:PTHR24082:SF15

Representative Members: Ppard (mouse)UniProtKB:P35396 PPARD (human)UniProtKB:Q03181

Function

nuclear receptor activityGO:0004879

Processes

peroxisome proliferator activated receptor signaling pathwayGO:0035357

Locations

nucleusGO:0005634

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.

PMID:19838202

PPAR-delta senses and orchestrates clearance of apoptotic cells to promote tolerance.

PPAR-delta is activated by apoptotic cells but not by other engulfed particles.

this transcriptional activation of PPAR-δ by apoptotic cells was specific, because necrotic cells and opsonized sRBCs failed to activate PPAR-δ

PMID:19838202

PPAR-delta senses and orchestrates clearance of apoptotic cells to promote tolerance.

PPAR-delta/RXR directly controls C1qb.

Deletion analysis of the mouse promoter affirmed that PPAR-δ/RXR heterodimers directly regulate C1qb gene expression

Fatty acid oxidation route: NAD+, SIRT1 and PBX1Signaling Pathwayfatty_acid_oxidation_route

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.

positive regulation of interleukin-10 productionGO:0032733

Annotons

Complex III (Rieske subunit deleted)

risp_complex_iii

Participant: Protein Complex: respiratory chain complex III

Protein Complex:

respiratory chain complex IIIGO:0045275

Active units:

Rieske iron-sulfur subunit (RISP)

Participant: Family: UQCRFS1 (RISP)

Family:

UQCRFS1 (RISP)PANTHER:PTHR10134

Representative Members: Uqcrfs1 (mouse)UniProtKB:Q9CR68 UQCRFS1 (human)UniProtKB:P47985

Function

quinol-cytochrome-c reductase activityGO:0008121

Locations

mitochondrial inner membraneGO:0005743

Couples oxidation of cargo fatty acids to NAD+ regeneration. Myeloid Risp deletion abolishes IL-10 after efferocytosis, and an NAD+ precursor rescues it.

PMID:30595481

Efferocytosis Fuels Requirements of Fatty Acid Oxidation and the Electron Transport Chain to Polarize Macrophages for Tissue Repair.

An NAD+ precursor rescues IL-10 in Risp-deficient macrophages, placing NAD+ downstream of complex III.

we added NAD+ precursor NMN to Rispfl/fl LysMcre macrophages during efferocytosis and found that NMN was sufficient to rescue IL-10 production

SIRT1 NAD-dependent deacetylase

sirt1_deacetylase

Participant: Family: SIRT1

Family:

SIRT1PANTHER:PTHR11085:SF9

Representative Members: Sirt1 (mouse)UniProtKB:Q923E4 SIRT1 (human)UniProtKB:Q96EB6

Function

NAD-dependent protein lysine deacetylase activityGO:0034979

Processes

positive regulation of interleukin-10 productionGO:0032733

Locations

nucleusGO:0005634

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.

PMID:30595481

Efferocytosis Fuels Requirements of Fatty Acid Oxidation and the Electron Transport Chain to Polarize Macrophages for Tissue Repair.

SIRT1 is needed for PBX1 occupancy of the IL-10 promoter.

Sirt1 deficiency reduced PBX-1 binding to the apoptotic cell response element of the IL-10 promoter (Figure 6F)

PBX1 at the IL-10 promoter

pbx1_tf

Participant: Family: PBX1

Family:

PBX1PANTHER:PTHR11850:SF89

Representative Members: Pbx1 (mouse)UniProtKB:P41778 PBX1 (human)UniProtKB:P40424

Function

DNA-binding transcription activator activity, RNA polymerase II-specificGO:0001228

Processes

positive regulation of interleukin-10 productionGO:0032733

Locations

nucleusGO:0005634

Transcription factor that drives Il10 after efferocytosis. siRNA only.

Tryptophan route: SLC36A4, IDO1 and AhRSignaling Pathwaytryptophan_ahr_route

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.

L-tryptophan catabolic processGO:0006569

Annotons

SLC36A4 exports tryptophan from the phagolysosome

slc36a4_trp_export

Participant: Family: SLC36A4 (PAT4)

Family:

SLC36A4 (PAT4)PANTHER:PTHR22950:SF190

Representative Members: Slc36a4 (mouse)UniProtKB:Q8CH36 SLC36A4 (human)UniProtKB:Q6YBV0

Function

L-tryptophan transmembrane transporter activityGO:0015196

Locations

phagolysosome membraneGO:0061474

Rises on phagolysosomes containing apoptotic cells. Knockdown in mouse and human macrophages blocks the downstream response but not engulfment.

