{"gene":"SPIC","run_date":"2026-04-28T20:42:08","timeline":{"discoveries":[{"year":1999,"finding":"Spi-C is a novel ETS transcription factor most closely related to PU.1 and Spi-B within the DNA-binding ETS domain, isolated by yeast one-hybrid screening. It binds DNA similarly to PU.1 (assessed by methylation interference, band-shift, and site selection analysis) and activates transcription of a kappaY element reporter gene upon co-transfection of HeLa cells.","method":"Yeast one-hybrid screen, methylation interference, EMSA (band-shift), site selection analysis, reporter gene co-transfection","journal":"The Journal of biological chemistry","confidence":"High","confidence_rationale":"Tier 1 — multiple in vitro and cell-based methods establishing DNA binding and transactivation activity","pmids":["10187812"],"is_preprint":false},{"year":2003,"finding":"SPI-C contains an acidic transactivation domain located at the N-terminus; mutation of four aspartic acid residues to alanines reduces transactivation activity to that of the DNA-binding domain alone. Unlike PU.1, SPI-C cannot form a ternary complex with the co-activator PIP on the Ig lambda light chain enhancer element.","method":"Deletion and point mutation analysis of transactivation domain, reporter assays, gel shift/ternary complex assay","journal":"Molecular immunology","confidence":"High","confidence_rationale":"Tier 1 — mutagenesis with functional reporter readout, multiple constructs tested","pmids":["12749910"],"is_preprint":false},{"year":2006,"finding":"SPI-C physically interacts with the C-terminus of STAT6, confirmed by yeast two-hybrid and co-immunoprecipitation in transfected COS7 cells. This interaction is functional: SPI-C and STAT6 synergistically stimulate IL-4-induced Iε (IgE germline) transcription only when both proteins are DNA-bound.","method":"Yeast two-hybrid, co-immunoprecipitation, reporter gene assay","journal":"Biochemical and biophysical research communications","confidence":"Medium","confidence_rationale":"Tier 2 — reciprocal interaction confirmed by two methods with functional reporter readout, single lab","pmids":["16647686"],"is_preprint":false},{"year":2008,"finding":"Spi-C selectively controls the development of red pulp macrophages (RPM) in a cell-autonomous manner. Spic−/− mice lack RPM but have normal monocytes and other tissue macrophages; retroviral Spi-C expression in bone marrow cells corrects this defect. Loss of RPM results in failure to phagocytose senescent red blood cells and iron overload localized to splenic red pulp.","method":"Knockout mouse model (Spic−/−), retroviral complementation in bone marrow, flow cytometry, phagocytosis assay, iron staining","journal":"Nature","confidence":"High","confidence_rationale":"Tier 2 — cell-autonomous rescue experiment with multiple orthogonal readouts, highly cited foundational study","pmids":["19037245"],"is_preprint":false},{"year":2008,"finding":"Transgenic overexpression of Spi-C in B cells impairs B-cell development and function by downregulating several BCR signaling mediators (including SYK and BLNK) and upregulating an inhibitor of BCR signaling, resulting in poor proliferative responses to anti-IgM or anti-CD40.","method":"B-cell-specific transgenic mouse (Eμ-Spi-C), flow cytometry, real-time RT-PCR, in vitro proliferation assay","journal":"European journal of immunology","confidence":"Medium","confidence_rationale":"Tier 2 — gain-of-function in vivo with defined molecular and cellular phenotype, single lab","pmids":["18792411"],"is_preprint":false},{"year":2010,"finding":"Spi-C, together with PU.1 and Spi-B, directly activates transcription of the Fcer2a gene (encoding CD23) to promote follicular B cell differentiation. Eμ-Spi-C transgene expression partially rescues CD23+ follicular B cell frequencies in Sfpi1+/−Spib−/− mice.","method":"Transgenic rescue experiment, in vitro reporter assay, chromatin immunoprecipitation (ChIP), gene expression analysis","journal":"Journal of immunology","confidence":"High","confidence_rationale":"Tier 2 — ChIP, reporter, and in vivo rescue with multiple orthogonal methods","pmids":["21057087"],"is_preprint":false},{"year":2014,"finding":"Heme induces proteasome-dependent degradation of the transcriptional repressor BACH1, derepressing Spic expression in monocytes to drive their differentiation into iron-recycling red pulp macrophages and bone marrow macrophages. Cysteine-proline dipeptide motifs in BACH1 are required for heme-dependent degradation. Spic also governs development of F4/80+VCAM1+ bone marrow macrophages.","method":"Genetic mouse models (Spic−/−, hemolysis models), proteasome inhibitor experiments, BACH1 mutant constructs (CP motif mutations), flow cytometry, gene expression","journal":"Cell","confidence":"High","confidence_rationale":"Tier 1-2 — mechanistic dissection using mutagenesis of BACH1 CP motifs, pharmacological inhibition of proteasome, and in vivo genetic models; replicated across multiple experimental approaches","pmids":["24630724"],"is_preprint":false},{"year":2015,"finding":"Spi-C functions as a negative regulator of B-cell development and function by repressing the Nfkb1 gene (encoding p50), opposing Spi-B which directly activates Nfkb1. Heterozygous loss of Spic in Spib−/− mice rescues B-cell frequencies, absolute numbers, and proliferative responses.","method":"Genetic epistasis (Spib−/−Spic+/− mice), reporter gene assay, gene expression analysis","journal":"Journal of immunology","confidence":"Medium","confidence_rationale":"Tier 2 — genetic epistasis with reporter assay validation, single lab","pmids":["25769919"],"is_preprint":false},{"year":2019,"finding":"RAG-generated DNA double-strand breaks in pre-B cells activate a SPIC/BCLAF1 transcription factor complex that displaces PU.1 genome-wide, represses SYK tyrosine kinase expression, and enforces the large-to-small pre-B cell transition. SPIC recruits BCLAF1 to gene-regulatory elements controlling key B-cell developmental genes.","method":"ChIP-seq, co-immunoprecipitation, gene expression analysis, SPIC/BCLAF1 complex characterization in pre-B cells with RAG-induced DSBs","journal":"Cell reports","confidence":"High","confidence_rationale":"Tier 2 — genome-wide ChIP-seq plus Co-IP of complex plus genetic and expression analyses, multiple orthogonal methods","pmids":["31644907"],"is_preprint":false},{"year":2019,"finding":"TLR signaling induces stress erythropoiesis by promoting erythrophagocytosis in splenic macrophages, which enables heme-dependent SPI-C expression. Elevated SPI-C, coupled with TLR signaling, then drives expression of Gdf15 and Bmp4 to initiate expansion of stress erythroid progenitors in the spleen.","method":"Mouse model of sterile inflammation, TLR signaling studies, erythrophagocytosis assay, gene expression analysis, cytokine treatment of progenitors","journal":"Science signaling","confidence":"Medium","confidence_rationale":"Tier 2 — in vivo mouse model with multiple molecular readouts, single lab","pmids":["31506384"],"is_preprint":false},{"year":2020,"finding":"TLR signaling induces Spic expression in patrolling monocytes and tissue macrophages via an NF-κB-dependent mechanism. SPIC then downregulates pro-inflammatory cytokines and promotes iron efflux by regulating ferroportin expression. Interferon-gamma blocks Spic expression in a STAT1-dependent manner.","method":"Genetically engineered mouse models, primary macrophage cultures, NF-κB/STAT1 pathway inhibition, ferroportin expression assay","journal":"Cell reports","confidence":"High","confidence_rationale":"Tier 2 — multiple genetic mouse models combined with primary cell assays and pathway-specific genetic manipulations","pmids":["32610126"],"is_preprint":false},{"year":2020,"finding":"RANKL stimulation induces nuclear translocation of Spi-C (from cytoplasm to nucleus) in bone marrow-derived monocytes/macrophages in a p38 MAPK- and PI3K-dependent manner. Spi-C positively regulates osteoclast differentiation by promoting expression of NFATc1, RANK, and TRAP, and regulates actin ring formation and bone