Efferocytosis-induced macrophage proliferation

After a macrophage engulfs an apoptotic cell, it can divide. Two signals converge to make it do so. Lysosomal DNase II digests the engulfed cell's DNA in the phagolysosome, and the resulting oligonucleotides activate DNA-PKcs, then mTORC2 and AKT. Separately, GAS6 bound to the apoptotic cell activates the MERTK receptor tyrosine kinase and ERK1/2. Both routes raise MYC, which induces the transcription factor BHLHE40. BHLHE40 represses the anti-proliferative factor c-MAF, and the macrophage enters the cell cycle. The daughter cells keep clearing apoptotic cells, so the programme expands the pool of pro-resolving macrophages at sites of injury.

MODULE:efferocytosis_induced_macrophage_proliferationDRAFTABSTRACTSignaling Pathwaymodules/efferocytosis_induced_macrophage_proliferation.yaml
macrophage proliferationGO:0061517
PMID:34784501
Efferocytosis induces macrophage proliferation to help resolve tissue injury.
The programme is triggered by digestion of the engulfed apoptotic cell, not by phagocytosis as such. Red cells, which have no DNA, are engulfed without effect, while red cells loaded with DNA trigger proliferation.
However, the macrophages that ingested IgG-RBCs did not show this response even though the uptake was similar to that of ACs
PMID:34784501
Efferocytosis induces macrophage proliferation to help resolve tissue injury.
DNA loaded into red cells is enough to trigger proliferation, and this depends on DNase II.
The DNA-loaded IgG-RBCs were able to stimulate macrophage EdU incorporation compared with unloaded IgG-RBCs, and this proliferative response was blunted in macrophages treated with siDnase2a
PMID:34784501
Efferocytosis induces macrophage proliferation to help resolve tissue injury.
Blocking phagolysosomal degradation does not block CSF1-driven proliferation, so the effect is specific to the cargo route.
As an important control, we showed that CSF1-induced macrophage proliferation, which should not involve phagolysosomes, was not blocked by bafilomycin

Boundary: this module starts with apoptotic-cell DNA in the phagolysosome and with GAS6-bound apoptotic cells at the macrophage surface, and ends with macrophage proliferation. Engulfment, phagosome maturation and the rest of cargo digestion belong to the phagocytosis modules (MODULE:phagocytic_engulfment, MODULE:phagosome_maturation). RUBCN and the V-ATPase are needed for this programme only because they are needed for phagolysosome formation, so they are not participants here. GO has no term for this programme. The closest is GO:0061517 macrophage proliferation, used as the module concept. The term "efferocytosis-induced macrophage proliferation" (is_a GO:0061517, preceded_by GO:0043277) has been proposed to the GO editors in go-ontology#32748. Taxon scope: the programme is shown in mouse and its proliferative phenotype in human monocyte-derived macrophages. DNase II and RICTOR are conserved across animals. An OpenScientist phylogenetic profile (file:human/PRKDC/PRKDC-hypotheses/prkdc-animal-distribution/openscientist.md) found DNA-PKcs (PTHR11139:SF68) ancestral to animals, present from sponges and cnidarians through most insects, and lost in Drosophila melanogaster and C. elegans, which keep the related PIKK kinases. All the components of the DNA-sensing route are therefore present in most animals, but the route has only been tested in mouse (see knowledge gaps).

5Nodes
4Parts
0Variant Sets
0Variants
10Annotons
9Connections

Derived QC

Recommended-field compliance

78.6% recommended fields populated
  • references[0] · findings (0/1)
  • knowledge_gaps[0].provenance[0] · reference_section_type (0/1)
  • knowledge_gaps[1].provenance[0] · reference_section_type (0/1)

Module deep research

✗ none found

No MODULE:efferocytosis_induced_macrophage_proliferation 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

11 gene-function check(s) reflected in core functions · 0 conflict(s) · 15 evidence or coverage gap(s) (28 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.