PMID:39242914

Efferocytosis drives a tryptophan metabolism pathway in macrophages to promote tissue resolution.

Cargo-free beads do not induce SLC36A4.

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

IDO1 converts cargo tryptophan

ido1_dioxygenase

Participant: Family: IDO1

Family:

IDO1PANTHER:PTHR28657:SF2

Representative Members: Ido1 (mouse)UniProtKB:P28776 IDO1 (human)UniProtKB:P14902

Function

indoleamine 2,3-dioxygenase activityGO:0033754

Processes

L-tryptophan catabolic processGO:0006569

Locations

cytosolGO:0005829

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.

PMID:39242914

Efferocytosis drives a tryptophan metabolism pathway in macrophages to promote tissue resolution.

IDO1 is needed for IL-10 and TGF-beta1 induction in efferocytosing macrophages.

We found that both siIdo1 and epacadostat markedly blocked the increases in levels of Tgfb1 and Il10 mRNAs in efferocytosing macrophages

AhR activated by kynurenine

ahr_trp_route

Participant: Family: AhR

Family:

AhRPANTHER:PTHR10649:SF9

Representative Members: Ahr (mouse)UniProtKB:P30561 AHR (human)UniProtKB:P35869

Function

ligand-modulated transcription factor activityGO:0098531

Processes

positive regulation of interleukin-10 productionGO:0032733

Locations

nucleusGO:0005634

Ligand-activated transcription factor that induces Il10 and Tgfb1. Knockout, myeloid knockout and an antagonist block the response.

PMID:39242914

Efferocytosis drives a tryptophan metabolism pathway in macrophages to promote tissue resolution.

Kynurenine plus cargo-free engulfment reconstitutes AhR activation; neither alone does.

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

DNA route: TLR9 and AhRSignaling Pathwaydna_tlr9_ahr_route

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.

toll-like receptor 9 signaling pathwayGO:0034162

Annotons

TLR9 senses apoptotic-cell DNA

tlr9_dna_sensor

Participant: Family: TLR9

Family:

TLR9PANTHER:PTHR47410:SF3

Representative Members: Tlr9 (mouse)UniProtKB:Q9EQU3 TLR9 (human)UniProtKB:Q9NR96

Function

pattern recognition receptor activityGO:0038187

Processes

toll-like receptor 9 signaling pathwayGO:0034162

Locations

endolysosome membraneGO:0036020

Needed for AhR activation after efferocytosis. An AhR agonist rescues Tlr9-/- cells, placing TLR9 upstream.

PMID:29760532

Apoptotic cell-induced AhR activity is required for immunological tolerance and suppression of systemic lupus erythematosus in mice and humans.

AhR does not enter the nucleus after efferocytosis without TLR9.

Tlr9−/− BMDMs did not show nuclear accumulation of AhR after efferocytosis (Fig. 3d)

AhR binds the Il10 promoter

ahr_dna_route

Participant: Family: AhR

Family:

AhRPANTHER:PTHR10649:SF9

Representative Members: Ahr (mouse)UniProtKB:P30561 AHR (human)UniProtKB:P35869

Function

ligand-modulated transcription factor activityGO:0098531

Processes

positive regulation of interleukin-10 productionGO:0032733

Locations

nucleusGO:0005634

Myeloid AhR deletion causes autoimmunity; AhR binds the Il10 promoter after efferocytosis. The ligand in this route is not identified.

PMID:29760532

Apoptotic cell-induced AhR activity is required for immunological tolerance and suppression of systemic lupus erythematosus in mice and humans.

AhR occupies the Il10 promoter after efferocytosis.

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

Methionine route: DNMT3A, ERK and prostaglandin E2Signaling Pathwaymethionine_dnmt3a_route

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.

positive regulation of transforming growth factor beta1 productionGO:0032914

Annotons

MAT2A makes SAM from cargo methionine

mat2a_sam

Participant: Family: MAT2A

Family:

MAT2APANTHER:PTHR11964:SF73

Representative Members: Mat2a (mouse)UniProtKB:Q3THS6 MAT2A (human)UniProtKB:P31153

Function

methionine adenosyltransferase activityGO:0004478

Processes

S-adenosylmethionine biosynthetic processGO:0006556

Inhibitor and siRNA block the response; added SAM bypasses it. Labelled methionine from corpses becomes SAM only in macrophages that engulfed them.

PMID:35361955

Macrophages use apoptotic cell-derived methionine and DNMT3A during efferocytosis to promote tissue resolution.

SAM made from cargo methionine needs phagolysosomal digestion.