resorption by controlling DC-STAMP and d2-ATPase expression.","method":"Spi-C knockdown and overexpression in BMMs, TRAP staining, actin ring assay, bone resorption assay, kinase inhibitor studies, immunofluorescence for localization","journal":"Experimental & molecular medicine","confidence":"Medium","confidence_rationale":"Tier 2 — direct localization experiment linked to functional consequence, combined with loss- and gain-of-function with defined cellular phenotype, single lab","pmids":["32341419"],"is_preprint":false},{"year":2020,"finding":"Spi-B and Spi-C differentially regulate Bach2 expression; ChIP-seq and reporter gene analyses show opposing effects on Bach2 transcription, with Spi-B and Spi-C having different regulatory impacts on plasma cell differentiation. Heterozygosity for Spic in Spib−/− mice rescues IgG1 secondary antibody responses and restores plasma cell differentiation kinetics.","method":"Genetic epistasis (Spib−/−Spic+/− mice), ChIP-seq, reporter gene analysis, gene expression analysis","journal":"Frontiers in immunology","confidence":"Medium","confidence_rationale":"Tier 2 — ChIP-seq and reporter assay with in vivo genetic rescue, single lab","pmids":["32457757"],"is_preprint":false},{"year":2022,"finding":"The Spic promoter has unidirectional transcriptional activity reduced by mutation of an NF-κB binding site. In B cells, Spic expression is repressed by an upstream regulatory region interacting with heme-binding regulator Bach2. External signals (BAFF+IL-4+IL-5, anti-IgM, LPS) downregulate Spic, partly through actin cytoskeleton-dependent mechanisms.","method":"Promoter deletion/mutation analysis, reporter assay, RT-qPCR, cytochalasin treatment, regulatory element identification","journal":"ImmunoHorizons","confidence":"Medium","confidence_rationale":"Tier 2 — promoter mutagenesis with functional reporter assay, interaction with Bach2 established, single lab","pmids":["38285436"],"is_preprint":false},{"year":2023,"finding":"Spi-C negatively regulates Igκ rearrangement in small pre-B cells by repressing both Igκ transcription and Rag1 transcription, opposing PU.1 which activates both. ChIP analysis identified Spi-C and PU.1 binding sites in the Rag1 promoter region.","method":"Inducible expression system in pre-B cell line, Spic−/− mice, RT-qPCR, ChIP analysis","journal":"Journal of immunology","confidence":"Medium","confidence_rationale":"Tier 2 — ChIP plus inducible system plus genetic knockout with consistent molecular phenotypes, single lab","pmids":["37195219"],"is_preprint":false},{"year":2023,"finding":"SPIC binds to enhancer elements and stabilizes NANOG binding to chromatin in ground-state embryonic stem cells, particularly at genes encoding enzymes of choline/one-carbon metabolism (Bhmt, Bhmt2, Dmgdh). SPIC controls the SAM-to-SAH flux, thereby modulating H3R17me2 and H3K4me3 histone methylation marks.","method":"Gain- and loss-of-function in ESCs, ChIP analysis, metabolic flux measurement (SAM/SAH), histone modification assay","journal":"Science advances","confidence":"Medium","confidence_rationale":"Tier 2 — multiple orthogonal methods (ChIP, metabolomics, histone modification) in single study","pmids":["37595034"],"is_preprint":false},{"year":2023,"finding":"In zebrafish, the ETS transcription factor Spic guides in situ generation of metaphocytes (tissue-resident macrophage/DC-like cells of non-hematopoietic origin) from local progenitors; Spic deficiency results in absence of metaphocytes. Metaphocytes are the major IL-22BP-producing cells, and their depletion causes dysregulated barrier immunity.","method":"Zebrafish spic knockout, lineage tracing, cell depletion, IL-22BP expression assay","journal":"Cell reports","confidence":"Medium","confidence_rationale":"Tier 2 — genetic loss-of-function in zebrafish ortholog with defined cellular and molecular phenotype","pmids":["37148242"],"is_preprint":false},{"year":2026,"finding":"Silencing of the m6A writer Zc3h13 stabilizes Spic mRNA in an m6A-dependent manner, thereby increasing SPIC protein levels, inhibiting NF-κB pathway activation, and attenuating LPS-induced inflammatory responses in macrophages. Co-silencing of Spic reverses the anti-inflammatory effects of Zc3h13 knockdown.","method":"siRNA knockdown of Zc3h13 and Spic in macrophages, m6A methylation assay, mRNA stability assay, NF-κB pathway analysis, in vivo mouse LPS model","journal":"Journal of immunology","confidence":"Medium","confidence_rationale":"Tier 2 — epistasis by co-silencing with mRNA stability and pathway readouts, multiple methods in single study","pmids":["41847860"],"is_preprint":false}],"current_model":"SPIC is an ETS-family transcription factor that, in response to heme-driven proteasomal degradation of the repressor BACH1, is induced in monocytes to direct their differentiation into iron-recycling red pulp macrophages and bone marrow macrophages; in macrophages it is additionally activated by NF-κB signaling downstream of TLRs to suppress pro-inflammatory cytokines and promote ferroportin-mediated iron efflux (counteracted by IFN-γ/STAT1); in B cells, SPIC acts as a transcriptional repressor that—following RAG-induced DNA double-strand breaks—forms a complex with BCLAF1, displaces PU.1 genome-wide, represses Nfkb1, Rag1, and Igκ transcription, and enforces the pre-B to small pre-B cell transition, while also cooperating with STAT6 to stimulate IgE germline transcription and opposing Spi-B to regulate plasma cell differentiation."},"narrative":{"teleology":[{"year":1999,"claim":"Identification of SPIC as a new ETS-family member established that the PU.1/Spi-B subfamily contained a third factor with similar DNA-binding specificity but potentially distinct functions.","evidence":"Yeast one-hybrid screen, EMSA, methylation interference, and reporter assay in HeLa cells","pmids":["10187812"],"confidence":"High","gaps":["No in vivo function determined","Expression pattern across tissues not fully characterized","Endogenous target genes unknown"]},{"year":2003,"claim":"Mapping of an N-terminal acidic transactivation domain and demonstration that SPIC cannot form ternary complexes with PIP on the Igλ enhancer distinguished SPIC mechanistically from PU.1.","evidence":"Deletion/point mutagenesis of transactivation domain with reporter assays and gel shift ternary complex assay","pmids":["12749910"],"confidence":"High","gaps":["Whether SPIC uses alternative co-activators not tested","Structural basis for inability to recruit PIP unknown"]},{"year":2006,"claim":"Discovery that SPIC physically interacts with STAT6 and synergistically activates IgE germline transcription revealed a first functional partnership linking SPIC to humoral immune regulation.","evidence":"Yeast two-hybrid, co-immunoprecipitation in COS7, reporter assay for Iε promoter","pmids":["16647686"],"confidence":"Medium","gaps":["Interaction not confirmed in primary B cells","Whether SPIC-STAT6 interaction occurs on endogenous chromatin not tested"]},{"year":2008,"claim":"Genetic knockout demonstrated that SPIC is uniquely required for red pulp macrophage development and iron recycling, establishing its non-redundant role relative to PU.1 and Spi-B, while transgenic overexpression in B cells revealed dose-dependent repression of BCR signaling components.","evidence":"Spic−/− mice with retroviral rescue, phagocytosis and iron staining assays; Eμ-Spi-C transgenic mice with flow cytometry and proliferation assays","pmids":["19037245","18792411"],"confidence":"High","gaps":["Transcriptional targets in RPM not mapped genome-wide","Whether B-cell repression is direct or indirect at individual loci unclear"]},{"year":2014,"claim":"Identification of the heme–BACH1–SPIC axis resolved how environmental iron sensing is transduced into a transcriptional program: heme triggers proteasomal BACH1 degradation via cysteine-proline motifs, derepressing Spic to drive RPM and bone marrow macrophage differentiation.","evidence":"Spic−/− and hemolysis mouse models, BACH1 CP-motif mutant constructs, proteasome inhibitor experiments","pmids":["24630724"],"confidence":"High","gaps":["Whether