DNA microarray analysis of gene expression in iris and ciliary body of rat eyes with endotoxin-induced uveitis

Single-cell RNA-sequencing analysis of the ciliary epithelium and contiguous tissues in the mouse eye

The ciliary epithelium plays a central role in ocular homeostasis but cells of the pigmented and non-pigmented layers are difficult to isolate physically and study. Here we used single-cell RNA-sequencing (scRNA-seq) to analyze the transcriptional signatures of cells harvested from the ciliary body and contiguous tissues. Microdissected tissue was dissociated by collagenase digestion and the transcriptomes of individual cells were obtained using a droplet-based scRNA-seq approach. In situ hybridization was used to verify the expression patterns of selected differentially-expressed genes. High quality transcriptomes were obtained from 10,024 cells and unsupervised clustering distinguished 22 cell types. Although efforts were made to specifically isolate the ciliary body, approximately half of the sequenced cells were derived from the adjacent retina. Cluster identities were assigned using expression of canonical markers or cluster-specific genes. The transcriptional signature of cells in the PCE and NPCE were distinct from each other and from cells in contiguous tissues. PCE cell transcriptomes were characterized by genes involved in melanin synthesis and transport proteins such as Slc4a4. Among the most differentially expressed genes in NPCE cells were those encoding members of the Zic family of transcription factors (Zic1, 2, 4), collagen XVIII (Col18a1), and corticotrophin-releasing hormone-binding protein (Crhbp). The ocular melanocyte population was distinguished by expression of the gap junction genes Gjb2 and Gjb6. Two fibroblast signatures were detected in the ciliary body preparation and shown by in situ hybridization to correspond to uveal and scleral populations. This cell atlas for the ciliary body and contiguous layers represents a useful resource that may facilitate studies into the development of the ciliary epithelium, the production of the aqueous and vitreous humors, and the synthesis of the ciliary zonule.

Study on the anti-endotoxin effect of sinomenine using an Agilent genome array

BACKGROUND

Endotoxin is a significant contributing factor underlying the occurrence of fever, diarrhea, inflammation, edema, coagulation, shock and other syndromes associated with gram-negative bacterial infections. To date, there is no effective treatment for endotoxemia.

AIM

The aim of this study was to characterize differentially expressed genes in sinomenine-treated and lipopolysaccharide (LPS)-induced endothelial cells by microarray analysis and to determine the potential pharmacological activity of sinomenine.

DESIGN

The cultured cells of five treatment groups (n = 3) were collected. Participants: total RNA was extracted and subjected to Agilent Porcine 4 × 44 K whole genome microarray.

METHODS

Kyoto encyclopedia of genes and genomes and gene ontology software were applied to screen and analyze differentially regulated genes.

RESULTS

The results showed that 723 differentially regulated genes were identified including 410 up-regulated genes and 313 down-regulated genes in therapy group vs. LPS group. Ten genes may be key controlled genes in the pathogenesis of LPS, including five up-regulated genes (ARG1, TLR2, IL1A, VCAM1, DKK3) and five down-regulated genes (HABP2, ID1, CHDH, GPX3, PTGFR), which primarily contribute to biological processes such as inflammatory response, vascular lesion, metabolic process and cell cycle. IL1A and FMO3 were considered as potent target genes.

CONCLUSION

Global gene expression profile analysis showed that sinomenine might effectively be useful to regulate inflammatory responses as part of future anti-endotoxin therapies.

Determination of Genes Related to Uveitis by Utilization of the Random Walk with Restart Algorithm on a Protein-Protein Interaction Network

Uveitis, defined as inflammation of the uveal tract, may cause blindness in both young and middle-aged people. Approximately 10–15% of blindness in the West is caused by uveitis. Therefore, a comprehensive investigation to determine the disease pathogenesis is urgent, as it will thus be possible to design effective treatments. Identification of the disease genes that cause uveitis is an important requirement to achieve this goal. To begin to answer this question, in this study, a computational method was proposed to identify novel uveitis-related genes. This method was executed on a large protein–protein interaction network and employed a popular ranking algorithm, the Random Walk with Restart (RWR) algorithm. To improve the utility of the method, a permutation test and a procedure for selecting core genes were added, which helped to exclude false discoveries and select the most important candidate genes. The five-fold cross-validation was adopted to evaluate the method, yielding the average F1-measure of 0.189. In addition, we compared our method with a classic GBA-based method to further indicate its utility. Based on our method, 56 putative genes were chosen for further assessment. We have determined that several of these genes (e.g., CCL4, Jun, and MMP9) are likely to be important for the pathogenesis of uveitis.

