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Copyright © 2001, The National Academy of Sciences Cell Biology Gene expression profiles of light-induced apoptosis in arrestin/rhodopsin kinase-deficient mouse retinas Division of Biology, 147-75, California Institute of Technology, Pasadena, CA 91125 *S.C. and W.H. contributed equally to this work. †To whom reprint requests should be addressed. E-mail: simonm/at/caltech.edu. Contributed by Melvin I. Simon Accepted August 8, 2001. This article has been cited by other articles in PMC.Abstract To examine the molecular processes that lead to light-induced retinal degeneration, mutant mice deficient in arrestin and rhodopsin kinase were raised in the dark and then subjected to relatively low doses of white light. The kinetics of the subsequent induction of apoptosis, change in mRNA transcript level, and photoreceptor cell death were monitored. Analysis of transcript profiles identified clusters of genes that responded differently to illumination, including a cluster of photoreceptor-specific genes that showed marked decreases in levels long before morphological damage could be readily ascertained. The behaviors of other gene clusters demonstrate the coordinate induction of stress gene responses early in the course of irradiation. There was little, if any, change in transcript levels corresponding to genes associated with the initiation of apoptosis or antiapoptotic effects. Transcript analysis provides insight into the patterns of gene expression that are associated with the different stages of retinal degeneration in this model system. Exposure to light can induce photoreceptor cell death and retinal degeneration in a variety of animals (1, 2). The extent of light damage highly depends on the light intensity, wavelength, and manner in which the animals are exposed to light. Nutrition, stress, age, previous history of light exposure, continuous versus cyclic light, and the genetic background of the animals all play important roles in determining the extent and nature of the damage (3–7). Under certain conditions the absence of specific genes, e.g., c-fos and Rpe65 (8, 9), can prevent light-induced degeneration, whereas the absence of other genes, e.g., arrestin and rhodopsin kinase (10, 11), can sensitize the retina to light damage. Specific growth factors have been shown to be involved both in increasing cell death and in rescuing cells from the effects of light-induced damage (12, 13). In addition to light induction, photoreceptor cell death can result from a variety of mutations in components of the pathway involved in generating the phototransduction cascade (14, 15). Many different processes have been suggested to account for light-induced degeneration, including rhodopsin regeneration and processing (16–18), induction of free radical formation (19), interactions between photoreceptor cells and other cells in the retina (12), and the formation of toxic products resulting from stimulation of the phototransduction cascade (20). Furthermore, it has been suggested that light damage may also play a role in late-onset retinal and macular degeneration diseases (21–23). It has been difficult to determine the specific molecular mechanisms responsible for the induction of apoptotic cell death and retinopathy under different conditions because of the complexity of the processes involved. There are presumably different molecular and biochemical events that can induce subsequent apoptosis, but the molecular mechanisms that initiate the process are not readily observed. In addition, the major assays that have been used to examine the process involve measuring changes in gross retinal morphology. Thus the ultimate degeneration that is far removed from causal events is assessed as the end point. Changes in the protocol for irradiation where light is applied over a relatively short interval and the animals are then put in the dark to allow damage to develop have been used (8) to try to separate the initiation processes from the degenerative processes. However, this regimen requires the application of a relatively large dose of irradiation, and again the immediate effects cannot easily be measured. To better determine the molecular and genetic processes involved, we propose to use mutant mice that are deficient in the regulation of the phototransduction cascade and are rendered highly sensitive to light damage. We have generated mutants deficient in arrestin and rhodopsin kinase. When the animals are raised in the dark they have normal retinal morphology. However, when exposed to continuous light they show rapid induction of photoreceptor cell death that appears to be the result of apoptosis (10, 11). The use of these mutant mice allows us to synchronize the initiation of light damage by raising the animals in the dark and initiating the experiment by using