Identification of key genes and pathways in scleral extracellular matrix remodeling in glaucoma: Potential therapeutic agents discovered using bioinformatics analysis

Genistein stimulates the viability and prevents myofibroblastic transformation in human trabecular meshwork cells stimulated by TGF-β

Primary open-angle glaucoma (POAG) is the most common type of glaucoma leading to blindness. The search for ways to prevent/treat this entity is one of the main challenges of today's ophthalmology. One of such solution seems to be biologically active substances of natural origin, such as genistein (GEN), which can affect the function of isolated trabecular meshwork by the inhibition of protein tyrosine kinase. However, the role of GEN in viability as well as myofibroblastic transformation in human trabecular meshwork cells stimulated by TGF-β is unknown. Using human trabecular meshwork cells (HTMCs) we investigated the effect of genistein on cell viability and myofibroblastic transformation stimulated by TGF-β1 and TGF-β2. Using Real-Time PCR, western blot and immunofluorescence we determined the effect on the expression changes of αSMA, TIMP1, collagen 1 and 3 at mRNA and protein level. We found that genistein increases the viability of HTMCs (1, 2, 3 μg/ml; P < 0.05 and 4, 5, 10, 15, 20 μg/ml; P < 0.01). Moreover, we found that addition of 10, 15 and 20 μg/ml is able to prevent myofibroblastic transformation of HTMCs by decreasing αSMA, TIMP1, collagen 1 and 3 mRNA and protein expression (P < 0.01). Based on the obtained results, we can conclude that genistein is a potential factor that can prevent the myofibroblastic transformation of HTMCs accompanying glaucoma. Describing GEN influence on myofibroblastic transformation processes in HTMC allows us to conclude that it can be considered a potential therapeutic agent or a substance supporting treatment in patients with glaucoma.

Scleral remodeling during myopia development in mice eyes: a potential role of thrombospondin-1

BACKGROUND

Scleral extracellular matrix (ECM) remodeling plays a crucial role in the development of myopia, particularly in ocular axial elongation. Thrombospondin-1 (THBS1), also known as TSP-1, is a significant cellular protein involved in matrix remodeling in various tissues. However, the specific role of THBS1 in myopia development remains unclear.

METHOD

We employed the HumanNet database to predict genes related to myopic sclera remodeling, followed by screening and visualization of the predicted genes using bioinformatics tools. To investigate the potential target gene Thbs1, we utilized lens-induced myopia models in male C57BL/6J mice and performed Western blot analysis to detect the expression level of scleral THBS1 during myopia development. Additionally, we evaluated the effects of scleral THBS1 knockdown on myopia development through AAV sub-Tenon's injection. The refractive status and axial length were measured using a refractometer and SD-OCT system.

RESULTS

During lens-induced myopia, THBS1 protein expression in the sclera was downregulated, particularly in the early stages of myopia induction. Moreover, the mice in the THBS1 knockdown group exhibited alterations in myopia development in both refraction and axial length changed compared to the control group. Western blotting analysis confirmed the effectiveness of AAV-mediated knockdown, demonstrating a decrease in COLA1 expression and an increase in MMP9 levels in the sclera.

CONCLUSION

Our findings indicate that sclera THBS1 levels decreased during myopia development and subsequent THBS1 knockdown showed a decrease in scleral COLA1 expression. Taken together, these results suggest that THBS1 plays a role in maintaining the homeostasis of scleral extracellular matrix, and the reduction of THBS1 may promote the remodeling process and then affect ocular axial elongation during myopia progression.

Searching for Essential Genes and Targeted Drugs Common to Breast Cancer and Osteoarthritis

BACKGROUND

It is documented that osteoarthritis can promote the progression of breast cancer (BC).

OBJECTIVE

This study aims to search for the essential genes associated with breast cancer (BC) and osteoarthritis (OA), explore the relationship between epithelial-mesenchymal transition (EMT)- related genes and the two diseases, and identify the candidate drugs.

METHODS

The genes related to both BC and OA were determined by text mining. Protein-protein Interaction (PPI) analysis was carried out, and as a result, the exported genes were found to be related to EMT. PPI and the correlation of mRNA of these genes were also analyzed. Different kinds of enrichment analyses were performed on these genes. A prognostic analysis was performed on these genes for examining their expression levels at different pathological stages, in different tissues, and in different immune cells. Drug-gene interaction database was employed for potential drug discovery.

RESULTS

A total number of 1422 genes were identified as common to BC and OA and 58 genes were found to be related to EMT. We found that HDAC2 and TGFBR1 were significantly poor in overall survival. High expression of HDAC2 plays a vital role in the increase of pathological stages. Four immune cells might play a role in this process. Fifty-seven drugs were identified that could potentially have therapeutic effects.

CONCLUSION

EMT may be one of the mechanisms by which OA affects BC. Using the drugs can have potential therapeutic effects, which may benefit patients with both diseases and broaden the indications for drug use.

