Commercially available antibodies against different growth factors, comprising
BDNF,
CNTF, interleukin 6 (
IL-6), transforming growth factor-beta 2 (
TGFb2), transforming growth factor-beta 1 (
TGFb1), pigment epithelium-derived factor (
PEDF), apolipoprotein E (
ApoE), nerve growth factor beta (
NGFb), vascular endothelial growth factor A (
VEGFA), clusterin (
CLU), complement Factor H (
CFH), and matrix metallopeptidase 9 (
MMP-9; detailed information can be seen in
Table 1) were used. These factors are known to be secreted by Müller cells and have an impact on the survival of RGCs. The antibodies were diluted in PBS and spotted in triplicate on a nitrocellulose slide using a non-contact array spotter (Scienion GmbH, Berlin, Germany) to create an antibody microarray. The conditioned medium (
n = 10 per group) was labeled with Dylight 649 (1:10 in PBS, Thermo Fisher Scientific, Waltham, MA, USA) for 1 hour in the dark and quenched with Tris-HCl for 1 hour. As a negative control, PBS was used. The slides were blocked with 5% BSA in 0.5% Tween-PBS for 1 hour, washed 3 times with 0.5% Tween-PBS, and subsequently incubated with the labeled conditioned medium for 2.5 hours. After washing the slides three times the microarrays were digitalized with an array scanner (Aviso GmbH, Aachen, Germany). For data analysis, spot intensity was quantified with ImaGene 5.0 Software (BioDiscovery, El Segundo, CA, USA). Defective spots were manually excluded from further evaluation. The fluorescence intensities were then determined, with the median signal of the respective triplicates being averaged. Fold-changes of the fluorescence intensities were calculated, a cutoff of 1.5 was used to determine the significantly differentially expressed secretome, as described before.
45–47 The overview of the workflow carried out in this study is presented in
Figure 1.