AnnotonParticipantFunctionAssessment
dnase2_cargo_dna Dnase2 (mouse)
UniProtKB:P56542
Family Representative 		deoxyribonuclease II activity
GO:0004531 		Review Missing
No ai-review exists for this protein; its function and core-function coverage cannot yet be checked.
dnase2_cargo_dna DNASE2 (human)
UniProtKB:O00115
Family Representative 		deoxyribonuclease II activity
GO:0004531 		Core Supported
The GO molecular function is reflected in core_functions (exact term or a reviewed subclass).
dna_pkcs_sensor Prkdc (mouse)
UniProtKB:P97313
Family Representative 		DNA-dependent protein kinase activity
GO:0004677 		Review Missing
No ai-review exists for this protein; its function and core-function coverage cannot yet be checked.
dna_pkcs_sensor PRKDC (human)
UniProtKB:P78527
Family Representative 		DNA-dependent protein kinase activity
GO:0004677 		Core Supported
The GO molecular function is reflected in core_functions (exact term or a reviewed subclass).
mtorc2_kinase PROTEIN_COMPLEX
Gene 		protein serine/threonine kinase activity
GO:0004674 		Participant Unchecked
No direct UniProt participant to compare. Abstract selectors and complex-wide activities cannot be inferred from donor or subunit gene reviews.
akt_kinase AKT1 (human)
UniProtKB:P31749
Family Representative 		protein serine/threonine kinase activity
GO:0004674 		Core Supported
The GO molecular function is reflected in core_functions (exact term or a reviewed subclass).
akt_kinase Akt1 (mouse)
UniProtKB:P31750
Family Representative 		protein serine/threonine kinase activity
GO:0004674 		Core Supported
The GO molecular function is reflected in core_functions (exact term or a reviewed subclass).
gas6_ligand Gas6 (mouse)
UniProtKB:Q61592
Family Representative 		receptor ligand activity
GO:0048018 		Core Supported
The GO molecular function is reflected in core_functions (exact term or a reviewed subclass).
gas6_ligand GAS6 (human)
UniProtKB:Q14393
Family Representative 		receptor ligand activity
GO:0048018 		Core Supported
The GO molecular function is reflected in core_functions (exact term or a reviewed subclass).
mertk_receptor 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.
mertk_receptor 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.
erk_kinase Mapk3 (mouse)
UniProtKB:Q63844
Family Representative 		MAP kinase activity
GO:0004707 		Core Supported
The GO molecular function is reflected in core_functions (exact term or a reviewed subclass).
erk_kinase MAPK1 (human)
UniProtKB:P28482
Family Representative 		MAP kinase activity
GO:0004707 		Core Supported
The GO molecular function is reflected in core_functions (exact term or a reviewed subclass).
myc_tf Myc (mouse)
UniProtKB:P01108
Family Representative 		DNA-binding transcription factor activity, RNA polymerase II-specific
GO:0000981 		Core Supported
The GO molecular function is reflected in core_functions (exact term or a reviewed subclass).
myc_tf MYC (human)
UniProtKB:P01106
Family Representative 		DNA-binding transcription factor activity, RNA polymerase II-specific
GO:0000981 		Core Supported
The GO molecular function is reflected in core_functions (exact term or a reviewed subclass).
bhlhe40_repressor Bhlhe40 (mouse)
UniProtKB:O35185
Family Representative 		DNA-binding transcription repressor activity, RNA polymerase II-specific
GO:0001227 		Review Missing
No ai-review exists for this protein; its function and core-function coverage cannot yet be checked.
bhlhe40_repressor BHLHE40 (human)
UniProtKB:O14503
Family Representative 		DNA-binding transcription repressor activity, RNA polymerase II-specific
GO:0001227 		Core Supported
The GO molecular function is reflected in core_functions (exact term or a reviewed subclass).
cmaf_brake Maf (mouse)
UniProtKB:P54843
Family Representative 		DNA-binding transcription factor activity, RNA polymerase II-specific
GO:0000981 		Review Missing
No ai-review exists for this protein; its function and core-function coverage cannot yet be checked.
cmaf_brake MAF (human)
UniProtKB:O75444
Family Representative 		DNA-binding transcription factor activity, RNA polymerase II-specific
GO:0000981 		Review Missing
No ai-review exists for this protein; its function and core-function coverage cannot yet be checked.
dnase2_cargo_dna DNase II alpha
PANTHER:PTHR10858:SF9
Family 		deoxyribonuclease II activity
GO:0004531 		Family Supported
Family review supports GO:0004531 FAMILY_WIDE. The modules phagolysosomal_cargo_degradation (family level) and efferocytosis_induced_macrophage_proliferation (SF9) use this activity. It has been shown for vertebrate DNase II-alpha, worm NUC-1 and Drosophila DNaseII. The catalytic histidine is conserved in every subfamily checked, including the divergent plancitoxin-1 and the bacterial members. The Dictyostelium paralog groups (SF22, SF25) are untested, but no evidence shows catalytic loss in them.
dna_pkcs_sensor DNA-PK catalytic subunit
PANTHER:PTHR11139:SF68
Family 		DNA-dependent protein kinase activity
GO:0004677 		Family Review Missing
No supported structured family review is available for PANTHER:PTHR11139:SF68.
akt_kinase AKT kinase
PANTHER:PTHR24356:SF171
Family 		protein serine/threonine kinase activity
GO:0004674 		Family Review Missing
No supported structured family review is available for PANTHER:PTHR24356:SF171.
gas6_ligand GAS6
PANTHER:PTHR24040:SF14
Family 		receptor ligand activity
GO:0048018 		Family Review Missing
No supported structured family review is available for PANTHER:PTHR24040:SF14.
mertk_receptor 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.
erk_kinase ERK1/ERK2
PANTHER:PTHR24055
Family 		MAP kinase activity
GO:0004707 		Family Function Unreviewed
Family review leaves GO:0004707 UNRESOLVED. The cucumber target has a MAP-kinase conserved-site signature, supporting MAPK-type phosphotransfer rather than an arbitrary kinase label. Classical MAPKs and divergent CMGC relatives nevertheless differ in activation-loop regulation and upstream kinases. The complete functional boundary cannot be inferred from a rule-generated catalytic equation or extended to every CMGC-like member without catalytic and activation-mechanism evidence.
myc_tf MYC
PANTHER:PTHR45851
Family 		DNA-binding transcription factor activity, RNA polymerase II-specific
GO:0000981 		Family Review Missing
No supported structured family review is available for PANTHER:PTHR45851.
bhlhe40_repressor BHLHE40 (DEC1)
PANTHER:PTHR10985:SF3
Family 		DNA-binding transcription repressor activity, RNA polymerase II-specific
GO:0001227 		Family Function Unreviewed
Family review leaves GO:0000981 UNRESOLVED. Zebrafish Hes6 contributes to a DNA-binding repressor with Her7. This does not imply autonomous Hes6 homodimer binding, and the evidence does not grant identical activity to all HES/HEY products or all possible dimer combinations.
cmaf_brake c-MAF
PANTHER:PTHR10129:SF9
Family 		DNA-binding transcription factor activity, RNA polymerase II-specific
GO:0000981 		Family Review Missing
No supported structured family review is available for PANTHER:PTHR10129:SF9.