moderate levels of illumination. The rapid degeneration provides an opportunity to study the kinetics of retinal degeneration in a reproducible fashion over a relatively short time period. The second approach we have taken to the analysis of this complex process is to use oligonucleotide microarrays to measure changes in RNA transcript levels as a function of time of exposure to light. Transcript analysis provides one measure of the molecular changes induced by light damage and points a way to developing experimental paradigms to more clearly define the molecules involved in the initiation and subsequent apoptotic cell death of the photoreceptors, as well as the responses of other cells in the layered retina. Materials and Methods Animals. All procedures involving mice were carried out in accordance with the statement by the Association for Research in Vision and Ophthalmology on the use of animals in ophthalmic and vision research. Arrestin and rhodopsin kinase knockout mice were generated (11, 24). These mice were crossed to each other, and the double-deficient (arrestin and rhodopsin kinase) mice were intercrossed for many generations. The mice were maintained as double mutants and reared in the dark. Wild-type mice were derived from an initial cross of 129sv and C57BL/6. These mice were intercrossed and also were reared in the dark. The mice used in this study ranged in age from 6 to 10 weeks. Light Illumination. To induce retinal degeneration with light, mice reared in the dark were placed in aluminum foil-wrapped polycarbonate cages that were covered with stainless steel wire tops, and the mice were supplied with food and water at the bottom of the cage. Constant illumination of 200 ft-c was generated by diffuse, cool, white fluorescent lamps. The temperature was controlled at 25°C during irradiation. Analysis of Retinal Morphology. Eyes were enucleated from anesthetized mice. After lenses were fixed and removed, eyecups were fixed overnight in 2.5% glutaraldehyde/2% paraformaldehyde in 0.1 M phosphate buffer (pH 7.4). The eyecups were then fixed for 2 h in 1% osmium tetroxide before they were processed and embedded in Epon. Sections 1 μm in thickness were cut along the vertical meridian with the optic nerve and stained with 1% toluidine blue. Measurements of outer nuclear layer (ONL) thickness were made on one section from each mouse as described (7). Briefly, ONL thickness was surveyed by measuring nine 250-μm-long segments in each of the superior and inferior hemispheres of the retina, starting from the optic nerve head. Within each segment, ONL thickness was represented by averaging measurements from three points spaced 50 μm apart. Microarray Probe Preparation. The RNA samples were processed as recommended by Affymetrix (Santa Clara, CA). Briefly, total RNA was prepared from frozen retinas with the use of Trizol reagent (Life Technologies, Rockville, MD). After the Trizol extraction procedure, cleanup was carried out with a Qiagen RNeasy Mini Kit (Qiagen, Chatsworth, CA). Reverse transcription was performed on 10 μg of total retinal RNA with the use of SuperScript polymerase (Life Technologies) and an oligo-(dT)24 primer with a T7 RNA polymerase promoter (Genset, La Jolla, CA). After second-strand synthesis, the double-stranded cDNA was cleaned up by extraction with phenol-chloroform-isoamyl alcohol and recovered by ethanol precipitation. An RNA Transcript Labeling Kit (Enzo Diagnostics) was used for the production of hybridizable biotin-labeled RNA targets by in vitro transcription from T7 RNA polymerase promoters. The cDNA prepared from total RNA was used as a template in the presence of a mixture of unlabeled ATP, CTP, GTP, and UTP and biotinylated CTP and UTP. In vitro transcription products were purified with an RNeasy Mini Kit (Qiagen) to remove unincorporated NTPs and fragmented to sizes from ≈ 50 to 200 bases by incubation at 94°C for 35 min. The fragmented sample cRNA (complementary RNA) was stored at −20°C until the hybridization was performed.Hybridization and Scan. Mouse GeneChips Mu11K and Mu19K, or U74 (Affymetrix) were used. The biotinylated cRNA was hybridized for 16 h at 40°C to a set of oligonucleotide arrays in the GeneChip Fluidics Station 400 (Affymetrix). The final concentration of fragmented cRNA was 0.28–0.35 μg/μl in the hybridization solutions. After hybridization, the GeneChip array underwent a series of stringency washes and was stained with streptavidin-conjugated phycoerythrin. Probe arrays were scanned with a Hewlett–Packard Scanner. Finally, the results were analyzed with genechip analysis software (Affymetrix), and the fold change between the hybridization intensities of reference and test samples was obtained. Quantification of Apoptosis in the Retina. Light-induced apoptosis in the retina was quantified with a cell death detection ELISA assay kit (Roche