Therapeutic benefit of melatonin in experimental feline uveitis

Uveitis is a frequent ophthalmic disorder which constitutes one of the main causes of blindness in domestic cats. The aim of this report was to analyze the effect of melatonin on experimentally induced uveitis in cats. Bacterial lipopolysaccharide (LPS) was injected intravitreally into one eye from intact cats, while the contralateral eye was injected with vehicle. Melatonin was orally administered every 24 hr to a group of ten cats, from 24 hr before until 45 days after intravitreal injections. Eyes were evaluated by means of clinical evaluation, intraocular pressure (IOP), blood-ocular barrier integrity (via measurement of protein concentration and cell content in samples of aqueous humor [AH]), electroretinogram (ERG), and histological examination of the retinas. In LPS-treated eyes, several clinical signs were observed until day 45 postinjection. The treatment with melatonin significantly decreased clinical signs and prevented the reduction in IOP induced by LPS. In LPS-injected eyes, melatonin significantly preserved the blood-ocular barrier integrity, as shown by a decrease in the number of infiltrating cells and protein concentration in the AH. Mean amplitudes of scotopic ERG a- and b-waves were significantly reduced in eyes injected with LPS, whereas melatonin significantly prevented the effect of LPS. At 45 days after injection, LPS induced alterations in photoreceptors and at the middle portion of the retina, whereas melatonin preserved the retinal structure. These results indicate that melatonin prevented clinical, biochemical, functional, and histological alterations induced by LPS injection. Thus, melatonin might constitute a useful tool for the treatment of feline uveitis.

Elevated levels of anti-endotoxin antibodies in patients with bilateral idiopathic acute anterior uveitis

PURPOSE

Endotoxins have been proved to be responsible for acute anterior uveitis (AAU) in animals in a well-established experimental model of endotoxin-induced uveitis (EIU). The purpose of our study was the detection of antibodies against endotoxins of selected enterobacteria in the serum of patients with idiopathic AAU and searching for correlations between the levels of these antibodies and the presence of HLA-B27 antigen as well as characteristic signs of EIU such as bilaterality and the absence of spontaneous recurrences of the disease.

METHODS

Reactions of serum IgG antibodies with lipopolysaccharides (LPSs) of Escherichia coli O1, E. coli O10, E. coli O111, E. coli J5, and Klebsiella pneumoniae O3 were determined for 60 patients with idiopathic AAU and 40 healthy volunteers. The presence of HLA-B27 antigen in patients was determined. Documentation of the frequency of recurrences of AAU during a follow-up period of 8 years was collected.

RESULTS

We have observed that the sera of patients with a first attack of AAU reacted stronger with the LPS of K. pneumoniae O3 than the sera of patients with relapse of the disease. Patients with bilateral AAU had markedly higher levels of antibodies against four of the five used LPSs than patients with one eye involved. A multiply comparison showed higher levels of IgG reacting with LPS of E. coli O111 in patients with bilateral eye inflammation admitted with the first attack of AAU comparing to controls. The incidence of recurrent form of AAU was significantly increased in HLA-B27-positive patients compared to HLA-B27-negative patients. However, we found in HLA-B27 carriers that those with the bilateral form of AAU had over three times smaller risk of recurrence and showed stronger immunization by endotoxins than patients with unilateral inflammation.

CONCLUSION

Our results suggest a potential role of endotoxins in the aetiology of the nonrecurrent bilateral form of AAU. We suggest that not only HLA-B27 status but also determination of number of involved eyes may be useful to assess the risk of recurrence of the idiopathic AAU.

Calcium channel blocker nilvadipine, but not diltiazem, inhibits ocular inflammation in endotoxin-induced uveitis

PURPOSE

Calcium channel blockers (CCBs), widely used for hypertensive patients, have recently been shown to inhibit atherosclerosis by their antioxidative action. The aim of the present study was to examine whether the CCBs nilvadipine and diltiazem reduce ocular inflammation in endotoxin-induced uveitis (EIU).