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.

  • bhlhe40_repressor ⊣ cmaf_brake [closed]
    bhlhe40_repressor is regulated by myc_tf: feedback loop closed

Gene-review completeness (11/22 grounded genes reviewed)

9 complete review(s) · 8 with deep research · 11 missing review · 3 reviewed but lacking deep research

Gene Review Complete Deep research
AKT1 P31749 ✓ 414/445 ✓
Akt1 P31750 ✓ 459/463 ✓
BHLHE40 O14503 ✓ ✓ ✗
DNASE2 O00115 ✓ ✓ ✗
GAS6 Q14393 ✓ ✓ ✓
Gas6 Q61592 ✓ ✓ ✓
MAPK1 P28482 ✓ ✓ ✓
Mapk3 Q63844 ✓ ✓ ✓
MYC P01106 ✓ ✓ ✓
Myc P01108 ✓ ✓ ✓
Bhlhe40 (mouse) O35185 ✗ — —
MAF (human) O75444 ✗ — —
TSC11/AVO3 (S. cerevisiae) P40061 ✗ — —
MTOR (human) P42345 ✗ — —
Maf (mouse) P54843 ✗ — —
Dnase2 (mouse) P56542 ✗ — —
Prkdc (mouse) P97313 ✗ — —
PRKDC P78527 ✓ ✓ ✗
MERTK (human) Q12866 ✗ — —
Mertk (mouse) Q60805 ✗ — —
Rictor (mouse) Q6QI06 ✗ — —
RICTOR (human) Q6R327 ✗ — —

Details

Context
MammaliaNCBITaxon:40674
macrophageCL:0000235
Efferocytosis-induced macrophage proliferationSignaling Pathwayefferocytosis_induced_macrophage_proliferation
macrophage proliferationGO:0061517
Context
MammaliaNCBITaxon:40674
macrophageCL:0000235

Connections

DNase II-generated oligonucleotides activate DNA-PKcs.
dna_pkcs_sensor -> mtorc2_kinase Positively Regulates
DNA-PKcs acts upstream of mTORC2; whether directly is not shown.
mtorc2_kinase -> akt_kinase Positively Regulates
mTORC2 phosphorylates AKT on Ser473.
gas6_ligand -> mertk_receptor Positively Regulates
mertk_receptor -> erk_kinase Positively Regulates
akt_kinase -> myc_tf Positively Regulates
Raises Myc mRNA and protein.
erk_kinase -> myc_tf Positively Regulates
myc_tf -> bhlhe40_repressor Positively Regulates
MYC induces Bhlhe40 transcription.
bhlhe40_repressor -> cmaf_brake Negatively Regulates
BHLHE40 represses c-Maf.
Part 1: cargo DNA digestion
Digestion of apoptotic-cell DNA in the phagolysosomeBiological Processcargo_dna_digestion

Lysosomal DNase II cuts the engulfed cell's DNA into oligonucleotides. This step makes the signal, so the programme needs phagolysosome formation as well as DNase II itself.

