Antibody microarrays were prepared by spotting purified antibodies in triplicate on nitrocellulose-coated slides (Oncyte, nitrocellulose 16 multipad slides; Grace Bio-Labs, Bend, OR) using a noncontact array spotter (sciFLEXARRAYER 3; Scienion, Berlin, Germany). Anti-IgG/IgM/IgA (1 μg/μL) served as a positive control. For the analysis of proinflammatory cytokines, antibodies against IL-1β, IL-6, IL-8, TNF-α, and IFN-γ (0.5 μg/μL; Biolegend, San Diego, CA) were spotted on slides. In addition, antibodies against lipocalin 1 (LCN1), cystatin SN (1 μg/μL), and α-antitrypsin (2.43 μg/μL) were used. As a negative control, we used spotting buffer. For incubation with tear samples, slides were covered with 16-pad frame hybridization chambers (FAST; Whatman, Maidstone, UK) followed by the blocking of unspecific binding sites using 120 μL buffer (PBS/3%, NFDM/3%, BSA/1%) per subarray for 1 hour at 10°C. The arrays were washed three times (120 μL PBS) for 5 minutes each time. Labeled sample proteins were incubated on subarrays overnight at 4°C. Afterward, slides were washed four times for 15 minutes each time using PBS-T (PBS containing 5% Tween-20). Finally, the slides were dried (SpeedVac; Thermo Scientific, Waltham, MA) and subsequently scanned using a high-resolution confocal scanner (array scanner 428 TM, AVISO; Affymetrix High Wycombe, UK).
The generated slide images were analyzed using image-processing software (Spotfinder 3.1.1, TM4; Dana-Faber Cancer Institute, Boston, MA).
28,29 Background subtraction was performed according to the formula: spot intensity = mean intensity
SP − [(sum
bkg − sum
top5bkg)/(number of pixel
SP − number of pixel
top5bkg)], where SP represents any spot, bkg represents the corresponding background, and top5bkg represents the top 5% of background pixel.
Data normalization was performed by calculating the mean immunoglobulin reactivity over all samples; thus, samples from different groups were normalized together, not separately, for each single group. Afterward, every single sample was adjusted to this mean immunoglobulin value, whereby the conversion factor was also applied to measured values of all other tested analytes of this patient, in due consideration of the tear volume. A comparison of raw data intensities obtained from total immunoglobulin measurements of the different study groups revealed no statistical difference (
P > 0.75;
Supplementary Fig. S1).
ANOVA and Tukey HSD post hoc testing were used for statistical comparison of the antibody intensities of the subgroups. Statistical analysis was performed with commercial software (Statistica 8.0; Statsoft, Tulsa, AZ). P < 5.00E-2 was considered to be statistically significant.