13C515N-SAM was found only in AC+ macrophages and, importantly, this was markedly inhibited when phagolysosomal hydrolysis was blocked by bafilomycin

DNMT3A silences Dusp4

dnmt3a_methyltransferase

Participant: Family: DNMT3A

Family:

DNMT3APANTHER:PTHR23068:SF10

Representative Members: Dnmt3a (mouse)UniProtKB:O88508 DNMT3A (human)UniProtKB:Q9Y6K1

Function

DNA (cytosine-5-)-methyltransferase activityGO:0003886

Processes

negative regulation of gene expression via chromosomal CpG island methylationGO:0044027

Locations

nucleusGO:0005634

Hematopoietic deletion blocks COX2, PGE2, TGF-beta1 and resolution in three in vivo models. Knockdown of Dusp4 rescues the DNMT3A defect.

PMID:35361955

Macrophages use apoptotic cell-derived methionine and DNMT3A during efferocytosis to promote tissue resolution.

DNMT3A methylates the Dusp4 promoter after efferocytosis.

the CpG-rich promoter region of the Dusp4 gene was methylated in response to ACs in wild-type but not DNMT3A-deficient macrophages

PMID:35361955

Macrophages use apoptotic cell-derived methionine and DNMT3A during efferocytosis to promote tissue resolution.

DNMT3A loss does not affect other macrophage activation pathways.

control and DNMT3A-KO macrophages, or macrophages treated with scrambled RNA or siDnmt3a, responded similarly to LPS

DUSP4 ERK phosphatase (silenced)

dusp4_phosphatase

Participant: Family: DUSP4

Family:

DUSP4PANTHER:PTHR10159:SF111

Representative Members: Dusp4 (mouse)UniProtKB:Q8BFV3 DUSP4 (human)UniProtKB:Q13115

Function

MAP kinase tyrosine/serine/threonine phosphatase activityGO:0017017

Locations

nucleusGO:0005634

Limits ERK activity. Its silencing lets ERK stay active; its knockdown rescues DNMT3A loss.

PTGS2 makes prostaglandin H2 for PGE2

ptgs2_cox2

Participant: Family: PTGS2 (COX2)

Family:

PTGS2 (COX2)PANTHER:PTHR11903:SF8

Representative Members: Ptgs2 (mouse)UniProtKB:Q05769 PTGS2 (human)UniProtKB:P35354

Function

prostaglandin-endoperoxide synthase activityGO:0004666

Processes

prostaglandin biosynthetic processGO:0001516

Locations

endoplasmic reticulum membraneGO:0005789

Induced by sustained ERK. Its knockdown or inhibition blocks TGF-beta1 induction; added PGE2 restores it.

Part 2: interpretation gate (optional)

Chloride sensing sets the anti-inflammatory readingRegulatory Stepchloride_sensing_gate

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

SLC12A2 chloride importer

slc12a2_chloride_import

Participant: Family: SLC12A2 (NKCC1)

Family:

SLC12A2 (NKCC1)PANTHER:PTHR11827:SF58

Representative Members: Slc12a2 (mouse)UniProtKB:P55012 SLC12A2 (human)UniProtKB:P55011

Function

sodium:potassium:chloride symporter activityGO:0008511

Locations

plasma membraneGO:0005886

Gate on the anti-inflammatory reading. Deletion or knockdown increases uptake and flips the response to pro-inflammatory; re-expression reverses this.

PMID:31792382

Interpreting an apoptotic corpse as anti-inflammatory involves a chloride sensing pathway.

Loss of SLC12A2 increases corpse uptake.

targeted deletion of Slc12a2 via CRISPR/Cas9 or siRNA-mediated knockdown in LR73 phagocytes resulted in significantly enhanced uptake of apoptotic corpses

PMID:31792382

Interpreting an apoptotic corpse as anti-inflammatory involves a chloride sensing pathway.

The pro-inflammatory flip is not caused by eating more.

Despite eating more corpses, the TIM4-overexpressing phagocytes did not show upregulation of pro-inflammatory signature genes, contrasting with Slc12a2-deficient phagocytes

Most mechanism is in hamster LR73 fibroblasts; macrophage evidence is mostly uptake phenotypes and inhibitors.

WNK1 chloride-sensing kinase

wnk1_chloride_sensor

Participant: Family: WNK1

Family:

WNK1PANTHER:PTHR13902

Representative Members: Wnk1 (mouse)UniProtKB:P83741 WNK1 (human)UniProtKB:Q9H4A3

Function

protein serine/threonine kinase activityGO:0004674

Upstream kinase of OSR1/SPAK and SLC12A2. Gene deletion only in LR73 cells; in macrophages only a pan-WNK inhibitor.

Treat as provisional in macrophages.