microglia/macrophage markers

Iba1 (AIF1)

General marker for all microglia and macrophages, essential for actin remodeling and phagocytosis.

CD11b (ITGAM)

Integrin marker for all myeloid cells, part of Complement Receptor 3 (CR3) used for synaptic pruning.

CD45 (PTPRC)

Distinguishes resident microglia (CD45-low) from infiltrating peripheral macrophages (CD45-high).

TMEM119

Highly specific marker for parenchymal microglia, absent on infiltrating macrophages and BAMs.

P2RY12

Homeostatic microglial marker, purinergic receptor that senses ATP/ADP, downregulated in DAM states.

SALL1

Transcriptional regulator unique to microglia, maintains homeostatic identity, lost during neuroinflammation.

CX3CR1

Fractalkine receptor, mediates communication with neurons, high in homeostatic microglia and BAMs.

HEXB

Lysosomal enzyme, considered one of the most stable specific markers for microglia across various states.

CD206 (MRC1)

Mannose receptor, specific for Border-Associated Macrophages (BAMs) and "M2-like" repair states.

CD163

Scavenger receptor for hemoglobin-haptoglobin, specifically labels BAMs (perivascular/meningeal).

LYVE1

Lymphatic vessel endothelial hyaluronan receptor 1, highly specific for perivascular and meningeal BAMs.

TREM2

Lipid sensor and master regulator of DAM, essential for clearing myelin debris in MS.

APOE

Major ligand for TREM2, upregulated in DAM/MGnD microglia to coordinate lipid metabolism.

CD68

Lysosomal protein, quantitative marker of phagocytic activity, highly upregulated in active MS lesions.

GPNMB

Glycoprotein nonmetastatic melanoma protein B, a hallmark marker for DAM and remyelinating microglia.

CLEC7A (Dectin-1)

Pattern recognition receptor, specific marker for the DAM/MGnD microglial phenotype.

AXL

TAM family receptor, helps microglia sense and clear apoptotic cells, upregulated in MS lesions.

CST7 (Cystatin F)

Endosomal/lysosomal cathepsin inhibitor, specifically upregulated in DAM microglia during demyelination.

MHCII (HLA-DR)

Innate antigen presentation marker, high in active MS lesions, indicates microglial-T cell interaction.

CD86

Co-stimulatory molecule (B7-2), marker of "M1-like" pro-inflammatory activation and T-cell priming.

CD11c (ITGAX)

Integrin often used to identify the DAM phenotype, high in microglia surrounding MS plaques.

iNOS (NOS2)

Inducible Nitric Oxide Synthase, marker of neurotoxic, oxidative stress-inducing microglial states.

Arg1 (Arginase-1)

Competes with iNOS, marker of anti-inflammatory, pro-repair microglial phenotypes.

NLRP3

Core component of the inflammasome, processes IL-1β, driver of innate-mediated focal damage in MS.

C3 (Complement C3)

Central complement marker, indicates neurotoxic "A1" astrocytes and C3-opsonized myelin/synapses.

C1q

Initiator of the classical complement pathway, produced by microglia to tag debris for phagocytosis.

TLR4

Toll-like receptor 4, senses DAMPs (like fibrinogen) to trigger innate microglial activation.

CCR2

Chemokine receptor, essential for the recruitment of peripheral monocytes into the CNS during MS relapses.

CSF1R

Growth factor receptor, essential for microglial survival and proliferation, a target for depletion studies.

TGFβR1

Transforming growth factor receptor, vital for maintaining the homeostatic signature (P2RY12/SALL1).