Molecular Biochemicals) that quantifies the soluble mono- and oligonucleosomes released in the cell lysate as a function of apoptosis (12, 25). One retina was homogenized with a 26-½ gauge needle in 200 μl of phosphate buffer with 1 mM PMSF. The lysate was centrifuged at 15,000 × g for 10 min at room temperature. One hundred microliters of supernatant was diluted 10 times with lysis buffer, and the rest of the supernatant was saved for the measurement of protein levels with the Bio-Rad protein assay procedure. Twenty microliters of diluted supernatant was used in the ELISA measurement according to the manufacturer's instructions. Real-Time Quantitative Reverse Transcription–PCR (RT-PCR). Real-time quantitative RT-PCR was performed on the GeneAmp 5700 Sequence Detection System (Applied Biosystems) by monitoring of the increase in fluorescence caused by the binding of SYBR Green to double-stranded DNA. Total RNA was prepared from frozen mouse retinas with the use of Trizol reagent (Life Technologies). To prepare cDNA templates, 50–100 ng of total RNA was mixed with 5.5 mM MgCl2, 0.5 mM each dNTP, 2.5 μM random hexamer, 0.4 unit/μl RNase inhibitor, and 1.25 units/μl MultiScribe reverse transcriptase from TaqMan Reverse Transcription Reagents (Applied Biosystems). RT was incubated at 25°C for 10 min and at 48°C for 30 min and inactivated at 95°C for 5 min. The PCR primers were designed with primer express software (Applied Biosystems), and their specificity in gene amplification was confirmed by measurement of the size and purity of the PCR product by 4% NuSieve agarose gel electrophoresis. For a 50-μl PCR, 4 μl cDNA template was mixed with 300 nM each of forward and reverse primers and 2× SYBR Green PCR Master Mix (Applied Systems). The reaction was first incubated at 50°C for 2 min, then at 95°C for 10 min, followed by 40 cycles of 95°C for 15 s and 60°C for 1 min. Each gene-specific PCR was performed in triplicate. Results In previous experiments we showed separately that the absence of arrestin (10) or the absence of rhodopsin kinase (11) individually sensitizes the photoreceptors of mutant mice to the induction of cell death by light. We crossed these mutant mice and generated doubly deficient animals. In the double mutants the major, rapid, reproducible mechanisms for inactivating rhodopsin have been eliminated. Extended activation of the phototransduction cascade is presumably responsible for initiating the subsequent processes that lead to cell death (20). Mice homozygous for both the arrestin deficiency and the rhodopsin kinase deficiency were raised in the dark and transferred to conditions of moderate-intensity, continuous light exposure. After 2, 5, 8, 16, 24, 48, or 96 h of continuous light, retinas were removed, and they were sectioned, stained, and used for measurements of nucleosome release, or harvested and extracted for total RNA to be used for microarray analysis. In many cases, a portion of the RNA sample used for DNA microarray analysis was used for real-time quantitative PCR analysis for specific mRNA transcripts. Control animals with similar genetic backgrounds that were homozygous wild type with respect to rhodopsin kinase and arrestin were raised in the dark and exposed to light in the same manner as the experimental animals and were used as controls. Fig. Fig.11
Staining and morphological assays suggested that, as early as 8 h after the initiation of irradiation, changes in nuclear morphology could be seen. To get other correlates of apoptotic cell death, we used the nucleosome release assay (12, 25). Entire retinas from irradiated mice were taken for each sample point, and damage to DNA resulting from the initiation of apoptosis was gauged by comparing nucleosome release at different times after illumination. Nucleosome release could be clearly seen by 10 h, and there was a very robust nucleosome release response after 16 h of irradiation, suggesting high levels of apoptosis. For the oligonucleotide microarray experiments Affymetrix mouse chips, Mu 11k and Mu 19k, were used. In addition, the U74 set, which is a revision of the Mu 11k and Mu 19k set, was used. All together, 34,325 probe sets were surveyed. Of those, 14,510 gave discernible and clear signals (i.e., 42.3%), and of those giving signals, 3,877 or 11.3% were changed for at least one of the time points in the experiments. A total of 2,673 probe sets displayed an increase or decrease in gene expression greater than 2-fold. The largest number of differentially expressed genes among the samples was observed at 16 h of irradiation. All of the data including the wild-type irradiated controls are presented at our web site (http://microarray.caltech.edu/pubs/). The data obtained from the irradiated mutant retinas were assembled and analyzed by the self-organizing map method described by Tamayo et al. (26). Twenty-four cluster groups were used (Fig. (Fig.3).3
