Patients. A pilot prospective clinical study was performed to evaluate topical 0.1% dexamethasone eye drops in patients with ROP. Dexamethasone was prescribed off label, and this study was approved by the local ethics committee (Dnr 2019–02321, Registration date 2019-05-02) and performed following the committee regulations. It adhered to the Declaration of Helsinki for human research.
The inclusion criteria were the first sign of Type 2 ROP with stage 3, zone II without plus disease, i.e., the beginning of neovascularization. Infants fulfilling the inclusion criteria were included over a period of one year (2019–2020). Treatment with topical 0.1% dexamethasone eye drops was started at the first sign of stage 3 ROP. If severe haziness occurred, three drops/day were initiated for three days, tapering to 2 drops for four days, whereafter one drop daily was administered. Patients with stage 3 zone II were given one drop daily until regression to stage 2, median five weeks (range 1–13 weeks), whereafter, one drop every other day was administered for one week. Screening was performed with standardized protocols, classification, and ROP diagnosis were performed according to international screening guidelines[19] once to twice a week with RetCam, for objective analyses, by three experienced ROP screeners (AH, MP, and PL).
Exclusion criteria were infection in the eye, and no patient was excluded.
Animals
C57BL/6J mice (#000664, Jackson Laboratory) were housed under a 12-hourly light/dark cycle. Pups weighing less than 5.0g or more than 7.5g at P17 were excluded[20]. Both littermate females and males were used. All animal care and experiments were in accordance with the Association for Research in Vision and Ophthalmology Statement for the Use of Animals in Ophthalmic and Vision Research and were approved by the Institutional Animal Care and Use Committee at Boston Children’s Hospital (Protocol Number: 00001619).
Oxygen-induced retinopathy mouse model and quantification
In mouse OIR, C57BL/6J pups and their nursing dam were placed in a 75% oxygen chamber from P7 to P12 to inhibit retinal vessel growth and induce vessel loss and then returned to room air at P12. Relative hypoxia of avascular retina induces both pathological neovascularization (NV) and re-vascularization (reflected by decreased vaso-obliteration, VO). Mice were euthanized using CO2 asphyxiation or ketamine/xylazine (depending on age) and both eyes were enucleated. After one-hour fixation with 4% paraformaldehyde, retinas were dissected and stained with isolectin GS-IB4 (Alexa Fluor 594, #I21413, Invitrogen) in 1 mmol/L CaCl2 in phosphate-buffered saline (PBS, (#10010-023, Gibco) overnight at room temperature to visualize blood vessels. Retinas were washed with PBS and mounted using ProLong Glass Antifade Mountant (#P36980, Invitrogen). Images were taken at 50X magnification using a Zeiss fluorescent microscope. VO and NV were quantified using Image J[21]. The percentages of NV and VO of the total retinal area were calculated and compared between interventions.
Treatments.
Dexamethasone sodium phosphate ophthalmic solution (0.1% (1mg/mL)), NDC 24208-720-02, Bausch Lomb Inc.) was topically administered (5 µL) once per day to each eye from P12 to P14 (prior to any neovessel formation), or P14 to P16 (prior to peak neovessel formation) or P17 to P19 (at peak neovessel formation and regression). PBS was topically administered to both eyes of littermates as vehicle control. Oligomycin A (#11342, Cayman Chemical) (0.25µg/g body weight, dissolved in PBS with 20% ethanol) or vehicle control (PBS with 20% ethanol) were intraperitoneally injected in OIR mice from P14 to P16. Retinas were collected at P17 and P20 to examine retinal vascular networks.
Labe-free LC-MS/MS proteomics
Sample preparation:
OIR mice were euthanized at P17 using ketamine/xylazine and retinas were immediately isolated. The two retina from each mouse were pooled for each sample and homogenized in RIPA buffer (#89900, Thermo Fisher Scientific) with protease inhibitor (#P0044, Sigma) and phosphatase inhibitor (#P8340, Sigma). Lysates were proteolyzed using the iST in-solution digestion kit (#P.O.00027, PreOmics GmbH) automated on the PreON robot (PreOmics). In brief, 50 µg retina protein sample in 10 µL was added to 40 µL LYSE buffer (PreOmics). The samples were trypsinized for 3 hours following the manufacturer’s instructions. Eluted peptides were dried in a speed vacuum (Vacufuge, Eppendorf) and resuspended in 40 µL LC-LOAD solution. In total, n = 6 vehicle control and n = 6 dexamethasone samples were prepared.
