Abstract
Purpose.:
We investigated the expression profile of and identify all microRNAs (miRNAs) that potentially regulate inflammation in a light-induced model of focal retinal degeneration.
Methods.:
Sprague Dawley (SD) rats aged 90 to 140 postnatal days were exposed to 1000 lux white fluorescent light for 24 hours. At 24 hours, and 3 and 7 days after exposure, the animals were euthanized and retinas processed for RNA. Expression of 750 miRNAs at 24 hours of exposure was assessed using low density array analysis. Significantly modulated miRNAs and their target mRNAs were used to assess the potential biological effects. Expression of seven miRNAs, potentially modulating inflammation, was investigated across a protracted time course after light exposure using quantitative PCR. Photoreceptor cell death was analyzed using TUNEL.
Results.:
Intense light exposure for 24 hours led to differential expression of a number of miRNAs, 37 of which were significantly modulated by 2-fold or more. Of those, 19 may potentially regulate the inflammatory immune response observed in the model. MicroRNAs -125-3p, -155, -207, -347, -449a, -351, and -542-3p are all upregulated at 24 hours of exposure along with peak photoreceptor cell death. The MiRNAs -542-3p and -351 reached maximum expression at 7 days after exposure, while -125-3p, -155, -207, -347, and -449 reached a peak expression at 3 days.
Conclusions.:
The results of the study show that miRNAs are modulated in response to light damage (LD). These miRNAs potentially regulate the inflammatory immune response, triggered as a result of the acute retinal damage, which is a key mediator of retinal degeneration in this model and age-related macular degeneration.
MicroRNAs (miRNAs) are small evolutionarily conserved noncoding RNA sequences that modulate a range of biological processes,
1 including cell death
2,3 and inflammation.
4 They are approximately 22 to 25 nucleotides long and provide a second layer of posttranscriptional gene regulation by targeting messenger RNAs (mRNAs) for degradation or repression of translation,
5 and are found in abundance in the central nervous system (CNS).
6,7
Age-related macular degeneration (AMD) is a progressive degenerative disease of the retina that causes irreversible vision loss and accounts for up to 50% of central blindness cases worldwide. The involvement of inflammatory processes in the pathogenesis of AMD was documented in the 1980s
8 and its central role confirmed by gene association studies.
9–11 Subsequently, a large number of inflammatory factors and cofactors, particularly in the complement pathways, have been implicated in the disease process (see review
12).
The acute retinal light damage (LD) model in rats has features in common with dry AMD,
13,14 including cell death and inflammation.
14 This model has been used to investigate the involvement of chemokines and macrophages in the progression of retinal degeneration.
15 Following LD, a lesion formed by the death of photoreceptors and atrophy of the RPE presents on the visual axis and enlarges over time, even in the absence of the damaging stimulus.
14 In this model photoreceptor death is associated with expression of chemokines by Müller glia, recruitment of macrophages, and deposition of C3,
16 and attenuation of macrophage recruitment, by silencing expression of the chemokine Ccl2, reduces photoreceptor cell death.
17 Similar patterns of chemokine expression, macrophage recruitment, C3 deposition, and photoreceptor cell death are present in the normally aging rat,
18 indicating that the model represents many of the features of normal aging of the retina.
Recent evidence supports the idea that miRNAs are involved in inflammation.
19,20 Many miRNAs are rapidly upregulated in response to inflammatory cues and may either promote the duration and magnitude of inflammation
21 or silence it.
22 In this study we investigated the modulation of miRNAs in the rat LD model of focal retinal degeneration and explored the transcriptional profile of their target genes in the retina following LD, with a focus on identifying miRNAs that modulate expression of genes involved in the inflammatory response.