DNA catabolic processGO:0006308

Annotons

DNase II digests apoptotic-cell DNA
dnase2_cargo_dna
Participant: Family: DNase II alpha
Family:
DNase II alphaPANTHER:PTHR10858:SF9
Representative Members: Dnase2 (mouse)UniProtKB:P56542 DNASE2 (human)UniProtKB:O00115

Function

deoxyribonuclease II activityGO:0004531

Locations

phagolysosomeGO:0032010

Makes the oligonucleotide signal from engulfed DNA. Its knockdown blocks proliferation after efferocytosis but not uptake, and blocks the response to DNA-loaded red cells.

PMID:34784501
Efferocytosis induces macrophage proliferation to help resolve tissue injury.
The proliferative signal comes from phagolysosomal hydrolysis of apoptotic-cell DNA.
We found that nucleotides derived from the phagolysosomal hydrolysis of AC-DNA during efferocytosis triggers a signaling pathway that promotes the proliferation of pro-resolving macrophages.
Part 2: oligonucleotide-triggered kinase signalling
DNA-PKcs, mTORC2 and AKT signallingSignaling Pathwaydna_pk_mtorc2_signaling

Cargo-derived oligonucleotides activate DNA-PKcs, which acts upstream of mTORC2. mTORC2 phosphorylates AKT on Ser473, and AKT signalling raises MYC. Phosphorylation of DNA-PKcs after efferocytosis depends on DNase II.

TORC2 signalingGO:0038203

Annotons

DNA-PKcs activated by cargo oligonucleotides
dna_pkcs_sensor
Participant: Family: DNA-PK catalytic subunit
Family:
DNA-PK catalytic subunitPANTHER:PTHR11139:SF68
Representative Members: Prkdc (mouse)UniProtKB:P97313 PRKDC (human)UniProtKB:P78527

Function

DNA-dependent protein kinase activityGO:0004677

Proposed sensor of the cargo oligonucleotides. Its knockdown blocks proliferation and AKT Ser473 phosphorylation. Direct binding of the oligonucleotides was not shown.

PMID:34784501
Efferocytosis induces macrophage proliferation to help resolve tissue injury.
DNA-PKcs is activated after efferocytosis, and this needs DNase II.
Further, phosphorylation of DNA-PKcs, which is a marker of its activation, was increased in AC+ versus AC− macrophages, and this increase was completely abrogated by siDnase2a
mTORC2 phosphorylates AKT
mtorc2_kinase
Participant: Protein Complex: TORC2 complex
Protein Complex:
TORC2 complexGO:0031932
Active units:
RICTOR
Participant: Family: RICTOR (AVO3)
Family:
RICTOR (AVO3)PANTHER:PTHR13298:SF11
Representative Members: Rictor (mouse)UniProtKB:Q6QI06 RICTOR (human)UniProtKB:Q6R327 TSC11/AVO3 (S. cerevisiae)UniProtKB:P40061
MTOR kinase
Participant: Family: MTOR
Family:
MTORPANTHER:PTHR11139:SF9
Representative Members: MTOR (human)UniProtKB:P42345

Function

protein serine/threonine kinase activityGO:0004674

Processes

TORC2 signalingGO:0038203

Relays the DNA-PKcs signal to AKT. Rictor knockdown blocks efferocytosis-induced proliferation but not CSF1-induced proliferation; Rictor deletion in bone marrow blocks proliferation of efferocytosing macrophages in the thymus.

PMID:34784501
Efferocytosis induces macrophage proliferation to help resolve tissue injury.
The authors place DNA-PKcs upstream of mTORC2 and AKT in this programme.
These combined data support a role for the following pathway in EIMP: Dnase2a-hydrolyzed AC-DNA → DNA-PKcs → mTORC2 → phospho-Akt → proliferation.
AKT downstream of mTORC2
akt_kinase
Participant: Family: AKT kinase
Family:
AKT kinasePANTHER:PTHR24356:SF171
Representative Members: AKT1 (human)UniProtKB:P31749 Akt1 (mouse)UniProtKB:P31750

Function

protein serine/threonine kinase activityGO:0004674

Its Ser473 phosphorylation is the readout of mTORC2 activity here. Its requirement rests on a pan-AKT inhibitor, and the isoform involved is not known.

