# Epigenetic control of microglial developmental milestones from proliferative progenitors to efficient phagocytes

**Authors:** Marta Pereira-Iglesias, Duncan Martinson, Carles Falco, Joel Maldonado-Teixido, Marco Gonzalez-Dominguez, Rodrigo Senovilla-Ganzo, Eva Benito, Sol Beccari, Jorge Valero, Bella Mora-Romero, Ivan Ballasch, Sarah Viguier, Philipp Hane, Molly Boettiger, Julie A. Reisz, Alba Elías-Tersa, Yasmina Manso, Laura Parkkinen, Ana María Aransay, Federico N. Soria, Angelo D’Alessandro, Eduardo Soriano, Morgane S. Thion, Sonia Garel, Melanie Greter, Albert Giralt, Alberto Pascual, Fernando García-Moreno, David A. Menassa, Jose A. Carrillo, Amanda Sierra

PMC · DOI: 10.21203/rs.3.rs-8344753/v1 · Research Square · 2026-02-20

## TL;DR

The study reveals key developmental stages of microglia, the brain's immune cells, showing how their growth and function are linked to epigenetic changes and early proliferation.

## Contribution

The paper identifies a proliferative-to-quiescent switch in microglia development and links it to epigenetic regulation by Ikaros.

## Key findings

- A proliferative-to-quiescent switch occurs around postnatal day 3/4 in microglia development.
- Pharmacological or genetic disruption of early proliferation impairs later morphological complexity and phagocytosis.
- Microglial maturation is driven by chromatin remodeling and the epigenetic regulator Ikaros.

## Abstract

Early immune perturbations increase the risk of brain disorders, yet the mechanisms underlying the functional maturation of microglia, the brain resident immune cells, remain poorly defined. Here, we used mathematical modeling of hippocampus and cerebellum to reconstruct postnatal microglial development. We identified a proliferative-to-quiescent (P/Q) switch around P3/P4 that preceded the acquisition of morphological complexity and efficient phagocytosis and was accompanied by changes in cell-cycle dynamics and metabolic state. This P/Q switch was recapitulated in repopulation contexts in mice and in the fetal human brain. Pharmacological and genetic perturbations of proliferation impaired subsequent morphological complexity and phagocytosis efficiency. Finally, microglial developmental maturation was associated with chromatin remodeling and driven by the epigenetic regulator Ikaros. These findings uncover the milestones of microglial development, revealing a potential period of early vulnerability and establishing an unexpected linkage between proliferation and phagocytosis essential to understanding how these processes are coordinated in neurodegenerative disorders.

## Linked entities

- **Genes:** IKZF1 (IKAROS family zinc finger 1) [NCBI Gene 10320]
- **Species:** Mus musculus (taxon 10090)

