id: MODULE:heme_induced_iron_recycling_macrophage_differentiation title: Heme-induced iron-recycling macrophage differentiation description: >- Macrophages that engulf aged or damaged red blood cells digest them in the phagolysosome and release heme. The heme transporter HRG1 carries heme out of the phagolysosome into the cytosol. Heme then switches on a differentiation programme. The transcriptional repressor BACH1 normally keeps the gene for the transcription factor SPI-C silent. Heme binds BACH1 through its cysteine-proline motifs and triggers its proteasomal degradation, which de-represses Spic. SPI-C drives monocytes to become iron-recycling macrophages: splenic red pulp macrophages and VCAM1-positive bone marrow macrophages. The same heme signal also de-represses the iron-recycling enzymes and transporters these cells use, heme oxygenase 1 and ferroportin. status: DRAFT scope: ABSTRACT references: - id: PMID:24630724 title: Heme-mediated SPI-C induction promotes monocyte differentiation into iron-recycling macrophages. reference_review: relevance: HIGH correctness: VERIFIED review_notes: >- PubMed-verified; full text cached and read in full. Mouse. Bach1-/- BMDM, a degradation-resistant BACH1 CP-to-AP mutant, Spic-igfp reporter mice, Spic-/- and Ho1-/- mice and adoptive transfer of monocytes. - id: PMID:23395172 title: HRG1 is essential for heme transport from the phagolysosome of macrophages during erythrophagocytosis. reference_review: relevance: HIGH correctness: VERIFIED review_notes: >- PubMed-verified; full text cached and read in full. Mouse BMDM erythrophagocytosis with latex-bead controls; Hrg1 siRNA; heme-transport reporters in yeast and macrophages. No knockout animal in this paper. - id: PMID:20179090 title: Heme controls ferroportin1 (FPN1) transcription involving Bach1, Nrf2 and a MARE/ARE sequence motif at position -7007 of the FPN1 promoter. reference_review: relevance: MEDIUM correctness: VERIFIED review_notes: >- PubMed-verified; abstract only in cache. RAW264.7 cells; BACH1 represses and NRF2 activates Fpn1 transcription in response to heme. evidence: - source_id: PMID:24630724 title: Heme-mediated SPI-C induction promotes monocyte differentiation into iron-recycling macrophages. statement: The authors' summary of the programme in vivo. supporting_text: Bach1 inhibition at sites of erythrophagocytosis controls RPM and BMM development through derepression of Spic. - source_id: PMID:24630724 title: Heme-mediated SPI-C induction promotes monocyte differentiation into iron-recycling macrophages. statement: The signal is heme itself, not a heme breakdown product. supporting_text: Bilirubin and biliverdin failed to induce SPIC-EGFP in Spicigfp/igfp BMDM notes: >- Boundary: this module starts with heme in the phagolysosome of a macrophage that has engulfed an erythrocyte, and ends with a differentiated iron-recycling macrophage that exports iron. Engulfment of the erythrocyte and its digestion belong to the phagocytosis modules. The programme is defined by heme, not by phagocytosis. Heme released by haemolysis induces Spic in the same way. Engulfed erythrocytes are the main physiological source of heme for these cells. GO has no term for red pulp macrophage differentiation. The module concept is GO:0030225 macrophage differentiation, and "splenic red pulp macrophage differentiation" (is_a GO:0030225, cell type CL:0000874) has been proposed to the GO editors in go-ontology#32748. The two arms are supported by separate papers in different cells. HRG1 work is in bone-marrow-derived macrophages and spleen and liver macrophages without red pulp markers; the BACH1/SPIC work is in bone-marrow-derived macrophages, monocytes and chimeric mice. The link between them, phagolysosomal heme reaching BACH1, is inferred. Taxon scope: the programme is shown only in mouse. An OpenScientist phylogenetic profile (file:human/SPIC/SPIC-hypotheses/spic-bach1-cooccurrence/openscientist.md) found SPIC orthologs from cartilaginous fish through all bony vertebrates but not in cyclostomes or