additional repressors besides BACH1 regulate Spic in non-macrophage lineages not addressed","Direct BACH1 binding to Spic locus not demonstrated by ChIP"]},{"year":2015,"claim":"Genetic epistasis between Spic and Spib showed that SPIC opposes Spi-B by repressing Nfkb1 transcription, establishing a balancing mechanism within the subfamily that tunes B-cell output.","evidence":"Spib−/−Spic+/− mice, reporter assay, gene expression analysis","pmids":["25769919"],"confidence":"Medium","gaps":["Whether SPIC directly binds the Nfkb1 promoter in primary B cells not shown by ChIP","Downstream NF-κB targets affected not mapped"]},{"year":2019,"claim":"Genome-wide ChIP-seq revealed that RAG-induced DNA breaks trigger a SPIC/BCLAF1 complex that displaces PU.1 from regulatory elements, represses SYK, and enforces the pre-B cell transition, connecting DNA damage signaling to lineage progression.","evidence":"ChIP-seq, co-immunoprecipitation, gene expression in pre-B cells with RAG-induced DSBs","pmids":["31644907"],"confidence":"High","gaps":["How DNA break signals induce SPIC protein or complex assembly not fully elucidated","Structural basis of SPIC-BCLAF1 interaction unknown"]},{"year":2019,"claim":"TLR signaling was shown to couple erythrophagocytosis-derived heme with SPIC induction in splenic macrophages, which then drives Gdf15 and Bmp4 expression to initiate stress erythropoiesis, extending SPIC's role beyond iron recycling to erythroid regeneration.","evidence":"Mouse sterile inflammation model, erythrophagocytosis assay, gene expression","pmids":["31506384"],"confidence":"Medium","gaps":["Whether SPIC directly binds Gdf15/Bmp4 regulatory regions not established","Relevance to human stress erythropoiesis not tested"]},{"year":2020,"claim":"Multiple studies established SPIC as an NF-κB-induced anti-inflammatory effector in macrophages that promotes ferroportin expression and iron efflux while being antagonized by IFN-γ/STAT1, and as a regulator of osteoclast differentiation and plasma cell fate.","evidence":"Genetic mouse models with NF-κB/STAT1 pathway manipulation; RANKL-stimulated BMMs with kinase inhibitors and localization assays; Spib−/−Spic+/− mice with ChIP-seq for Bach2","pmids":["32610126","32341419","32457757"],"confidence":"Medium","gaps":["Direct SPIC binding at ferroportin locus not mapped","Osteoclast findings from single lab without in vivo bone phenotype","SPIC nuclear translocation mechanism in osteoclasts not fully defined"]},{"year":2022,"claim":"Promoter dissection revealed that NF-κB binding is required for Spic promoter activity and that Bach2 represses Spic through an upstream regulatory region in B cells, while external B-cell activating signals downregulate Spic partly through actin-dependent mechanisms.","evidence":"Promoter deletion/mutation reporter assay, RT-qPCR, cytochalasin treatment","pmids":["38285436"],"confidence":"Medium","gaps":["Actin-dependent repression mechanism molecularly undefined","Whether Bach2 directly binds the identified upstream element not confirmed by ChIP"]},{"year":2023,"claim":"Three studies expanded SPIC's functional scope: it represses Igκ rearrangement by directly opposing PU.1 at Rag1 and Igκ loci in pre-B cells; it stabilizes NANOG on enhancers of one-carbon metabolism genes in ESCs to control histone methylation; and its zebrafish ortholog drives metaphocyte generation for barrier immunity.","evidence":"ChIP plus inducible expression in pre-B cells and Spic−/− mice; ChIP, metabolomics, and histone modification in ESCs; zebrafish spic knockout with lineage tracing","pmids":["37195219","37595034","37148242"],"confidence":"Medium","gaps":["ESC function awaits confirmation in mammalian embryonic development in vivo","Whether metaphocyte specification by Spic is conserved in mammals unknown","SPIC occupancy at Rag1 in primary small pre-B cells not validated genome-wide"]},{"year":2026,"claim":"Demonstration that m6A methylation by ZC3H13 destabilizes Spic mRNA revealed a post-transcriptional layer of SPIC regulation, with SPIC protein levels controlling NF-κB-dependent inflammatory responses in macrophages.","evidence":"siRNA knockdown/co-silencing of Zc3h13 and Spic in macrophages, m6A and mRNA stability assays, in vivo LPS model","pmids":["41847860"],"confidence":"Medium","gaps":["Specific m6A sites on Spic mRNA not mapped","Whether other m6A readers/erasers participate not tested"]},{"year":null,"claim":"Key unresolved questions include the structural basis of SPIC's context-dependent switching between transcriptional activation and repression, how DNA damage signals post-translationally activate SPIC in pre-B cells, and whether SPIC's role in ESC chromatin and zebrafish metaphocytes reflects conserved mammalian developmental functions.","evidence":"","pmids":[],"confidence":"Low","gaps":["No crystal or cryo-EM structure available","Post-translational modifications controlling SPIC activity largely uncharacterized","No genome-wide target comparison across cell types (macrophage vs. B cell vs. ESC)"]}],"mechanism_profile":{"molecular_activity":[{"term_id":"GO:0003677","term_label":"DNA binding","supporting_discovery_ids":[0,1,5,8,14,15]},{"term_id":"GO:0140110","term_label":"transcription regulator activity","supporting_discovery_ids":[0,1,5,7,8,10,14,15]}],"localization":[{"term_id":"GO:0005634","term_label":"nucleus","supporting_discovery_ids":[8,11,15]}],"pathway":[{"term_id":"R-HSA-168256","term_label":"Immune System","supporting_discovery_ids":[3,6,8,10,14]},{"term_id":"R-HSA-74160","term_label":"Gene expression (Transcription)","supporting_discovery_ids":[0,1,5,7,10,15]},{"term_id":"R-HSA-1266738","term_label":"Developmental Biology","supporting_discovery_ids":[3,6,8,11,16]},{"term_id":"R-HSA-382551","term_label":"Transport of small molecules","supporting_discovery_ids":[3,6,10]}],"complexes":["SPIC-BCLAF1 complex"],"partners":["BCLAF1","STAT6","BACH1","SPI1","SPIB","NANOG","BACH2"],"other_free_text":[]},"mechanistic_narrative":"SPIC is an ETS-family transcription factor that orchestrates iron homeostasis, myeloid cell fate, and B-cell developmental checkpoints through context-dependent transcriptional activation and repression. In monocytes and macrophages, heme-driven proteasomal degradation of the repressor BACH1 derepresses SPIC expression, which is essential for differentiation of red pulp macrophages and bone marrow macrophages that recycle iron from senescent erythrocytes via ferroportin; TLR/NF-κB signaling further induces SPIC to suppress pro-inflammatory cytokines, while IFN-γ/STAT1 antagonizes this pathway [PMID:19037245, PMID:24630724, PMID:32610126]. In pre-B cells, RAG-induced DNA double-strand breaks activate a SPIC/BCLAF1 complex that displaces PU.1 genome-wide, represses Nfkb1, Rag1, and Igκ transcription, and enforces the large-to-small pre-B cell transition, while in mature B cells SPIC opposes Spi-B to regulate plasma cell differentiation and cooperates with STAT6 to stimulate IgE germline transcription [PMID:31644907, PMID:37195219, PMID:25769919, PMID:16647686]. SPIC also functions in embryonic stem cells, where it stabilizes NANOG binding at enhancers controlling one-carbon metabolism genes and modulates histone methylation through SAM-to-SAH flux [PMID:37595034]."