Pathogenesis of Common Ocular Diseases: Emerging Trends in Extracellular Matrix Remodeling

The prevalence of visual impairments in human societies is worrying due to retinopathy complications of several chronic diseases such as diabetes, cardiovascular diseases, and many more that are on the rise worldwide. Since the proper function of this organ plays a pivotal role in people's quality of life, identifying factors affecting the development/exacerbation of ocular diseases is of particular interest among ophthalmology researchers. The extracellular matrix (ECM) is a reticular, three-dimensional (3D) structure that determines the shape and dimensions of tissues in the body. The ECM remodeling/hemostasis is a critical process in both physiological and pathological conditions. It consists of ECM deposition, degradation, and decrease/increase in the ECM components. However, disregulation of this process and an imbalance between the synthesis and degradation of ECM components are associated with many pathological situations, including ocular disorders. Despite the impact of ECM alterations on the development of ocular diseases, there is not much research conducted in this regard. Therefore, a better understanding in this regard, can pave the way toward discovering plausible strategies to either prevent or treat eye disorders. In this review, we will discuss the importance of ECM changes as a sentimental factor in various ocular diseases based on the research done up to now.

Identification of Drug Compounds for Capsular Contracture Based on Text Mining and Deep Learning

BACKGROUND

Capsular contracture is a common and unpredictable complication after breast implant placement. Currently, the pathogenesis of capsular contracture is unclear, and the effectiveness of nonsurgical treatment is still doubtful. The authors' study aimed to investigate new drug therapies for capsular contracture by using computational methods.

METHODS

Genes related to capsular contracture were identified by text mining and GeneCodis. Then, the candidate key genes were selected through protein-protein interaction analysis in Search Tool for the Retrieval of Interacting Genes/Proteins and Cytoscape. Drugs targeting the candidate genes with relation to capsular contracture were screened out in Pharmaprojects. Based on the drug-target interaction analysis by DeepPurpose, candidate drugs with highest predicted binding affinity were obtained eventually.

RESULTS

The authors' study identified 55 genes related to capsular contracture. Gene set enrichment analysis and protein-protein interaction analysis generated eight candidate genes. One hundred drugs targeting the candidate genes were selected. The seven candidate drugs with the highest predicted binding affinity were determined by DeepPurpose, including tumor necrosis factor alpha antagonist, estrogen receptor agonist, insulin-like growth factor 1 receptor, tyrosine kinase inhibitor, and matrix metallopeptidase 1 inhibitor.

CONCLUSION

Text mining and DeepPurpose can be used as a promising tool for drug discovery in exploring nonsurgical treatment to capsular contracture.

CLINICAL QUESTION/LEVEL OF EVIDENCE

Therapeutic, V.

Bioinformatics analysis of key candidate genes and pathways in Chinese patients with keratoconus

Keratoconus (KC) is a multifactorial disease in which genetic factors played important roles in its pathogenesis. The purpose of the current study was to identify the key candidate genes and pathways in Chinese patients with KC through bioinformatics analysis. Totally, we identified 71 candidate genes by analyzing the results of whole exome sequencing on 51 Chinese patients with KC, combining with previous reports on differential expression at transcription and protein levels in KC. Gene enrichment analysis with GeneCodis demonstrated that two significantly enriched terms including 21 genes in biological process (BP) were detected, and six significantly enriched terms containing 14 genes in Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway were discovered. The STRING was utilized to construct the protein-protein interaction (PPI) network of identified genes. The result showed that a PPI network consisted of 14 nodes with 14 edges was constructed, and two gene modules were obtained. Eight hub genes (LAMB3, LAMA3, LAMA1, ITGA6, ITGA3, COL6A3, COL6A2, and COL6A1) were identified as key candidate genes for KC by cytoHubba in Cytoscape. Functional enrichment analysis with ClueGO and CluePedia indicated that the ECM-receptor interaction was the key pathway accounted for KC. The findings might provide novel insights on the genetic basis of KC.

ZD6474 attenuates TGF-β1-induced fibrosis in human Tenon fibroblasts and inhibits neovascularization via AKT-mTOR signaling pathway

PURPOSE

To investigate the anti-fibrotic effect of ZD6474 (a novel inhibitor of VEGF and EGF) in TGF-β1 stimulated human Tenon's capsule fibroblasts (HTFs) and the anti-angiogenetic role in HUVECs, compared to that of mitomycin C (MMC).

METHODS

The effects of ZD6474 on cell proliferation or migration in TGF-β1-stimulated HTFs and HUVECs were determined, using CCK8 or wound healing assay, respectively. The typical markers of fibrosis in TGF-β1-stimuated HTFs were detected, vimentin by immunofluorescence, α-SMA and snail by western blot. Tube formation was applied to validate the anti-angiogenesis effect in HUVECs following ZD6474 treatment. Furthermore, phosphorylated AKT and mTOR (p-AKT and p-mTOR) were evaluated, compared to the standardized total AKT and mTOR, using western blot.

