Eyes from CFA-injected B10.RIII, MyD88 KO, Rag1 KO, TLR4 KO, TNF-αKO, and caspase 7KO mice (D5 p.i.; n = 6–12 of each group) and their proper control mice were quickly embedded in compound (Tissue-Tek OCT; Sakura Finetek, Torrance, CA). Retinal cryosections (5–7 μm thickness) were fixed with 4% paraformaldehyde and further permeabilized/blocked in the blocking solution (5% bovine serum and 0.1% Triton X-100). Sections were incubated overnight at 4°C with combinations of the following primary antibodies (1:100 dilution) in the blocking solution: rat anti-mouse CD11b (Serotec, Raleigh, NC), rabbit anti-mouse TLR4 (Santa Cruz Biotechnology, Santa Cruz, CA), mouse anti-major histocompatibility complex (MHC) class II (Santa Cruz Biotechnology), goat anti-mouse glial fibrillary acidic protein (GFAP; Santa Cruz Biotechnology), rabbit anti-cytochrome c oxidase, subunit IV (Invitrogen), goat anti-8-hydroxy-deoxy-guanosine (8-OHdG; Millipore, Billerica, MA), mouse anti-TNF-α (Millipore), rabbit anti-TNFR1 (Stressgen, San Diego, CA), rabbit anti-iNOS/NOS type II (BD, San Jose, CA), and mouse anti-caspase 7 (Santa Cruz Biotechnology). The sections were further incubated for 1 hour at room temperature (RT) with secondary antibodies: Cy-3, Cy-5, and/or Cy-2-conjugated donkey anti-mouse, -rat, -goat and/or -rabbit antibody (1:200; Jackson ImmunoResearch Laboratories, West Grove, PA) and then were mounted using mounting medium containing DAPI (Vectashield; Vector Laboratories, Burlingame, CA). A negative control was processed using the same protocol with the omission of the primary antibody to assess nonspecific labeling and isotype control. Sections were analyzed with a confocal laser scanning microscope (510; Zeiss, Thornwood, NY).
The additional sections were stained with hematoxylin and eosin (H&E) and were examined by light microscopy for inflammatory cell infiltration and morphologic change.