Cluster c23 (Fig. (Fig.3)3 To further confirm the microarray results we used quantitative RT-PCR with oligonucleotides that were specific for some of the genes that showed kinetic patterns of increase or decrease as a function of time of irradiation. Selected results are shown in Fig. Fig.5.5
Discussion Analysis of the results of single-photon absorption experiments indicates that both arrestin and rhodopsin kinase contribute directly to attenuation of the ability of activated rhodopsin to engage the phototransduction cascade and that eliminating both genes leads to a prolonged response. It is this elimination of the two genes (10, 11, 20) that presumably initiates the sensitivity of the photoreceptors to cell death. The effect of irradiation is clearly seen on levels of mRNA that are photoreceptor-specific in the experimental animals but not in the controls. Levels of rhodopsin, recoverin, cGMP-specific rod phosphodiesterase gamma, rod photoreceptor 1, rod outer segment membrane protein 1, and message corresponding to other photoreceptor-specific proteins begin to decrease rapidly well before there is any readily discernible morphological effect on photoreceptor cells (cluster c0). There are also photoreceptor-specific genes whose transcript levels initially decrease slowly but show marked decreases after 8 h of irradiation (cluster c2). Cluster c2 contains rod transducin alpha, cGMP gated channel, cGMP-specific rod phosphodiesterase beta, peripherin 2, etc. On the other hand, there are marked increases in transcript levels corresponding to stress response genes or early response genes, such as DNA damage-inducible transcript 3, c-Fos, Jun, activating transcription factor 4, by 5 h of irradiation (cluster c23). Transcripts corresponding to a variety of heat shock proteins, DNA repair genes, and genes that encode methylating enzymes are coordinately increased, and their levels begin to decrease after 8 h. On the other hand, mRNAs corresponding to a number of transcription factors, such as signal transducer and activator of transcription 1 and 3, activating transcription factor 3, CCAAT/enhancer binding protein, Jun-B, and myeloid differentiation primary response gene 118, initially increase slowly but show a marked increase after 8 h (clusters 21 and 22). It is not clear that all of these changes are occurring in photoreceptors. There may be marked changes in neighboring cells, particularly after 16 h of irradiation, when we can biochemically and morphologically detect cell loss. Many of the probe sets in the arrays that we used correspond to expressed sequence tags or to unannotated genes. The association of changes in the levels of transcripts from these genes with specific gene clusters may help in the assignment of their function. We can begin to divide the changes that we observe into early (<8 h), middle (8–24 h), and late (>24 h) changes and focus more clearly on each stage in the process. In the early events, 0–8 h of irradiation, the predominant effects are presumably induced directly by the effects of light on the phototransduction cascade. Little or no increase in nucleosome release is observed during this period (Fig. (Fig.22 The period after 16 h of irradiation (corresponding to the “middle period”) includes the biochemical events that are part of the process of apoptosis (e.g., nucleosome release is detected). We have shown that if the animals are removed from irradiation after 5 h (unpublished observations) and put back in the dark, there are only low levels of morphological damage seen after 5 days. On the other hand, after 16 h of irradiation permanent damage is seen even if the animals are maintained in the dark. Thus we also may be able to distinguish between permanent and reversible events. Certainly after 24 h of irradiation a large proportion of the photoreceptor cells have been eliminated. The level of irreversible damage to the other cells in the layered retina is not clear. The precise nature of the events that induce apoptosis is not revealed by these experiments; however, they provide a series of markers, i.e., specific patterns of change in gene expression that result from the induction events, and help divide the processes so that they can be analyzed in terms of some of the molecular events that accompany the induction of cell death. We can now begin to modify the conditions of the experiment, e.g., use different mutations, different light intensities, and discontinuous illumination, and follow patterns of change in transcript levels to parse out the different mechanisms involved in light-induced degeneration. Acknowledgments We thank Rebecca Udwary and Hong Dang for their invaluable assistance with data analysis and setting up the web site. 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Science. 1971 Apr 2; 172(978):76-9.