},"prefetch_data":{"uniprot":{"accession":"Q8N5J4","full_name":"Transcription factor Spi-C","aliases":[],"length_aa":248,"mass_kda":29.2,"function":"Controls the development of red pulp macrophages required for red blood cells recycling and iron homeostasis. Transcription factor that binds to the PU-box, a purine-rich DNA sequence (5'-GAGGA[AT]-3') that can act as a lymphoid-specific enhancer. Regulates VCAM1 gene expression (By similarity)","subcellular_location":"Nucleus","url":"https://www.uniprot.org/uniprotkb/Q8N5J4/entry"},"depmap":{"release":"DepMap","has_data":true,"is_common_essential":false,"resolved_as":"","url":"https://depmap.org/portal/gene/SPIC","classification":"Not Classified","n_dependent_lines":165,"n_total_lines":1208,"dependency_fraction":0.13658940397350994},"opencell":{"profiled":false,"resolved_as":"","ensg_id":"","cell_line_id":"","localizations":[],"interactors":[],"url":"https://opencell.sf.czbiohub.org/search/SPIC","total_profiled":1310},"omim":[{"mim_id":"612568","title":"SPIC TRANSCRIPTION FACTOR; SPIC","url":"https://www.omim.org/entry/612568"},{"mim_id":"608871","title":"NIPSNAP HOMOLOG 3A; NIPSNAP3A","url":"https://www.omim.org/entry/608871"}],"hpa":{"profiled":true,"resolved_as":"","reliability":"","locations":[],"tissue_specificity":"Tissue enriched","tissue_distribution":"Detected in some","driving_tissues":[{"tissue":"lymphoid tissue","ntpm":29.0}],"url":"https://www.proteinatlas.org/search/SPIC"},"hgnc":{"alias_symbol":["MGC40611","SPI-C"],"prev_symbol":[]},"alphafold":{"accession":"Q8N5J4","domains":[{"cath_id":"1.10.10.10","chopping":"114-202","consensus_level":"high","plddt":97.4987,"start":114,"end":202}],"viewer_url":"https://alphafold.ebi.ac.uk/entry/Q8N5J4","model_url":"https://alphafold.ebi.ac.uk/files/AF-Q8N5J4-F1-model_v6.cif","pae_url":"https://alphafold.ebi.ac.uk/files/AF-Q8N5J4-F1-predicted_aligned_error_v6.png","plddt_mean":67.56},"mouse_models":{"mgi_url":"https://www.informatics.jax.org/marker/summary?nomen=SPIC","jax_strain_url":"https://www.jax.org/strain/search?query=SPIC"},"sequence":{"accession":"Q8N5J4","fasta_url":"https://rest.uniprot.org/uniprotkb/Q8N5J4.fasta","uniprot_url":"https://www.uniprot.org/uniprotkb/Q8N5J4/entry","alphafold_viewer_url":"https://alphafold.ebi.ac.uk/entry/Q8N5J4"}},"corpus_meta":[{"pmid":"19037245","id":"PMC_19037245","title":"Role for Spi-C in the development of red pulp macrophages and splenic iron homeostasis.","date":"2008","source":"Nature","url":"https://pubmed.ncbi.nlm.nih.gov/19037245","citation_count":360,"is_preprint":false},{"pmid":"24630724","id":"PMC_24630724","title":"Heme-mediated SPI-C induction promotes monocyte differentiation into iron-recycling macrophages.","date":"2014","source":"Cell","url":"https://pubmed.ncbi.nlm.nih.gov/24630724","citation_count":337,"is_preprint":false},{"pmid":"31506384","id":"PMC_31506384","title":"Inflammation induces stress erythropoiesis through heme-dependent activation of SPI-C.","date":"2019","source":"Science signaling","url":"https://pubmed.ncbi.nlm.nih.gov/31506384","citation_count":68,"is_preprint":false},{"pmid":"12174087","id":"PMC_12174087","title":"SpiC is required for secretion of Salmonella Pathogenicity Island 2 type III secretion system proteins.","date":"2002","source":"Cellular microbiology","url":"https://pubmed.ncbi.nlm.nih.gov/12174087","citation_count":64,"is_preprint":false},{"pmid":"12950921","id":"PMC_12950921","title":"The Salmonella SpiC protein targets the mammalian Hook3 protein function to alter cellular trafficking.","date":"2003","source":"Molecular microbiology","url":"https://pubmed.ncbi.nlm.nih.gov/12950921","citation_count":52,"is_preprint":false},{"pmid":"12427096","id":"PMC_12427096","title":"Identification of a NIPSNAP homologue as host cell target for Salmonella virulence protein SpiC.","date":"2002","source":"Cellular microbiology","url":"https://pubmed.ncbi.nlm.nih.gov/12427096","citation_count":52,"is_preprint":false},{"pmid":"15491354","id":"PMC_15491354","title":"SsaM and SpiC interact and regulate secretion of Salmonella pathogenicity island 2 type III secretion system effectors and translocators.","date":"2004","source":"Molecular microbiology","url":"https://pubmed.ncbi.nlm.nih.gov/15491354","citation_count":49,"is_preprint":false},{"pmid":"32610126","id":"PMC_32610126","title":"Counter Regulation of Spic by NF-κB and STAT Signaling Controls Inflammation and Iron Metabolism in Macrophages.","date":"2020","source":"Cell reports","url":"https://pubmed.ncbi.nlm.nih.gov/32610126","citation_count":47,"is_preprint":false},{"pmid":"10187812","id":"PMC_10187812","title":"Spi-C, a novel Ets protein that is temporally regulated during B lymphocyte development.","date":"1999","source":"The Journal of biological chemistry","url":"https://pubmed.ncbi.nlm.nih.gov/10187812","citation_count":40,"is_preprint":false},{"pmid":"21057087","id":"PMC_21057087","title":"Regulation of follicular B cell differentiation by the related E26 transformation-specific transcription factors PU.1, Spi-B, and Spi-C.","date":"2010","source":"Journal of immunology (Baltimore, Md. : 1950)","url":"https://pubmed.ncbi.nlm.nih.gov/21057087","citation_count":36,"is_preprint":false},{"pmid":"12874347","id":"PMC_12874347","title":"Construction, characterization, and immunogenicity of an attenuated Salmonella enterica serovar typhimurium pgtE vaccine expressing fimbriae with integrated viral epitopes from the spiC promoter.","date":"2003","source":"Infection and immunity","url":"https://pubmed.ncbi.nlm.nih.gov/12874347","citation_count":32,"is_preprint":false},{"pmid":"33429286","id":"PMC_33429286","title":"WbaP is required for swarm motility and intramacrophage multiplication of Salmonella Enteritidis spiC mutant by glucose use ability.","date":"2020","source":"Microbiological research","url":"https://pubmed.ncbi.nlm.nih.gov/33429286","citation_count":19,"is_preprint":false},{"pmid":"31644907","id":"PMC_31644907","title":"RAG-Mediated DNA Breaks Attenuate PU.1 Activity in Early B Cells through Activation of a SPIC-BCLAF1 Complex.","date":"2019","source":"Cell 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advances","url":"https://pubmed.ncbi.nlm.nih.gov/37595034","citation_count":16,"is_preprint":false},{"pmid":"32457757","id":"PMC_32457757","title":"Opposing Roles for the Related ETS-Family Transcription Factors Spi-B and Spi-C in Regulating B Cell Differentiation and Function.","date":"2020","source":"Frontiers in immunology","url":"https://pubmed.ncbi.nlm.nih.gov/32457757","citation_count":15,"is_preprint":false},{"pmid":"9616339","id":"PMC_9616339","title":"Long-term survival effect of metoprolol in dilated cardiomyopathy. The SPIC (Italian Multicentre Cardiomyopathy Study) Group.","date":"1998","source":"Heart (British Cardiac Society)","url":"https://pubmed.ncbi.nlm.nih.gov/9616339","citation_count":14,"is_preprint":false},{"pmid":"12749910","id":"PMC_12749910","title":"SPI-C, a PU-box binding ETS protein expressed temporarily during B-cell development and in macrophages, contains an acidic transactivation domain located to the N-terminus.","date":"2003","source":"Molecular immunology","url":"https://pubmed.ncbi.nlm.nih.gov/12749910","citation_count":14,"is_preprint":false},{"pmid":"33551301","id":"PMC_33551301","title":"Salmonella Pullorum spiC mutant is a desirable LASV candidate with proper virulence, high immune protection and easy-to-use oral administration.","date":"2021","source":"Vaccine","url":"https://pubmed.ncbi.nlm.nih.gov/33551301","citation_count":12,"is_preprint":false},{"pmid":"12459275","id":"PMC_12459275","title":"Genomic structure of mouse SPI-C and genomic structure and expression pattern of human SPI-C.","date":"2002","source":"Gene","url":"https://pubmed.ncbi.nlm.nih.gov/12459275","citation_count":12,"is_preprint":false},{"pmid":"31801257","id":"PMC_31801257","title":"Evaluation of the Safety and Protection Efficacy of spiC and nmpC or rfaL Deletion Mutants of Salmonella Enteritidis as Live Vaccine Candidates for Poultry Non-Typhoidal Salmonellosis.","date":"2019","source":"Vaccines","url":"https://pubmed.ncbi.nlm.nih.gov/31801257","citation_count":11,"is_preprint":false},{"pmid":"18792411","id":"PMC_18792411","title":"Transgenic expression of Spi-C impairs B-cell development and function by affecting genes associated with BCR signaling.","date":"2008","source":"European journal of immunology","url":"https://pubmed.ncbi.nlm.nih.gov/18792411","citation_count":11,"is_preprint":false},{"pmid":"25769919","id":"PMC_25769919","title":"Identification of a negative regulatory role for spi-C in the murine B cell lineage.","date":"2015","source":"Journal of immunology (Baltimore, Md. : 1950)","url":"https://pubmed.ncbi.nlm.nih.gov/25769919","citation_count":10,"is_preprint":false},{"pmid":"24564945","id":"PMC_24564945","title":"SPIC: a novel similarity metric for