Mass spectrometry:
Mass spectra were acquired on Orbitrap Fusion Lumos coupled to an Easy-nLC1000 HPLC pump (Thermo Fisher Scientific). The peptides were diluted 5-fold using sample loading buffer and 4 ul injections separated using a dual column set-up: an Acclaim™ PepMap™ 100 C18 HPLC Column, 75 µm X 70 mm (Thermo Fisher Scientific, #164946); and an EASY-Spray™ HPLC Column, 75 µm X 250 mm (Thermo Fisher Scientific, #ES902). The column was heated at a constant temperature of 45 ˚C. The gradient flow rate was 300 nL/min from 5 to 21% solvent B (0.1% formic acid in acetonitrile) for 75 minutes, 21 to 30% solvent B for 15 minutes, and another 10 minutes of a 95%-5% solvent B in a jigsaw wash. Solvent A was 0.1% formic acid in mass spectrometry-grade water. The mass spectrometer was set to 120,000 resolution, and the top N precursor ions in a 3 second cycle time (within a scan range of m/z 400–1500; isolation window, 1.6 m/z) were subjected to collision-induced dissociation (CID, collision energy 30%) for peptide sequencing.
The acquired peptide spectra, comprising 12 retinal samples (n = 6 vehicle control and n = 6 dexamethasone) were searched with the Proteome Discoverer package (PD, Version 2.5) using the SEQUEST-HT search algorithm against the Mouse UniProt database (63,603 entries, updated January 2022). The digestion enzyme was set to trypsin and up to two missed cleavages were allowed. The precursor tolerance was set to 10 ppm and the fragment tolerance window to 0.6 Da. Methionine oxidation and n-terminal acetylation were set as dynamic modifications, and cysteine carbamidomethylation as a static modification. The PD Percolator algorithm calculated the peptide false discovery rate (FDR) and peptides were filtered based on an FDR threshold of 1.0%. Peptides that were only assigned to one given protein group and not detected in any other protein group were considered unique and used for further analyses. A minimum of 2 unique peptides for each protein were required for the protein to be included in the analyses. The Feature Mapper was enabled in PD to quantify peptide precursors detected in the MS1 but may not have been sequenced in all samples. Chromatographic alignment was performed with a maximum retention time shift of 10 minutes, mass tolerance of 10 ppm and signal-to-noise minimum of 5. Precursor peptide abundances were based on their chromatographic intensities and total peptide amount was used for PD normalization.
Analysis:
Data were further analyzed using the statistical software, Qlucore (Qlucore, Sweden, version 3.5). We performed a two-group comparison (dexamethasone vs. control eye drops) using the log-transformed protein group means, the student’s t-test for each protein’s comparison (p-value), and the Benjamini-Hochberg procedure to calculate the FDR adjusted p-value (q value). We employed Ingenuity Pathway Analysis (IPA, QIAGEN) to evaluate signaling pathways from gene expression data. IPA calculates Fisher’s exact p-value for overlapping differentially expressed genes with curated gene sets representing canonical biological pathways. In addition, IPA calculates a Z-score for the direction of gene expression for a pathway based on the observed gene expression in the dataset. The Z-score signifies whether expression changes for genes within pathways are consistent with what is expected based on previously published analyses annotated in the Ingenuity Knowledge Base[22]. Significant pathways were defined as those with a Z-score absolute value > 1 or an overlap p-value < 0.05. Principal component analysis was performed on unfiltered proteome (p = 1).
Real-time quantitative PCR (RT-qPCR)
Mice were euthanized at P17 using ketamine/xylazine and retinas were immediately isolated. Total RNA was extracted from pooled retinas of both eyes with PureLinkTM RNA Mini Kit (#12183025, Invitrogen), and cDNA was generated with iScriptTM Reverse Transcription Supermix (#1708841, Bio-Rad). RT-qPCR was performed using SYBR Green qPCR Master Mix (#522076, Bimake.com) and CFX96TM Real-Time PCR Detection System (Bio-Rad, California, USA). Data were quantified using the ∆∆Ct method with Cyclophilin A as the internal control Supplementary Table 1 shows primer sequences of target genes.
Single-cell RNA sequencing and transcriptome analysis
In the single-cell datasets of “Study - Single-cell RNAseq of Normoxic and OIR mouse retina by Drop-seq” (NCBI’s Gene Expression Omnibus accession no. GSE150703)[23], gene expression of inflammatory markers was analyzed.
Statistics
All data are presented as the mean ± SEM. The normality and variance of the data set were confirmed using a histogram, normality test, and a quantile-quantile plot. Mann-Whitney U test was used if the data set was not normally distributed. When normality was given, two-tailed unpaired t-test was used when the data set showed equal variance, and Welch’s test was used if the data set had unequal variance (Prism v9.0, GraphPad Software, Inc.). P values < 0.05 were considered statistically significant.