## Full-text entities

- **Genes:** Camk2b (calcium/calmodulin-dependent protein kinase II, beta) [NCBI Gene 12323] {aka CaMKII}, Spi1 (Spi-1 proto-oncogene) [NCBI Gene 20375] {aka Dis-1, Dis1, PU.1, Sfpi-1, Sfpi1, Spi-1}, Kdm5b (lysine demethylase 5B) [NCBI Gene 75605] {aka 2010009J12Rik, 2210016I17Rik, D1Ertd202e, Jarid1b, PLU-1, PUT1}, Tgfb1 (transforming growth factor, beta 1) [NCBI Gene 21803] {aka TGF-beta1, TGFbeta1, Tgfb, Tgfb-1}, Mki67 (antigen identified by monoclonal antibody Ki 67) [NCBI Gene 17345] {aka D630048A14Rik, Ki-67, Ki67}, Il34 (interleukin 34) [NCBI Gene 76527] {aka 2010004A03Rik}, CSF2 (colony stimulating factor 2) [NCBI Gene 1437] {aka CSF, GMCSF}, IL34 (interleukin 34) [NCBI Gene 146433] {aka C16orf77, IL-34}, Irf8 (interferon regulatory factor 8) [NCBI Gene 15900] {aka ICSBP, IRF-8, Icsbp1, Myls}, Csf1 (colony stimulating factor 1 (macrophage)) [NCBI Gene 12977] {aka BAP025, Csfm, MCSF, Mhdabap25, PG-M-CSF, op}, IKZF1 (IKAROS family zinc finger 1) [NCBI Gene 10320] {aka CVID13, Hs.54452, IK1, IKAROS, LYF1, LyF-1}, Ybx3 (Y box protein 3) [NCBI Gene 56449] {aka Csda, Dpba, MSY3, MSY4, Yb2, dbpA}, P2ry1 (purinergic receptor P2Y, G-protein coupled 1) [NCBI Gene 18441] {aka P2Y1, P2y1r}, Mb (myoglobin) [NCBI Gene 17189], Irf5 (interferon regulatory factor 5) [NCBI Gene 27056] {aka mirf5}, Ctsb (cathepsin B) [NCBI Gene 13030] {aka APPM, CB}, Gapdh (glyceraldehyde-3-phosphate dehydrogenase) [NCBI Gene 14433] {aka Gapd}, CSF1R (colony stimulating factor 1 receptor) [NCBI Gene 1436] {aka BANDDOS, C-FMS, CD115, CSF-1R, CSFR, FIM2}, Fscn1 (fascin actin-bundling protein 1) [NCBI Gene 14086] {aka Fan1, fascin-1}, Ikzf1 (IKAROS family zinc finger 1) [NCBI Gene 22778] {aka 5832432G11Rik, Ikaros, LyF-1, Zfpn1a1, Znfn1a1, hlk-1}, Mydgf (myeloid derived growth factor) [NCBI Gene 28106] {aka D17Wsu104e, Il25, Ly6elg}, Kif2c (kinesin family member 2C) [NCBI Gene 73804] {aka 4930402F02Rik, ESTM5, Knsl6, MCAK}, MBD2 (methyl-CpG binding domain protein 2) [NCBI Gene 8932] {aka DMTase, NY-CO-41}, P2ry12 (purinergic receptor P2Y, G-protein coupled 12) [NCBI Gene 70839] {aka 2900079B22Rik, 4921504D23Rik, P2Y12}, Casp3 (caspase 3) [NCBI Gene 12367] {aka A830040C14Rik, AC-3, CASP-3, CC3, CPP-32, CPP32}, ATM (ATM serine/threonine kinase) [NCBI Gene 472] {aka AT1, ATA, ATC, ATD, ATDC, ATE}, Iba1 (induction of brown adipocytes 1) [NCBI Gene 114737], Reln (reelin) [NCBI Gene 19699] {aka reeler, rl}, Tmem119 (transmembrane protein 119) [NCBI Gene 231633] {aka obif}, Ms6hm (minisatellite 6 hypermutable) [NCBI Gene 17653] {aka PC-1}, Lncppara (long noncoding RNA near Ppara) [NCBI Gene 102800312] {aka Lincppara, Mirlet7bhg, linc-Ppara}, Tmcc3 (transmembrane and coiled coil domains 3) [NCBI Gene 319880] {aka A230066D03Rik, C630016B22Rik, Gm1556, Tmcc1}, APOE (apolipoprotein E) [NCBI Gene 348] {aka AD2, APO-E, ApoE4, LDLCQ5, LPG}, Csf1r (colony stimulating factor 1 receptor) [NCBI Gene 12978] {aka CD115, CSF-1R, Csfmr, Fim-2, Fim2, Fms}, Cx3cr1 (C-X3-C motif chemokine receptor 1) [NCBI Gene 13051] {aka mCX3CR1}, Nes (nestin) [NCBI Gene 18008] {aka ESTM46, Ifaprc2, Marc2, RC2}, Iqgap3 (IQ motif containing GTPase activating protein 3) [NCBI Gene 404710] {aka D030034H08}
- **Diseases:** brain damage (MESH:D001925), brain diseases (MESH:D001927), infection (MESH:D007239), periventricular leukomalacia (MESH:D007969), neurodevelopmental disorders (MESH:D002658), congenital abnormalities (MESH:D000013), inflammation (MESH:D007249), neurodegenerative (MESH:D019636), brain trauma (MESH:D000070642), tumors (MESH:D009369), Alzheimer (MESH:D000544), hypoxic ischaemic encephalopathy (MESH:D002534), genetic disorders (MESH:D030342)
- **Chemicals:** haematoxylin (MESH:D006416), HEPES (MESH:D006531), CuSO4 (MESH:D019327), unsaturated fatty acids (MESH:D005231), sodium citrate (MESH:D000077559), NaHCO3 (MESH:D017693), H3K4 (-), thymidine (MESH:D013936), ribose phosphate (MESH:C031626), agarose (MESH:D012685), sucrose (MESH:D013395), Lipid (MESH:D008055), GMP (MESH:C066524), ammonium acetate (MESH:C018824), CO2 (MESH:D002245), GSH (MESH:D005978), citric acid (MESH:D019343), calcium (MESH:D002118), DAPI (MESH:C007293), formalin (MESH:D005557), hexose phosphate (MESH:D006600), glucose (MESH:D005947), DAB (MESH:C000469), sodium tetraborate (MESH:C010634), Tween20 (MESH:D011136), carbogen (MESH:C011700), PBS (MESH:D007854), KCl (MESH:D011189), formic acid (MESH:C030544), NaCl (MESH:D012965), methanol (MESH:D000432), Paraffin (MESH:D010232), pyruvate (MESH:D019289), MgCl2 (MESH:D015636), pentose phosphate (MESH:D010428), carbon (MESH:D002244), Triton-X-100 (MESH:D017830), acetonitrile (MESH:C032159), IMP (MESH:D007291), urate (MESH:D014527), EDTA (MESH:D004492), TMX (MESH:D013629), xylene (MESH:D014992), 5-bromodeoxyuridine (MESH:D001973), GW2580 (MESH:C506269), nucleotides (MESH:D009711), free fatty acid (MESH:D005230), water (MESH:D014867), phospholipids (MESH:D010743), methyl green (MESH:D008739), PLX (MESH:C000600259), ethanol (MESH:D000431), HCl (MESH:D006851), isopropanol (MESH:D019840), SDS (MESH:D012967), L-ascorbic acid (MESH:D001205), 5-ethynyl-2'-deoxyuridine (MESH:C031086), CaCl2 (MESH:D002122), DTT (MESH:D004229), EdU (MESH:C022811)
- **Species:** Danio rerio (leopard danio, species) [taxon 7955], Homo sapiens (human, species) [taxon 9606], Gallus gallus (bantam, species) [taxon 9031], Mus musculus (house mouse, species) [taxon 10090]
- **Mutations:** A 63X, P to Q
- **Cell lines:** C57BL/6 — Mus musculus (Mouse), Transformed cell line (CVCL_C0MU)

## Full text

_Full body text omitted from this summary view._ Fetch the complete paper as Markdown: https://tomesphere.com/paper/PMC12934985/full.md

## Figures

7 figures with captions in the complete paper: https://tomesphere.com/paper/PMC12934985/full.md

## References

99 references — full list in the complete paper: https://tomesphere.com/paper/PMC12934985/full.md

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Source: https://tomesphere.com/paper/PMC12934985