comparing transcription factor binding site motifs based on information contents.","date":"2013","source":"BMC systems biology","url":"https://pubmed.ncbi.nlm.nih.gov/24564945","citation_count":10,"is_preprint":false},{"pmid":"19706157","id":"PMC_19706157","title":"Involvement of SPI-2-encoded SpiC in flagellum synthesis in Salmonella enterica serovar Typhimurium.","date":"2009","source":"BMC microbiology","url":"https://pubmed.ncbi.nlm.nih.gov/19706157","citation_count":8,"is_preprint":false},{"pmid":"8529848","id":"PMC_8529848","title":"[Dilated cardiomyopathy: a new natural history? The experience of the Italian Multicenter Cardiomyopathy Study (SPIC)].","date":"1995","source":"Giornale italiano di cardiologia","url":"https://pubmed.ncbi.nlm.nih.gov/8529848","citation_count":8,"is_preprint":false},{"pmid":"16647686","id":"PMC_16647686","title":"SPI-C and STAT6 can cooperate to stimulate IgE germline transcription.","date":"2006","source":"Biochemical and biophysical research communications","url":"https://pubmed.ncbi.nlm.nih.gov/16647686","citation_count":8,"is_preprint":false},{"pmid":"32341419","id":"PMC_32341419","title":"Spi-C positively regulates RANKL-mediated osteoclast differentiation and function.","date":"2020","source":"Experimental & molecular medicine","url":"https://pubmed.ncbi.nlm.nih.gov/32341419","citation_count":7,"is_preprint":false},{"pmid":"31440219","id":"PMC_31440219","title":"Controversy Surrounding the Function of SpiC Protein in Salmonella: An Overview.","date":"2019","source":"Frontiers in microbiology","url":"https://pubmed.ncbi.nlm.nih.gov/31440219","citation_count":6,"is_preprint":false},{"pmid":"34869728","id":"PMC_34869728","title":"Evaluation of Safety and Protective Efficacy of a waaJ and spiC Double Deletion Korean Epidemic Strain of Salmonella enterica Serovar Gallinarum.","date":"2021","source":"Frontiers in veterinary science","url":"https://pubmed.ncbi.nlm.nih.gov/34869728","citation_count":6,"is_preprint":false},{"pmid":"37148242","id":"PMC_37148242","title":"Metaphocytes are IL-22BP-producing cells regulated by ETS transcription factor Spic and essential for zebrafish barrier immunity.","date":"2023","source":"Cell reports","url":"https://pubmed.ncbi.nlm.nih.gov/37148242","citation_count":5,"is_preprint":false},{"pmid":"26683183","id":"PMC_26683183","title":"Preparation of Monoclonal Antibodies Against SpiC Protein Secreted by T3SS-2 of Salmonella spp.","date":"2015","source":"Monoclonal antibodies in immunodiagnosis and immunotherapy","url":"https://pubmed.ncbi.nlm.nih.gov/26683183","citation_count":3,"is_preprint":false},{"pmid":"38285436","id":"PMC_38285436","title":"The E26 Transformation-Specific Family Transcription Factor Spi-C Is Dynamically Regulated by External Signals in B Cells.","date":"2022","source":"ImmunoHorizons","url":"https://pubmed.ncbi.nlm.nih.gov/38285436","citation_count":3,"is_preprint":false},{"pmid":"34730294","id":"PMC_34730294","title":"Lineage-instructive functions of the E26-transformation-specific-family transcription factor Spi-C in immune cell development and disease.","date":"2021","source":"WIREs mechanisms of disease","url":"https://pubmed.ncbi.nlm.nih.gov/34730294","citation_count":2,"is_preprint":false},{"pmid":"39674031","id":"PMC_39674031","title":"Salmonella enterica serovar typhimurium effectors spiA and spiC promote replication by modulating iron metabolism and oxidative stress.","date":"2024","source":"Veterinary microbiology","url":"https://pubmed.ncbi.nlm.nih.gov/39674031","citation_count":1,"is_preprint":false},{"pmid":"40073238","id":"PMC_40073238","title":"Burn injury-induced G-CSF secretion reduces spic+ erythroblastic island macrophages in the bone marrow and impairs medullary erythropoiesis.","date":"2025","source":"Journal of immunology (Baltimore, Md. : 1950)","url":"https://pubmed.ncbi.nlm.nih.gov/40073238","citation_count":1,"is_preprint":false},{"pmid":"25652851","id":"PMC_25652851","title":"[Prokaryotic expression and application of SpiC protein of Salmonella pullorum].","date":"2015","source":"Xi bao yu fen zi mian yi xue za zhi = Chinese journal of cellular and molecular immunology","url":"https://pubmed.ncbi.nlm.nih.gov/25652851","citation_count":1,"is_preprint":false},{"pmid":"37195219","id":"PMC_37195219","title":"Spi-C and PU.1 Counterregulate Rag1 and Igκ Transcription to Effect Vκ-Jκ Recombination in Small Pre-B Cells.","date":"2023","source":"Journal of immunology (Baltimore, Md. : 1950)","url":"https://pubmed.ncbi.nlm.nih.gov/37195219","citation_count":1,"is_preprint":false},{"pmid":"41847860","id":"PMC_41847860","title":"Silencing of Zc3h13 attenuates LPS-induced inflammatory response in macrophages via m6A-dependent stabilization of Spic mRNA.","date":"2026","source":"Journal of immunology (Baltimore, Md. : 1950)","url":"https://pubmed.ncbi.nlm.nih.gov/41847860","citation_count":0,"is_preprint":false},{"pmid":"41751866","id":"PMC_41751866","title":"The Emerging Role of Transcription Factor Spi-C in Macrophage Biology and Inflammatory Pathogenesis.","date":"2026","source":"International journal of molecular sciences","url":"https://pubmed.ncbi.nlm.nih.gov/41751866","citation_count":0,"is_preprint":false},{"pmid":null,"id":"bio_10.1101_2025.03.25.645219","title":"Myeloid FtH Regulates Macrophage Response to Kidney Injury by Modulating Snca and Ferroptosis","date":"2025-03-28","source":"bioRxiv","url":"https://doi.org/10.1101/2025.03.25.645219","citation_count":0,"is_preprint":true},{"pmid":null,"id":"bio_10.1101_2025.01.16.25320656","title":"Cohort profile of the ICMR-Stillbirth Pooled India Cohort (ICMR-SPIC): Estimating Prevalence, Analyzing Risk Factors, and Developing Prediction Models for Stillbirths in India","date":"2025-01-17","source":"bioRxiv","url":"https://doi.org/10.1101/2025.01.16.25320656","citation_count":0,"is_preprint":true}],"cost":{"stage1":{"model":"claude-sonnet-4-6","input_tokens":21933,"output_tokens":4376,"usd":0.06572},"stage2":{"model":"claude-opus-4-6","input_tokens":7935,"output_tokens":3258,"usd":0.181688},"total_usd":0.247408,"stage1_batch_id":"msgbatch_011rkcQdVV1RaFq9XhcG6df6","stage2_batch_id":"msgbatch_01RzgrJafdF4EWHhj5mNi6dh","note":"batch pricing = 50% of standard"},"stage1_raw":"```json\n{\n  \"discoveries\": [\n    {\n      \"year\": 1999,\n      \"finding\": \"Spi-C is a novel ETS transcription factor most closely related to PU.1 and Spi-B within the DNA-binding ETS domain, isolated by yeast one-hybrid screening. It binds DNA similarly to PU.1 (assessed by methylation interference, band-shift, and site selection analysis) and activates transcription of a kappaY element reporter gene upon co-transfection of HeLa cells.\",\n      \"method\": \"Yeast one-hybrid screen, methylation interference, EMSA (band-shift), site selection analysis, reporter gene co-transfection\",\n      \"journal\": \"The Journal of biological chemistry\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 — multiple in vitro and cell-based methods establishing DNA binding and transactivation activity\",\n      \"pmids\": [\"10187812\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2003,\n      \"finding\": \"SPI-C contains an acidic transactivation domain located at the N-terminus; mutation of four aspartic acid residues to alanines reduces transactivation activity to that of the DNA-binding domain alone. Unlike PU.1, SPI-C cannot form a ternary complex with the co-activator PIP on the Ig lambda light chain enhancer element.\",\n      \"method\": \"Deletion and point mutation analysis of transactivation domain, reporter assays, gel shift/ternary complex assay\",\n      \"journal\": \"Molecular immunology\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 — mutagenesis with functional reporter readout, multiple constructs tested\",\n      \"pmids\": [\"12749910\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2006,\n      \"finding\": \"SPI-C physically interacts with the C-terminus of STAT6, confirmed by yeast two-hybrid and co-immunoprecipitation in transfected COS7 cells. This interaction is functional: SPI-C and STAT6 synergistically stimulate IL-4-induced Iε (IgE germline) transcription only when both proteins are DNA-bound.