METHODS

EIU was induced in male C57/B6 mice with a single intraperitoneal injection of lipopolysaccharide (LPS). The animals received intraperitoneal injections of either nilvadipine, diltiazem, or vehicle for 5 days before the LPS application. Twenty-four hours after EIU induction, adherent leukocytes to the retinal vasculature were counted with a concanavalin A lectin perfusion-labeling technique. The protein concentration in the aqueous humor was measured to assess blood-ocular barrier breakdown. Retinal levels of intercellular adhesion molecule (ICAM)-1 and monocyte chemotactic protein (MCP)-1 were analyzed by enzyme-linked immunosorbent assay. LPS-stimulated generation of superoxide in murine microvascular endothelial cells was examined with a nitroblue tetrazolium assay.

RESULTS

Compared to vehicle treatment, application of nilvadipine, but not diltiazem, led to significant suppression of EIU-associated retinal leukocyte adhesion, together with anterior-chamber protein leakage, retinal expression of ICAM-1 and MCP-1, and LPS-induced superoxide generation in vitro.

CONCLUSIONS

The CCB nilvadipine exercises an inhibitory effect on the pathogenesis of ocular inflammation through the suppression of inflammation-related molecules.

Mammalian telomeric DNA suppresses endotoxin-induced uveitis

Telomeric regions of mammalian chromosomes contain suppressive TTAGGG motifs that inhibit several proinflammatory and Th1-biased immune responses. Synthetic oligodeoxynucleotides (ODN) expressing suppressive motifs can reproduce the down-regulatory activity of mammalian telomeric repeats and have proven effective in the prevention and treatment of several autoimmune and autoinflammatory diseases. Endotoxin-induced uveitis (EIU) is an established animal model of acute ocular inflammation induced by LPS administration. Augmented expression of proinflammatory cytokines/chemokines such as TNFalpha, IL-6, and MCP1 and bactericidal nitric oxide production mediated by LPS contribute to the development of EIU. Suppressing these mediators using agents that are devoid of undesirable systemic side effects may help prevent the development of EIU. This study demonstrates the selective down-regulatory role of suppressive ODN after (i) local or (ii) systemic treatment in EIU-induced rabbits and mice. Our results indicate that suppressive ODN down-regulate at both the transcript and protein levels of several proinflammatory cytokines and chemokines as well as nitric oxide and co-stimulatory surface marker molecules when administrated prior to, simultaneously with, or even after LPS challenge, thereby significantly reducing ocular inflammation in both rabbit and mouse eyes. These findings strongly suggest that suppressive ODN is a potent candidate for the prevention of uveitis and could be applied as a novel DNA-based immunoregulatory agent to control other autoimmune or autoinflammatory diseases.

Use of bioanalyzer electropherograms for quality control and target evaluation in microarray expression profiling studies of ocular tissues

Expression profiling with DNA microarrays has been used to examine the transcriptome of a wide spectrum of vertebrate cells and tissues. The sensitivity and accuracy of the data generated is dependent on the quality and composition of the input RNA. In this report, we examine the quality and array performance of over 200 total RNA samples extracted from ocular tissues and cells that have been processed in a microarray core laboratory over a 7-year period. Total RNA integrity and cRNA target size distribution were assessed using the 2100 Bioanalyzer. We present Affymetrix GeneChip array performance metrics for different ocular samples processed according to a standard microarray assay workflow including several quality control checkpoints. Our review of ocular sample performance in the microarray assay demonstrates the value of considering tissue-specific characteristics in evaluating array data. Specifically, we show that Bioanalyzer electropherograms reveal highly abundant mRNAs in lacrimal gland targets that are correlated with variation in array assay performance. Our results provide useful benchmarks for other gene expression studies of ocular systems.

Study on the antiendotoxin action of Pulsatillae Decoction using an Affymetrix rat genome array

A high-throughput and efficient Affymetrix rat genome array was used to investigate the pharmacological mechanism of the traditional Chinese medicine, Pulsatillae Decoction (PD), used for the treatment of diseases induced by lipopolysaccharide (LPS). Rat intestinal microvascular endothelial cells (RIMECs) were challenged with 1mug/ml LPS for 3h, and then treated with PD at a concentration of 1mg/ml for 24h. Total RNA from each treatment group was extracted from cultured RIMECs for detection by the Affymetrix Rat Genome 230 2.0 Array. The results showed that 36 genes were upregulated and 33 genes were downregulated in the LPS group vs. the blank control group; 566 genes were upregulated and 12 genes were downregulated in the PD-treated group vs. the LPS group; and 93 genes were upregulated and 29 genes were downregulated in the PD-treated group vs. the blank control group. The analysis of these data suggested that PD specifically and effectively reduce damage induced by LPS, and improved physiological and biochemical responses to counteract the effects of LPS.