invertebrates, and found the BACH1 C-terminal cysteine-proline motif conserved in every curated bony-vertebrate BACH1 checked. No lineage has SPIC without BACH1. The parts of the switch therefore co-occur across jawed vertebrates, but whether the switch operates outside mammals is untested. HRG1 is conserved more widely across animals (C. elegans hrg-1 imports heme), so the heme-export step is broader than the differentiation programme. A second profile (file:human/SLC48A1/SLC48A1-hypotheses/hrg1-protist-distribution/openscientist.md) found the HRG1 family almost only in animals and choanoflagellates, with one ortholog in Acanthamoeba and none in Dictyostelium. module: id: heme_induced_iron_recycling_macrophage_differentiation label: Heme-induced iron-recycling macrophage differentiation module_type: DEVELOPMENTAL_PROCESS concepts: - preferred_term: macrophage differentiation term: id: GO:0030225 label: macrophage differentiation notes: >- Nearest existing term. "splenic red pulp macrophage differentiation" has been proposed to GO (go-ontology#32748). context: taxa: - preferred_term: Mammalia term: id: NCBITaxon:40674 label: Mammalia notes: Mechanism shown in mouse. cell_types: - preferred_term: splenic red pulp macrophage term: id: CL:0000874 label: splenic red pulp macrophage notes: Also VCAM1-positive bone marrow macrophages, which have no CL term. parts: - order: 1 role: heme export from the phagolysosome node: id: phagolysosomal_heme_export label: HRG1 exports heme from the phagolysosome module_type: TRANSPORT_STEP description: >- Haemoglobin is digested in the phagolysosome and its heme is released there. Heme oxygenase faces the cytosol, so heme must cross the phagolysosomal membrane. HRG1 is recruited to that membrane during erythrophagocytosis and moves heme into the cytosol. concepts: - preferred_term: heme export from vacuole to cytoplasm term: id: GO:0140357 label: heme export from vacuole to cytoplasm annotons: - id: hrg1_heme_transporter label: HRG1 heme transporter participant: selector_type: FAMILY family: preferred_term: HRG1 heme transporter term: id: PANTHER:PTHR31525:SF1 label: HEME TRANSPORTER HRG1 representative_members: - preferred_term: Slc48a1 (mouse) term: id: UniProtKB:Q9D8M3 label: Heme transporter HRG1 - preferred_term: SLC48A1 (human) term: id: UniProtKB:Q6P1K1 label: Heme transporter HRG1 - preferred_term: hrg-1 (C. elegans) term: id: UniProtKB:Q21642 label: Heme transporter hrg-1 notes: hrg-1 shows the family is shared with nematodes, where it imports heme; it is not claimed to act in phagolysosomes. function: preferred_term: heme transmembrane transporter activity term: id: GO:0015232 label: heme transmembrane transporter activity locations: - preferred_term: phagolysosome membrane term: id: GO:0061474 label: phagolysosome membrane role_description: >- Delivers heme from engulfed erythrocytes to the cytosol. Its knockdown blunts induction of heme-responsive genes during erythrophagocytosis. evidence: - source_id: PMID:23395172 title: HRG1 is essential for heme transport from the phagolysosome of macrophages during erythrophagocytosis. statement: HRG1 moves to the phagolysosome only when red cells, not beads, are engulfed. supporting_text: Hrg1 was recruited to the phagolysosomal membranes specifically during phagocytosis of RBCs but not latex beads - source_id: PMID:23395172 title: HRG1 is essential for heme transport from the phagolysosome of macrophages during erythrophagocytosis. statement: The loss-of-function readout is indirect, through heme-responsive transcripts. supporting_text: Hrg1 knockdown resulted in a significant attenuation of Hmox1 and Fpn1 mRNA induction during EP - order: 2 role: heme sensing node: id: bach1_derepression label: Heme-triggered BACH1 degradation de-represses Spic module_type: REGULATORY_STEP description: >- BACH1 represses Spic. Heme binds BACH1 through its C-terminal cysteine-proline motifs and triggers its proteasomal degradation. A BACH1 mutant without these motifs resists degradation and blocks Spic induction