\",\n      \"method\": \"Yeast two-hybrid, co-immunoprecipitation, reporter gene assay\",\n      \"journal\": \"Biochemical and biophysical research communications\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 — reciprocal interaction confirmed by two methods with functional reporter readout, single lab\",\n      \"pmids\": [\"16647686\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2008,\n      \"finding\": \"Spi-C selectively controls the development of red pulp macrophages (RPM) in a cell-autonomous manner. Spic−/− mice lack RPM but have normal monocytes and other tissue macrophages; retroviral Spi-C expression in bone marrow cells corrects this defect. Loss of RPM results in failure to phagocytose senescent red blood cells and iron overload localized to splenic red pulp.\",\n      \"method\": \"Knockout mouse model (Spic−/−), retroviral complementation in bone marrow, flow cytometry, phagocytosis assay, iron staining\",\n      \"journal\": \"Nature\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 — cell-autonomous rescue experiment with multiple orthogonal readouts, highly cited foundational study\",\n      \"pmids\": [\"19037245\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2008,\n      \"finding\": \"Transgenic overexpression of Spi-C in B cells impairs B-cell development and function by downregulating several BCR signaling mediators (including SYK and BLNK) and upregulating an inhibitor of BCR signaling, resulting in poor proliferative responses to anti-IgM or anti-CD40.\",\n      \"method\": \"B-cell-specific transgenic mouse (Eμ-Spi-C), flow cytometry, real-time RT-PCR, in vitro proliferation assay\",\n      \"journal\": \"European journal of immunology\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 — gain-of-function in vivo with defined molecular and cellular phenotype, single lab\",\n      \"pmids\": [\"18792411\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2010,\n      \"finding\": \"Spi-C, together with PU.1 and Spi-B, directly activates transcription of the Fcer2a gene (encoding CD23) to promote follicular B cell differentiation. Eμ-Spi-C transgene expression partially rescues CD23+ follicular B cell frequencies in Sfpi1+/−Spib−/− mice.\",\n      \"method\": \"Transgenic rescue experiment, in vitro reporter assay, chromatin immunoprecipitation (ChIP), gene expression analysis\",\n      \"journal\": \"Journal of immunology\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 — ChIP, reporter, and in vivo rescue with multiple orthogonal methods\",\n      \"pmids\": [\"21057087\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2014,\n      \"finding\": \"Heme induces proteasome-dependent degradation of the transcriptional repressor BACH1, derepressing Spic expression in monocytes to drive their differentiation into iron-recycling red pulp macrophages and bone marrow macrophages. Cysteine-proline dipeptide motifs in BACH1 are required for heme-dependent degradation. Spic also governs development of F4/80+VCAM1+ bone marrow macrophages.\",\n      \"method\": \"Genetic mouse models (Spic−/−, hemolysis models), proteasome inhibitor experiments, BACH1 mutant constructs (CP motif mutations), flow cytometry, gene expression\",\n      \"journal\": \"Cell\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1-2 — mechanistic dissection using mutagenesis of BACH1 CP motifs, pharmacological inhibition of proteasome, and in vivo genetic models; replicated across multiple experimental approaches\",\n      \"pmids\": [\"24630724\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2015,\n      \"finding\": \"Spi-C functions as a negative regulator of B-cell development and function by repressing the Nfkb1 gene (encoding p50), opposing Spi-B which directly activates Nfkb1. Heterozygous loss of Spic in Spib−/− mice rescues B-cell frequencies, absolute numbers, and proliferative responses.\",\n      \"method\": \"Genetic epistasis (Spib−/−Spic+/− mice), reporter gene assay, gene expression analysis\",\n      \"journal\": \"Journal of immunology\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 — genetic epistasis with reporter assay validation, single lab\",\n      \"pmids\": [\"25769919\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2019,\n      \"finding\": \"RAG-generated DNA double-strand breaks in pre-B cells activate a SPIC/BCLAF1 transcription factor complex that displaces PU.1 genome-wide, represses SYK tyrosine kinase expression, and enforces the large-to-small pre-B cell transition. SPIC recruits BCLAF1 to gene-regulatory elements controlling key B-cell developmental genes.\",\n      \"method\": \"ChIP-seq, co-immunoprecipitation, gene expression analysis, SPIC/BCLAF1 complex characterization in pre-B cells with RAG-induced DSBs\",\n      \"journal\": \"Cell reports\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 — genome-wide ChIP-seq plus Co-IP of complex plus genetic and expression analyses, multiple orthogonal methods\",\n      \"pmids\": [\"31644907\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2019,\n      \"finding\": \"TLR signaling induces stress erythropoiesis by promoting erythrophagocytosis in splenic macrophages, which enables heme-dependent SPI-C expression. Elevated SPI-C, coupled with TLR signaling, then drives expression of Gdf15 and Bmp4 to initiate expansion of stress erythroid progenitors in the spleen.\",\n      \"method\": \"Mouse model of sterile inflammation, TLR signaling studies, erythrophagocytosis assay, gene expression analysis, cytokine treatment of progenitors\",\n      \"journal\": \"Science signaling\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 — in vivo mouse model with multiple molecular readouts, single lab\",\n      \"pmids\": [\"31506384\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2020,\n      \"finding\": \"TLR signaling induces Spic expression in patrolling monocytes and tissue macrophages via an NF-κB-dependent mechanism. SPIC then downregulates pro-inflammatory cytokines and promotes iron efflux by regulating ferroportin expression. Interferon-gamma blocks Spic expression in a STAT1-dependent manner.\",\n      \"method\": \"Genetically engineered mouse models, primary macrophage cultures, NF-κB/STAT1 pathway inhibition, ferroportin expression assay\",\n      \"journal\": \"Cell reports\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 — multiple genetic mouse models combined with primary cell assays and pathway-specific genetic manipulations\",\n      \"pmids\": [\"32610126\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2020,\n      \"finding\": \"RANKL stimulation induces nuclear translocation of Spi-C (from cytoplasm to nucleus) in bone marrow-derived monocytes/macrophages in a p38 MAPK- and PI3K-dependent manner. Spi-C positively regulates osteoclast differentiation by promoting expression of NFATc1, RANK, and TRAP, and regulates actin ring formation and bone resorption by controlling DC-STAMP and d2-ATPase expression.\",\n      \"method\": \"Spi-C knockdown and overexpression in BMMs, TRAP staining, actin ring assay, bone resorption assay, kinase inhibitor studies, immunofluorescence for localization\",\n      \"journal\": \"Experimental & molecular medicine\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 — direct localization experiment linked to functional consequence, combined with loss- and gain-of-function with defined cellular phenotype, single lab\",\n      \"pmids\": [\"32341419\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2020,\n      \"finding\": \"Spi-B and Spi-C differentially regulate Bach2 expression; ChIP-seq and reporter gene analyses show opposing effects on Bach2 transcription, with Spi-B and Spi-C having different regulatory impacts on plasma cell differentiation. Heterozygosity for Spic in Spib−/− mice rescues IgG1 secondary antibody responses and restores plasma cell differentiation kinetics.