A quantitative analysis of flat mount retinas revealed three major changes of microglial cells relevant to their morphology, density, and immunoreactivity in glaucomatous retinas. In the IPL of control retinas, microglia had small round or triangular somata and exhibited ramified morphology with smooth, continuous Iba1 labeling of processes extending tens of microns (
Figs. 3A,
3B). All presumed microglia cells showed Iba1+/MHCII− expression under control conditions and formed a regular mosaic arrangement with non-overlapping neighboring cells. By 1 week after microbead injection, the number of Iba1+ cells increased by 23% from 111 ± 8 under control conditions to 144 ± 7 (
P < 0.01,
n = 4 eyes), and cells appeared with altered morphology exhibiting larger somata and retracted, thicker processes (
Figs. 3C,
3D,
3M). Virtually no MHCII+ cells were observed at this time point (
Fig. 3N). At 4 weeks after initial microbead injection, the soma shape was altered markedly and the cell density was increased further by 45% (177 ± 5 cells) relative to control values (
P < 0.05,
n = 4 eyes) (
Figs. 3E,
3F,
3M). We observed 18% (
P < 0.001,
n = 4 eyes) of cells with Iba1+/MHCII+ immunoreactivity at this phase of disease progression (
Fig. 3N). At 8 weeks after microbead injection, the morphology of presumed microglial cells was altered dramatically with fewer processes and elongated somata (
Figs. 3G,
3H). The density of Iba1+ cells increased by 82% to 222 ± 9 cells (
P < 0.001,
n = 6 eyes) relative to controls (
Fig. 3M), and most cells (79%;
P < 0.001,
n = 6 eyes) showed Iba1+/MHCII+ immunolabeling (
Fig. 3N). It is important to note that we observed dense clustering of MHCII+ cells in the marginal regions of the retina at 4 and 8 weeks of microbead injection, which may have been a result of a direct mechanical trauma.
33,34 Therefore, we excluded retinal edges and used regions primarily from the mid-periphery in our quantitative analyzes. Interestingly, the timing of MHCII protein expression, indicating microglial activation, beginning at week 4 closely coincides with the earliest loss of RGCs (
Figs. 3I–
3L,
3O) reported previously for the microbead occlusion mouse model used here.
30