RESULTS

There was almost no decreased cell viability in HTFs following ZD6474 (≤ 1 μM/mL) treatment, but MMC (> 50 μg/mL) significantly impaired cell viability. ZD6474 significantly inhibited TGF-β1-stimulated proliferation and migration in HTFs, compared to control group (**P < 0.01). ZD6474 also significantly attenuated the TGF-β1-stimulated expression of vimentin, α-SMA and snail in HTFs. Tube formation was notably interrupted in HUVECs following ZD6474 treatment (**P < 0.01). P-AKT and p-mTOR were significantly decreased in response to ZD6474 treatment in TGF-β1- induced HTFs and HUVECs.

CONCLUSIONS

ZD6474 exerts anti-proliferation and anti-fibrotic effects in TGF-β1-stimulated HTFs perhaps via regulating AKT-mTOR signaling pathway. ZD6474 also inhibited proliferation, migration and tube formation in HUVECs via the same signaling pathway. We concluded that ZD6474 may be potentially a novel agent in preventing bleb dysfunction following glaucoma filtration surgery (GFS).

Influence of a Polyherbal Choline Source in Dogs: Body Weight Changes, Blood Metabolites, and Gene Expression

Choline chloride is used to provide choline in dog foods; however, in other domestic species, it has been replaced with a polyherbal containing phosphatidylcholine. A polyherbal containing Achyrantes aspera, Trachyspermum ammi, Citrullus colocynthis, Andrographis paniculata, and Azadirachta indica was evaluated in adult dogs through body weight changes, subcutaneous fat thickness, blood metabolites, and gene expression. Forty dogs (4.6 ± 1.6 years old) who were individually housed in concrete kennels were randomly assigned to the following treatments: unsupplemented diet (377 mg choline/kg), choline chloride (3850 mg/kg equivalent to 2000 mg choline/kg diet), and polyherbal (200, 400, and 800 mg/kg) for 60 days. Blood samples were collected on day 59 for biochemistry, biometry, and gene expression analysis through microarray assays. Intake, final body weight, and weight changes were similar for the two choline sources. Feed intake variation among dogs (p = 0.01) and dorsal fat (p = 0.03) showed a quadratic response to herbal choline. Dogs that received the polyherbal diet had reduced blood cholesterol levels (Quadratic, p = 0.02). The gene ontology analysis indicated that 15 biological processes were modified (p ≤ 0.05) with implications for preventing cardiovascular and metabolic diseases, cancer prevention, inflammatory and immune response, and behavior and cognitive process. According to these results that were observed in a 60 day trial, the polyherbal form could replace choline chloride in dog diets at a concentration of 400 mg/kg.

Identification of Key Genes and Pathways in Persistent Hyperplastic Primary Vitreous of the Eye Using Bioinformatic Analysis

Background: The failure of the embryonic hyaloid vascular system to regress naturally causes persistent hyperplastic primary vitreous (PHPV), a congenital eye disease. PHPVs molecular pathway, candidate genes, and drug targets are unknown. The current paper describes a comprehensive analysis using bioinformatics to identify the key genes and molecular pathways associated with PHPV, and to evaluate potential therapeutic agents for disease management. Methods: The genes associated with PHPV were identified using the pubmed2ensembl text mining platform. GeneCodis was employed to evaluate the Gene Ontology (GO) biological process terms and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways. Search Tool for the Retrieval of Interacting Genes (STRING) constructed a protein-protein interaction (PPI) network from the text mining genes (TMGs) in Cytoscape. The significant modules were clustered using Molecular Complex Detection (MCODE), and the GO and KEGG analysis for the hub genes were analyzed with the Database of Annotation, Visualization and Integrated Discovery (DAVID) tool. ClueGO, CluePedia, and ShinyGo were used to illustrate the functions and pathways of the clustered hub genes in a significant module. The Drug-Gene Interaction database (DGIdb) was used to evaluate drug-gene interactions of the hub genes to identify potential PHPV drug candidates. Results: A total of 50 genes associated with PHPV were identified. Overall, 35 enriched GO terms and 15 KEGG pathways were discovered by the gene functional enrichment analysis. Two gene modules were obtained from the PPI network constructed with 31 nodes with 42 edges using MCODE. We selected 14 hub genes as core candidate genes: TP53, VEGFA, SMAD2, CDKN2A, FOXC, FZD4, LRP5, KDR, FZD5, PAX6, MYCN, NDP, PITX2, and PAX2, primarily associated with camera-type eye morphogenesis, pancreatic cancer, the apoptotic process involved in morphogenesis, and the VEGF receptor signaling pathway. We discovered that 26 Food and Drug Administration (FDA)-approved drugs could target 7 of the 14 hub genes. Conclusions: In conclusion, the results revealed a total of 14 potential genes, 4 major pathways, 7 drug gene targets, and 26 candidate drugs that could provide the basis of novel targeted therapies for targeted treatment and management of PHPV.