\",\n      \"method\": \"Genetic epistasis (Spib−/−Spic+/− mice), ChIP-seq, reporter gene analysis, gene expression analysis\",\n      \"journal\": \"Frontiers in immunology\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 — ChIP-seq and reporter assay with in vivo genetic rescue, single lab\",\n      \"pmids\": [\"32457757\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2022,\n      \"finding\": \"The Spic promoter has unidirectional transcriptional activity reduced by mutation of an NF-κB binding site. In B cells, Spic expression is repressed by an upstream regulatory region interacting with heme-binding regulator Bach2. External signals (BAFF+IL-4+IL-5, anti-IgM, LPS) downregulate Spic, partly through actin cytoskeleton-dependent mechanisms.\",\n      \"method\": \"Promoter deletion/mutation analysis, reporter assay, RT-qPCR, cytochalasin treatment, regulatory element identification\",\n      \"journal\": \"ImmunoHorizons\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 — promoter mutagenesis with functional reporter assay, interaction with Bach2 established, single lab\",\n      \"pmids\": [\"38285436\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2023,\n      \"finding\": \"Spi-C negatively regulates Igκ rearrangement in small pre-B cells by repressing both Igκ transcription and Rag1 transcription, opposing PU.1 which activates both. ChIP analysis identified Spi-C and PU.1 binding sites in the Rag1 promoter region.\",\n      \"method\": \"Inducible expression system in pre-B cell line, Spic−/− mice, RT-qPCR, ChIP analysis\",\n      \"journal\": \"Journal of immunology\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 — ChIP plus inducible system plus genetic knockout with consistent molecular phenotypes, single lab\",\n      \"pmids\": [\"37195219\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2023,\n      \"finding\": \"SPIC binds to enhancer elements and stabilizes NANOG binding to chromatin in ground-state embryonic stem cells, particularly at genes encoding enzymes of choline/one-carbon metabolism (Bhmt, Bhmt2, Dmgdh). SPIC controls the SAM-to-SAH flux, thereby modulating H3R17me2 and H3K4me3 histone methylation marks.\",\n      \"method\": \"Gain- and loss-of-function in ESCs, ChIP analysis, metabolic flux measurement (SAM/SAH), histone modification assay\",\n      \"journal\": \"Science advances\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 — multiple orthogonal methods (ChIP, metabolomics, histone modification) in single study\",\n      \"pmids\": [\"37595034\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2023,\n      \"finding\": \"In zebrafish, the ETS transcription factor Spic guides in situ generation of metaphocytes (tissue-resident macrophage/DC-like cells of non-hematopoietic origin) from local progenitors; Spic deficiency results in absence of metaphocytes. Metaphocytes are the major IL-22BP-producing cells, and their depletion causes dysregulated barrier immunity.\",\n      \"method\": \"Zebrafish spic knockout, lineage tracing, cell depletion, IL-22BP expression assay\",\n      \"journal\": \"Cell reports\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 — genetic loss-of-function in zebrafish ortholog with defined cellular and molecular phenotype\",\n      \"pmids\": [\"37148242\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2026,\n      \"finding\": \"Silencing of the m6A writer Zc3h13 stabilizes Spic mRNA in an m6A-dependent manner, thereby increasing SPIC protein levels, inhibiting NF-κB pathway activation, and attenuating LPS-induced inflammatory responses in macrophages. Co-silencing of Spic reverses the anti-inflammatory effects of Zc3h13 knockdown.\",\n      \"method\": \"siRNA knockdown of Zc3h13 and Spic in macrophages, m6A methylation assay, mRNA stability assay, NF-κB pathway analysis, in vivo mouse LPS model\",\n      \"journal\": \"Journal of immunology\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 — epistasis by co-silencing with mRNA stability and pathway readouts, multiple methods in single study\",\n      \"pmids\": [\"41847860\"],\n      \"is_preprint\": false\n    }\n  ],\n  \"current_model\": \"SPIC is an ETS-family transcription factor that, in response to heme-driven proteasomal degradation of the repressor BACH1, is induced in monocytes to direct their differentiation into iron-recycling red pulp macrophages and bone marrow macrophages; in macrophages it is additionally activated by NF-κB signaling downstream of TLRs to suppress pro-inflammatory cytokines and promote ferroportin-mediated iron efflux (counteracted by IFN-γ/STAT1); in B cells, SPIC acts as a transcriptional repressor that—following RAG-induced DNA double-strand breaks—forms a complex with BCLAF1, displaces PU.1 genome-wide, represses Nfkb1, Rag1, and Igκ transcription, and enforces the pre-B to small pre-B cell transition, while also cooperating with STAT6 to stimulate IgE germline transcription and opposing Spi-B to regulate plasma cell differentiation.\"\n}\n```","stage2_raw":"```json\n{\n  \"mechanistic_narrative\": \"SPIC is an ETS-family transcription factor that orchestrates iron homeostasis, myeloid cell fate, and B-cell developmental checkpoints through context-dependent transcriptional activation and repression. In monocytes and macrophages, heme-driven proteasomal degradation of the repressor BACH1 derepresses SPIC expression, which is essential for differentiation of red pulp macrophages and bone marrow macrophages that recycle iron from senescent erythrocytes via ferroportin; TLR/NF-κB signaling further induces SPIC to suppress pro-inflammatory cytokines, while IFN-γ/STAT1 antagonizes this pathway [PMID:19037245, PMID:24630724, PMID:32610126]. In pre-B cells, RAG-induced DNA double-strand breaks activate a SPIC/BCLAF1 complex that displaces PU.1 genome-wide, represses Nfkb1, Rag1, and Igκ transcription, and enforces the large-to-small pre-B cell transition, while in mature B cells SPIC opposes Spi-B to regulate plasma cell differentiation and cooperates with STAT6 to stimulate IgE germline transcription [PMID:31644907, PMID:37195219, PMID:25769919, PMID:16647686]. SPIC also functions in embryonic stem cells, where it stabilizes NANOG binding at enhancers controlling one-carbon metabolism genes and modulates histone methylation through SAM-to-SAH flux [PMID:37595034].\",\n  \"teleology\": [\n    {\n      \"year\": 1999,\n      \"claim\": \"Identification of SPIC as a new ETS-family member established that the PU.1/Spi-B subfamily contained a third factor with similar DNA-binding specificity but potentially distinct functions.\",\n      \"evidence\": \"Yeast one-hybrid screen, EMSA, methylation interference, and reporter assay in HeLa cells\",\n      \"pmids\": [\"10187812\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"No in vivo function determined\", \"Expression pattern across tissues not fully characterized\", \"Endogenous target genes unknown\"]\n    },\n    {\n      \"year\": 2003,\n      \"claim\": \"Mapping of an N-terminal acidic transactivation domain and demonstration that SPIC cannot form ternary complexes with PIP on the Igλ enhancer distinguished SPIC mechanistically from PU.1.\",\n      \"evidence\": \"Deletion/point mutagenesis of transactivation domain with reporter assays and gel shift ternary complex assay\",\n      \"pmids\": [\"12749910\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Whether SPIC uses alternative co-activators not tested\", \"Structural basis for inability to recruit PIP unknown\"]\n    },\n    {\n      \"year\": 2006,\n      \"claim\": \"Discovery that SPIC physically interacts with STAT6 and synergistically activates IgE germline transcription revealed a first functional partnership linking SPIC to humoral immune regulation.\",\n      \"evidence\": \"Yeast two-hybrid, co-immunoprecipitation in COS7, reporter assay for Iε promoter\",\n      \"pmids\": [\"16647686\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Interaction not confirmed in primary B cells\", \"Whether SPIC-STAT6 interaction occurs on endogenous chromatin not tested\"]\n    },\n    {\n      \"year\": 2008,\n      \"claim\": \"Genetic knockout demonstrated that SPIC is uniquely required for red pulp macrophage development and iron recycling, establishing its non-redundant role relative to PU.1 and Spi-B, while transgenic overexpression in B cells revealed dose-dependent repression of BCR signaling components.