AKT1 is shown as an orienting member only; the paper does not resolve the isoform.

Part 3: receptor arm
GAS6, MERTK and ERK1/2 signallingSignaling Pathwaygas6_mertk_erk_arm

GAS6 bound to the apoptotic cell activates MERTK, likely before the cell is engulfed, and MERTK activates ERK1/2. This arm does not need phagolysosomal degradation and adds to the DNA-sensing arm in raising MYC.

ERK1 and ERK2 cascadeGO:0070371

Annotons

MERTK receptor tyrosine kinase
mertk_receptor
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

Locations

plasma membraneGO:0005886

Signals to ERK1/2 and MYC. Myeloid Mertk deletion blunts MYC induction in macrophages that have engulfed an apoptotic cell. MERTK also helps engulfment itself, so the analysis was gated on cells that had engulfed.

PMID:34784501
Efferocytosis induces macrophage proliferation to help resolve tissue injury.
The MERTK route acts alongside the phagolysosomal route.
Thus, two separate pathways contribute to EIMP: a pathway requiring degradation of ACs in phagolysosomes and a pathway downstream of MerTK, which likely becomes activated by AC-bound Gas6 prior to AC engulfment.
ERK1/2 downstream of MERTK
erk_kinase
Participant: Family: ERK1/ERK2
Family:
ERK1/ERK2PANTHER:PTHR24055
Representative Members: Mapk3 (mouse)UniProtKB:Q63844 MAPK1 (human)UniProtKB:P28482

Function

MAP kinase activityGO:0004707

Required for MYC induction by the MERTK arm. The evidence is a MEK inhibitor, so ERK1 and ERK2 are not separated.

Part 4: transcriptional switch
MYC and BHLHE40 relieve c-MAF restraintRegulatory Stepmyc_bhlhe40_switch

The two arms together raise MYC to a level that induces BHLHE40. BHLHE40 represses c-MAF, a transcription factor that holds macrophages out of the cell cycle, and proliferation follows.

Annotons

MYC induces BHLHE40
myc_tf
Participant: Family: MYC
Family:
MYCPANTHER:PTHR45851
Representative Members: Myc (mouse)UniProtKB:P01108 MYC (human)UniProtKB:P01106

Function

DNA-binding transcription factor activity, RNA polymerase II-specificGO:0000981

Locations

nucleusGO:0005634

Point where the two arms converge. Myc knockdown blocks proliferation and BHLHE40 induction.

PMID:34784501
Efferocytosis induces macrophage proliferation to help resolve tissue injury.
Both arms converge on MYC, which is needed for the programme.
Thus, the phagolysosomal and MerTK pathways, via mTORC2 and ERK1/2, respectively, combine to increase Myc in efferocytosing macrophages, which is necessary for EIMP.
BHLHE40 represses c-MAF
bhlhe40_repressor
Participant: Family: BHLHE40 (DEC1)
Family:
BHLHE40 (DEC1)PANTHER:PTHR10985:SF3
Representative Members: Bhlhe40 (mouse)UniProtKB:O35185 BHLHE40 (human)UniProtKB:O14503

Function

DNA-binding transcription repressor activity, RNA polymerase II-specificGO:0001227

Locations

nucleusGO:0005634

Its knockdown completely blocks proliferation after efferocytosis but not after CSF1, so it is the programme-specific step.

PMID:34784501
Efferocytosis induces macrophage proliferation to help resolve tissue injury.
BHLHE40 drives proliferation by repressing c-MAF.
Bhlhe40 then represses the cell-cycling-inhibitor c-Maf to drive proliferation
c-MAF anti-proliferative factor (repressed)
cmaf_brake
Participant: Family: c-MAF
Family:
c-MAFPANTHER:PTHR10129:SF9
Representative Members: Maf (mouse)UniProtKB:P54843 MAF (human)UniProtKB:O75444

Function

DNA-binding transcription factor activity, RNA polymerase II-specificGO:0000981

Locations

nucleusGO:0005634

Holds macrophages out of the cycle. It falls after efferocytosis, and its overexpression blocks the programme.

The overexpression construct is called a "Maf1 plasmid" in the paper's methods. MAF1 is an unrelated gene, so this is probably a naming slip for c-Maf, but it is unverified.