completely. annotons: - id: bach1_repressor label: BACH1 heme-sensing repressor participant: selector_type: FAMILY family: preferred_term: BACH1 term: id: PANTHER:PTHR46105:SF1 label: TRANSCRIPTION REGULATOR PROTEIN BACH1 representative_members: - preferred_term: Bach1 (mouse) term: id: UniProtKB:P97302 label: Transcription regulator protein BACH1 - preferred_term: BACH1 (human) term: id: UniProtKB:O14867 label: Transcription regulator protein BACH1 function: preferred_term: DNA-binding transcription repressor activity, RNA polymerase II-specific term: id: GO:0001227 label: DNA-binding transcription repressor activity, RNA polymerase II-specific locations: - preferred_term: nucleus term: id: GO:0005634 label: nucleus role_description: >- The heme sensor of the programme. Bach1-/- macrophages express Spic without heme, and a degradation-resistant mutant blocks induction. Whether BACH1 binds the Spic locus directly is not known. evidence: - source_id: PMID:24630724 title: Heme-mediated SPI-C induction promotes monocyte differentiation into iron-recycling macrophages. statement: BACH1 represses Spic and heme relieves the repression. supporting_text: These results demonstrate that Bach1 is a transcriptional repressor of Spic that is inhibited by heme. - source_id: PMID:24630724 title: Heme-mediated SPI-C induction promotes monocyte differentiation into iron-recycling macrophages. statement: The cysteine-proline motifs are required for heme to induce Spic. supporting_text: This demonstrates the requirement of heme-BACH1 interactions via CP motifs for heme-mediated Spic expression. - order: 3 role: lineage transcription factor node: id: spic_differentiation label: SPI-C drives iron-recycling macrophage differentiation module_type: DEVELOPMENTAL_PROCESS description: >- De-repressed SPI-C drives monocytes to become red pulp macrophages and VCAM1-positive bone marrow macrophages. Spic-/- mice lack both. annotons: - id: spic_tf label: SPI-C transcription factor participant: selector_type: FAMILY family: preferred_term: SPI-C term: id: PANTHER:PTHR11849:SF17 label: TRANSCRIPTION FACTOR SPI-C representative_members: - preferred_term: Spic (mouse) term: id: UniProtKB:Q6P3D7 label: Transcription factor Spi-C - preferred_term: SPIC (human) term: id: UniProtKB:Q8N5J4 label: Transcription factor Spi-C 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: macrophage differentiation term: id: GO:0030225 label: macrophage differentiation locations: - preferred_term: nucleus term: id: GO:0005634 label: nucleus role_description: Lineage factor of iron-recycling macrophages, induced by heme. evidence: - source_id: PMID:24630724 title: Heme-mediated SPI-C induction promotes monocyte differentiation into iron-recycling macrophages. statement: SPI-C is required for red pulp macrophages (earlier work) and for VCAM1-positive bone marrow macrophages (this paper). supporting_text: mice were found to be deficient in F4/80hi VCAM1hi BMM in addition to the previously reported loss of RPM - order: 4 role: iron-recycling outputs optional: true node: id: iron_recycling_outputs label: Heme catabolism and iron export module_type: BIOLOGICAL_PROCESS description: >- Heme also de-represses, through BACH1, the genes for heme oxygenase 1 and ferroportin. HMOX1 breaks heme down to release iron, and ferroportin exports the iron. These are the work the differentiated macrophage does, and the same derepression step controls them. annotons: - id: hmox1_enzyme label: Heme oxygenase 1 participant: selector_type: FAMILY family: preferred_term: heme oxygenase 1 term: id: PANTHER:PTHR10720:SF1 label: HEME OXYGENASE 1 representative_members: - preferred_term: HMOX1 (human) term: id: UniProtKB:P09601 label: Heme oxygenase 1 - preferred_term: Hmox1 (mouse) term: id: UniProtKB:P14901 label: Heme oxygenase 1 ancestral_nodes: - preferred_term: PAINT node PTN007456885 term: id: PANTHER:PTN007456885 label: PTN007456885 description: >- PAINT IBD node in PTHR10720 propagating F:GO:0004392 heme oxygenase (decyclizing) activity, with HMOX1 (P09601) among the seeds. evidence: - source_id: GO_REF:0000033 statement: IBD propagation of heme oxygenase (decyclizing) activity from PAINT node PTN007456885 in PTHR10720. function: preferred_term: heme oxygenase (decyclizing) activity term: id: GO:0004392 label: heme oxygenase (decyclizing) activity processes: - preferred_term: heme catabolic process term: id: GO:0042167 label: heme catabolic process role_description: Releases iron from heme in the cytosol. Its gene is de-repressed by heme through BACH1. evidence: - source_id: file:genes/human/HMOX1/HMOX1-ai-review.yaml title: HMOX1 gene review statement: The HMOX1 review covers its heme oxygenase activity. - id: ferroportin_exporter label: Ferroportin iron exporter participant: selector_type: FAMILY family: preferred_term: ferroportin term: id: PANTHER:PTHR11660:SF47 label: SOLUTE CARRIER FAMILY 40 MEMBER 1 representative_members: - preferred_term: SLC40A1 (human) term: id: UniProtKB:Q9NP59 label: Ferroportin - preferred_term: Slc40a1 (mouse) term: id: UniProtKB:Q9JHI9 label: Ferroportin ancestral_nodes: - preferred_term: PAINT node PTN002616802 term: id: PANTHER:PTN002616802 label: PTN002616802 description: >- Vertebrate-level PAINT IBD node (taxon:117571) in PTHR11660 propagating F:GO:0005381 iron ion transmembrane transporter activity, with SLC40A1 (Q9NP59) among the seeds. evidence: - source_id: GO_REF:0000033 statement: IBD propagation of iron ion transmembrane transporter activity from PAINT node PTN002616802 in PTHR11660. function: preferred_term: iron ion transmembrane transporter activity term: id: GO:0005381 label: iron ion transmembrane transporter activity processes: - preferred_term: iron ion export across plasma membrane term: id: GO:1903988 label: iron ion export across plasma membrane locations: - preferred_term: plasma membrane term: id: GO:0005886 label: plasma membrane role_description: Exports the recycled iron. Its gene is de-repressed by heme through BACH1. evidence: - source_id: PMID:24630724 title: Heme-mediated SPI-C induction promotes monocyte differentiation into iron-recycling macrophages. statement: Heme de-represses Spic, Ho1 and Slc40a1 through BACH1. supporting_text: derepression of Spic, Ho1, and SLC40A1 by heme was dependent on Bach1 connections: - source: hrg1_heme_transporter target: bach1_repressor connection_type: PROVIDES_INPUT_FOR description: >- Heme exported from the phagolysosome is the input that inactivates BACH1. This link is inferred; the two steps were studied separately. - source: hrg1_heme_transporter target: hmox1_enzyme connection_type: PROVIDES_INPUT_FOR description: Heme oxygenase faces the cytosol, so it needs exported heme. - source: bach1_repressor target: spic_tf connection_type: NEGATIVELY_REGULATES description: BACH1 represses Spic until heme triggers its degradation. - source: bach1_repressor target: hmox1_enzyme connection_type: NEGATIVELY_REGULATES - source: bach1_repressor target: ferroportin_exporter connection_type: NEGATIVELY_REGULATES - source: hmox1_enzyme target: ferroportin_exporter connection_type: PROVIDES_INPUT_FOR description: Iron released from heme is exported by ferroportin. knowledge_gaps: - gap_statement: >- How BACH1 represses Spic, and which heme-dependent step besides BACH1 degradation is needed for red pulp macrophage development, are unknown. boundary: >- The Spic locus has no classic MARE, NRF2 is not needed, and Bach1-/- mice have normal red pulp macrophage numbers, so the authors propose an additional heme-dependent, BACH1-independent step. gap_kind: - BIOLOGY dark_aspect: BP_DARK status: OPEN significance: The chain heme to BACH1 to SPIC is incomplete, and BACH1 may act indirectly on Spic. resolution: >- ChIP for BACH1 and its partner at the Spic locus in monocytes, and a screen for heme-induced, BACH1-independent factors needed for red pulp macrophage maturation (TremL4 is one candidate output). provenance: - reference_id: PMID:24630724 supporting_text: RPM development may involve an additional step that is heme-dependent but Bach1-independent