\",\n      \"evidence\": \"Spic−/− mice with retroviral rescue, phagocytosis and iron staining assays; Eμ-Spi-C transgenic mice with flow cytometry and proliferation assays\",\n      \"pmids\": [\"19037245\", \"18792411\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Transcriptional targets in RPM not mapped genome-wide\", \"Whether B-cell repression is direct or indirect at individual loci unclear\"]\n    },\n    {\n      \"year\": 2014,\n      \"claim\": \"Identification of the heme–BACH1–SPIC axis resolved how environmental iron sensing is transduced into a transcriptional program: heme triggers proteasomal BACH1 degradation via cysteine-proline motifs, derepressing Spic to drive RPM and bone marrow macrophage differentiation.\",\n      \"evidence\": \"Spic−/− and hemolysis mouse models, BACH1 CP-motif mutant constructs, proteasome inhibitor experiments\",\n      \"pmids\": [\"24630724\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Whether additional repressors besides BACH1 regulate Spic in non-macrophage lineages not addressed\", \"Direct BACH1 binding to Spic locus not demonstrated by ChIP\"]\n    },\n    {\n      \"year\": 2015,\n      \"claim\": \"Genetic epistasis between Spic and Spib showed that SPIC opposes Spi-B by repressing Nfkb1 transcription, establishing a balancing mechanism within the subfamily that tunes B-cell output.\",\n      \"evidence\": \"Spib−/−Spic+/− mice, reporter assay, gene expression analysis\",\n      \"pmids\": [\"25769919\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Whether SPIC directly binds the Nfkb1 promoter in primary B cells not shown by ChIP\", \"Downstream NF-κB targets affected not mapped\"]\n    },\n    {\n      \"year\": 2019,\n      \"claim\": \"Genome-wide ChIP-seq revealed that RAG-induced DNA breaks trigger a SPIC/BCLAF1 complex that displaces PU.1 from regulatory elements, represses SYK, and enforces the pre-B cell transition, connecting DNA damage signaling to lineage progression.\",\n      \"evidence\": \"ChIP-seq, co-immunoprecipitation, gene expression in pre-B cells with RAG-induced DSBs\",\n      \"pmids\": [\"31644907\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"How DNA break signals induce SPIC protein or complex assembly not fully elucidated\", \"Structural basis of SPIC-BCLAF1 interaction unknown\"]\n    },\n    {\n      \"year\": 2019,\n      \"claim\": \"TLR signaling was shown to couple erythrophagocytosis-derived heme with SPIC induction in splenic macrophages, which then drives Gdf15 and Bmp4 expression to initiate stress erythropoiesis, extending SPIC's role beyond iron recycling to erythroid regeneration.\",\n      \"evidence\": \"Mouse sterile inflammation model, erythrophagocytosis assay, gene expression\",\n      \"pmids\": [\"31506384\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Whether SPIC directly binds Gdf15/Bmp4 regulatory regions not established\", \"Relevance to human stress erythropoiesis not tested\"]\n    },\n    {\n      \"year\": 2020,\n      \"claim\": \"Multiple studies established SPIC as an NF-κB-induced anti-inflammatory effector in macrophages that promotes ferroportin expression and iron efflux while being antagonized by IFN-γ/STAT1, and as a regulator of osteoclast differentiation and plasma cell fate.\",\n      \"evidence\": \"Genetic mouse models with NF-κB/STAT1 pathway manipulation; RANKL-stimulated BMMs with kinase inhibitors and localization assays; Spib−/−Spic+/− mice with ChIP-seq for Bach2\",\n      \"pmids\": [\"32610126\", \"32341419\", \"32457757\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Direct SPIC binding at ferroportin locus not mapped\", \"Osteoclast findings from single lab without in vivo bone phenotype\", \"SPIC nuclear translocation mechanism in osteoclasts not fully defined\"]\n    },\n    {\n      \"year\": 2022,\n      \"claim\": \"Promoter dissection revealed that NF-κB binding is required for Spic promoter activity and that Bach2 represses Spic through an upstream regulatory region in B cells, while external B-cell activating signals downregulate Spic partly through actin-dependent mechanisms.\",\n      \"evidence\": \"Promoter deletion/mutation reporter assay, RT-qPCR, cytochalasin treatment\",\n      \"pmids\": [\"38285436\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Actin-dependent repression mechanism molecularly undefined\", \"Whether Bach2 directly binds the identified upstream element not confirmed by ChIP\"]\n    },\n    {\n      \"year\": 2023,\n      \"claim\": \"Three studies expanded SPIC's functional scope: it represses Igκ rearrangement by directly opposing PU.1 at Rag1 and Igκ loci in pre-B cells; it stabilizes NANOG on enhancers of one-carbon metabolism genes in ESCs to control histone methylation; and its zebrafish ortholog drives metaphocyte generation for barrier immunity.\",\n      \"evidence\": \"ChIP plus inducible expression in pre-B cells and Spic−/− mice; ChIP, metabolomics, and histone modification in ESCs; zebrafish spic knockout with lineage tracing\",\n      \"pmids\": [\"37195219\", \"37595034\", \"37148242\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"ESC function awaits confirmation in mammalian embryonic development in vivo\", \"Whether metaphocyte specification by Spic is conserved in mammals unknown\", \"SPIC occupancy at Rag1 in primary small pre-B cells not validated genome-wide\"]\n    },\n    {\n      \"year\": 2026,\n      \"claim\": \"Demonstration that m6A methylation by ZC3H13 destabilizes Spic mRNA revealed a post-transcriptional layer of SPIC regulation, with SPIC protein levels controlling NF-κB-dependent inflammatory responses in macrophages.\",\n      \"evidence\": \"siRNA knockdown/co-silencing of Zc3h13 and Spic in macrophages, m6A and mRNA stability assays, in vivo LPS model\",\n      \"pmids\": [\"41847860\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Specific m6A sites on Spic mRNA not mapped\", \"Whether other m6A readers/erasers participate not tested\"]\n    },\n    {\n      \"year\": null,\n      \"claim\": \"Key unresolved questions include the structural basis of SPIC's context-dependent switching between transcriptional activation and repression, how DNA damage signals post-translationally activate SPIC in pre-B cells, and whether SPIC's role in ESC chromatin and zebrafish metaphocytes reflects conserved mammalian developmental functions.\",\n      \"evidence\": \"\",\n      \"pmids\": [],\n      \"confidence\": \"Low\",\n      \"gaps\": [\"No crystal or cryo-EM structure available\", \"Post-translational modifications controlling SPIC activity largely uncharacterized\", \"No genome-wide target comparison across cell types (macrophage vs. B cell vs. ESC)\"]\n    }\n  ],\n  \"mechanism_profile\": {\n    \"molecular_activity\": [\n      {\"term_id\": \"GO:0003677\", \"supporting_discovery_ids\": [0, 1, 5, 8, 14, 15]},\n      {\"term_id\": \"GO:0140110\", \"supporting_discovery_ids\": [0, 1, 5, 7, 8, 10, 14, 15]}\n    ],\n    \"localization\": [\n      {\"term_id\": \"GO:0005634\", \"supporting_discovery_ids\": [8, 11, 15]}\n    ],\n    \"pathway\": [\n      {\"term_id\": \"GO:0140110\", \"supporting_discovery_ids\": []},\n      {\"term_id\": \"R-HSA-168256\", \"supporting_discovery_ids\": [3, 6, 8, 10, 14]},\n      {\"term_id\": \"R-HSA-74160\", \"supporting_discovery_ids\": [0, 1, 5, 7, 10, 15]},\n      {\"term_id\": \"R-HSA-1266738\", \"supporting_discovery_ids\": [3, 6, 8, 11, 16]},\n      {\"term_id\": \"R-HSA-382551\", \"supporting_discovery_ids\": [3, 6, 10]}\n    ],\n    \"complexes\": [\n      \"SPIC-BCLAF1 complex\"\n    ],\n    \"partners\": [\n      \"BCLAF1\",\n      \"STAT6\",\n      \"BACH1\",\n      \"SPI1\",\n      \"SPIB\",\n      \"NANOG\",\n      \"BACH2\"\n    ],\n    \"other_free_text\": []\n  }\n}\n```"}