Animal handling and treatment protocols were done in accordance with the ARVO Statement for the Use of Animals in Ophthalmic and Vision Research, and were approved by the Australian National University (ANU) Animal Ethics Committee. Sprague Dawley (SD) rats aged 90 to 140 postnatal days raised in dim (5 lux) cyclic light (“dim-reared”) were used for the study. Light damage was induced by exposure to bright light (1000 lux) from an overhead white fluorescent source (COLDF2 2 × 36W IHF; Thorn Lighting, Brisbane, Australia) for a period of 24 hours. Food was provided ad libitum. At the end of the exposure period animals were either euthanized immediately by intraperitoneal injection of barbiturate overdose (60 mg/kg bodyweight, Valabarb; Virbac, Carros, France), or were returned to dim light (5 lux) conditions for 3 or 7 days before euthanasia. Retinal tissue was collected immediately for analysis. Age-matched, dim-reared animals were used as controls. All experimental groups were n = 5, unless otherwise stated.
The retina from the right eye of each animal was excised through a corneal incision and placed in RNAlater solution (Ambion Biosystems, Austin, TX, USA), stored at 4°C overnight then transferred to −80°C. The left eye from each animal was enucleated, the superior margin marked, then immersed in 4% paraformaldehyde for 3 hours at 4°C. The anterior segment was removed, then the eye cups replaced in fresh 4% paraformaldehyde overnight at 4°C, and subsequently prepared for paraffin embedding. Eyes were sectioned at 6 μm on a microtome on the vertical axis. Only sections containing the optic nerve were used for analysis.
Total RNA was extracted from retinal samples using the mirVana miRNA isolation kit (Ambion Biosystems), according to manufacturer's protocol. The concentration of the RNA was determined by ND-1000 spectrophotometer (Nanodrop Technologies, Wilmington, DE, USA) and quality using the 2100-Bioanalyser (Agilent Technologies, Santa Clara, CA, USA). Only RNA samples with a A260/A280 ratio above 1.9 and an RNA integrity number (RIN) greater than 8.0 were used for the study. The RNA samples were stored at −80°C before performing TaqMan miRNA array studies.
The results of this study showed that miRNAs are modulated in response to LD. Indeed, two of the most highly regulated gene clusters targeted by these miRNAs are “positive regulation of the transcription from RNA polymerase II promoter” and “negative regulation of DNA dependent transcription.” This essentially reflects that light damage causes regulation of the retinal transcriptome. The other clusters include genes that regulate cell proliferation, cell adhesion, angiogenesis, and our target category, the inflammatory response.
Cell Proliferation and Angiogenesis in LD.
A surprising finding of the functional clustering analysis is the high representation of target genes involved in cell proliferation and angiogenesis, since neither of these functions feature prominently in the LD model. There are two possible explanations for this. The first is that, because a single miRNA can regulate translation of multiple genes, the list of “target genes” introduced into Partek for clustering is not necessarily the actual targets of the miRNAs we have identified. For example, miR-449a is enriched in “inflammatory response” and “angiogenesis” clusters exhibiting putative binding sites for interleukin 23 receptor mRNA, involved in the immune response, and angiopoietin-1 receptor mRNA, which facilitates blood vessel formation.
A second possibility is that genes in cell proliferation pathways and/or angiogenic pathways may be upregulated so that the tissues are induced into a “pro-angiogenesis” or “pro-proliferation” state, without activating all the genes required for angiogenesis or proliferation to take place. Proliferation of non-neuronal retinal cells (astrocytes, microglia, and Müller cells) has been well documented in retinal degenerations, including AMD as a response to intense retinal stress.
28–30 While angiogenesis has not been reported in the LD model previously, it is possible that leukostasis could cause local hypoxia leading to modulation of angiogenic factors, the effects of which might only be detected following much longer survival periods than explored here.
Cell Adhesion and Inflammation in LD.
In this study, we identified 37 miRNAs upregulated by LD, including seven that regulated the inflammatory response, which is a key mediator of retinal degeneration in this model, and in AMD. The miRNAs are endogenously-occurring molecules that can be safely introduced in vivo without triggering a nonspecific immune response. Because these miRNAs regulate multiple genes and pathways simultaneously, they provide new potential therapeutic targets with far-reaching biological outcomes suitable for management of complex retinal disorders, like AMD.
Supported by the Australian Research Council Centres of Excellence Program Grant CE0561903 and National Health and Medical Research Council Grant 1049990.
Disclosure: K. Saxena, None; M.V. Rutar, None; J.M. Provis, None; R.C. Natoli, None