[Science. 1971]Invest Ophthalmol Vis Sci. 1987 Jul; 28(7):1043-8.
[Invest Ophthalmol Vis Sci. 1987]Nat Med. 1997 Mar; 3(3):346-9.
[Nat Med. 1997]Nat Genet. 2000 May; 25(1):63-6.
[Nat Genet. 2000]Invest Ophthalmol Vis Sci. 1999 Nov; 40(12):2978-82.
[Invest Ophthalmol Vis Sci. 1999]Invest Ophthalmol Vis Sci. 1999 Nov; 40(12):2978-82.
[Invest Ophthalmol Vis Sci. 1999]Proc Natl Acad Sci U S A. 1999 Mar 30; 96(7):3718-22.
[Proc Natl Acad Sci U S A. 1999]Proc Natl Acad Sci U S A. 1999 Mar 30; 96(7):3718-22.
[Proc Natl Acad Sci U S A. 1999]Nature. 1997 Oct 2; 389(6650):505-9.
[Nature. 1997]Invest Ophthalmol Vis Sci. 1987 Jul; 28(7):1043-8.
[Invest Ophthalmol Vis Sci. 1987]Neuron. 2000 May; 26(2):533-41.
[Neuron. 2000]J Immunol. 1994 Aug 15; 153(4):1778-88.
[J Immunol. 1994]Invest Ophthalmol Vis Sci. 1999 Nov; 40(12):2978-82.
[Invest Ophthalmol Vis Sci. 1999]Proc Natl Acad Sci U S A. 1999 Mar 30; 96(7):3718-22.
[Proc Natl Acad Sci U S A. 1999]Invest Ophthalmol Vis Sci. 1999 Nov; 40(12):2770-2.
[Invest Ophthalmol Vis Sci. 1999]Invest Ophthalmol Vis Sci. 1999 Nov; 40(12):2978-82.
[Invest Ophthalmol Vis Sci. 1999]Neuron. 2000 May; 26(2):533-41.
[Neuron. 2000]J Immunol. 1994 Aug 15; 153(4):1778-88.
[J Immunol. 1994]Proc Natl Acad Sci U S A. 1999 Mar 16; 96(6):2907-12.
[Proc Natl Acad Sci U S A. 1999]Proc Natl Acad Sci U S A. 1998 Dec 8; 95(25):14863-8.
[Proc Natl Acad Sci U S A. 1998]Science. 1999 Jan 1; 283(5398):83-7.
[Science. 1999]Alcohol Clin Exp Res. 2001 Jun; 25(6):810-8.
[Alcohol Clin Exp Res. 2001]Invest Ophthalmol Vis Sci. 1999 Nov; 40(12):2978-82.
[Invest Ophthalmol Vis Sci. 1999]Proc Natl Acad Sci U S A. 1999 Mar 30; 96(7):3718-22.
[Proc Natl Acad Sci U S A. 1999]Invest Ophthalmol Vis Sci. 1999 Nov; 40(12):2770-2.
[Invest Ophthalmol Vis Sci. 1999]