Whole eyes from 0.5 (14 days), 0.75 (21 days), 1-, 3-, 6-, and 9-month WT and PAD4KO mice were fixed in 4% paraformaldehyde in PBS, pH 7.4 overnight at 4°C, cryoprotected in 30% sucrose in PBS, pH 7.4, frozen in optimal cutting temperature (OCT) medium, and cryosectioned into 10 μm-thick sections. After washing away the OCT, sections were treated using heat-mediated antigen retrieval by boiling in 10mM sodium citrate, pH 6.0 with 0.05% Tween-20 for 1 hour. After cooling, slides were washed in PBS and subsequently blocked in 10% goat serum/5% BSA/0.5% Triton X-100 in PBS for 1 hour at RT. Following blocking, sections were incubated with one of the following primary antibody combinations in the same buffer overnight at 4°C: rabbit anti-PAD2/4 and mouse anti-citrullinated peptide clone F95; rabbit anti-PAD4 and mouse anti-citrullinated peptide clone F95; or rabbit anti-β-tubulin, mouse anti-GS, and chicken anti-NFH. After washing in PBS, slides were probed using either goat anti-rabbit IgG conjugated to AlexaFluor 488 (A-11034; Invitrogen, Carlsbad, CA, USA) and goat anti-mouse IgM conjugated to AlexaFluor 555 (A-24126; Invitrogen), or goat anti-rabbit IgG conjugated to AlexaFluor 488, goat anti-chicken IgY conjugated to AlexaFluor555 (A-21437; Invitrogen), goat anti-mouse IgG conjugated to AlexaFluor 647 (A-21236; Invitrogen), and DAPI (D-1306; Invitrogen). After washing in PBS, slides were mounted using Prolong Diamond Anti-Fade Mountant (P-36961; Invitrogen) and imaged using a Zeiss 710 Laser Scanning Confocal Microscope. All images were captured as Z-stacks and expressed as maximum intensity projections using the same laser power and gain settings to ensure comparability for intensity analysis. After background subtraction (obtained from no primary controls), fluorescent intensities were quantified using ImageJ and analyzed using the quotient of mean intensity and the area of the region-of-interest (neural retina/retinal pigment epithelium [RPE]).
Preplanned comparisons to investigate the effect of age on expression levels conducted by 1-way analysis of variance (ANOVA). An α-level of 0.05 was used to designate the level significance for these analyses. Post-hoc comparisons of average expression levels between individual time points and between genotypes were conducted by two-tailed
t-tests. The Dunn-Sidák method was used to correct for multiple post-hoc comparisons made among the expression levels at each time point and between genotypes
16 (see
Supplementary Tables S1–
S3 for detailed analytical methods and summary statistics).