Unique molecular signatures of microRNAs in ocular fluids and plasma in diabetic retinopathy

MiR-9-3 hypermethylation is associated with stages of diabetic retinopathy

Purpose

To investigate the potential relation between methylation of miR-9-3 and stages of diabetic retinopathy (DR). Additionally, we explored whether miR-9-3 methylation impacts the serum levels of Vascular Endothelial Growth Factor (VEGF).

Methods

A cross-sectional study was conducted with 170 participants with type 2 diabetes, including a control group (n = 64) and a diabetes retinopathy group (n = 106), which was further divided into NPDR (n = 58) and PDR (n = 48) subgroups. Epidemiological, clinical, anthropometric, biochemical ELISA assay were analysed. DNA extracted from leukocytes was used to profile miR-9-3 methylation using PCR-MSP.

Results

MiR-9-3 hypermethylated profile was higher in the DR group (p < 0.001) and PDR subgroup compared to DM2 control group (p < 0.001). The hypermethylated profile in the PDR subgroup was also higher compared to NPDR subgroup (p < 0.001). There was no difference between DM2 control and NPDR group (p = 0.234). Logistic regression showed that miR-9-3 hypermethylation increases the odds of presenting DR (OR: 2.826; p = 0.002) and PDR (OR: 5.472; p < 0.001). In addition, hypermethylation of miR-9-3 in the DR and NPDR subgroup was associated with higher serum VEGF-A levels (p = 0.012 and p = 0.025, respectively).

Conclusion

The methylation profile of the miR-9-3 promoter increases the risk of developing PDR. Higher levels of VEGF-A are associated with miR-9-3 hypermethylated profile in patients in the DR and NPDR stages.

Supplementary Information

The online version contains supplementary material available at 10.1007/s40200-024-01411-9.

miR-92a and integrin expression in fibrovascular membranes in proliferative diabetic retinopathy

Diabetic retinopathy (DR) is a leading cause of vision impairment. The proliferative form of DR (PDR) involves fibrovascular membrane (FVM) formation at the vitreoretinal interface. MicroRNAs (miRNAs) are a class of non-coding RNA molecules that play an important role in gene regulation; a single miRNA could regulate multiple genes. We previously reported that miR-92a, a suppressor of integrins α₅ and α_v, was downregulated in DR. Considering the integrin's role in FVM pathology and the potential involvement of miR-92a in DR, we asked a question whether miR-92a could play a critical role in FVM pathology. We collected the FVM and epiretinal membranes of individuals with PDR and macular pucker (control) undergoing pars plana vitrectomy. The frozen sections of membranes were stained for α₅ and α_vβ₃ integrins. The miR-92a levels were assessed using real-time quantitative PCR. The FVMs of individuals with PDR stained brighter for integrin subunits α₅ and α_vβ₃ compared to the epiretinal membranes of subjects with macular pucker. miR-92a levels were decreased in FVM subjects. In conclusion, our studies demonstrate that miR-92a decrease is associated with an increase in integrins α₅ and α_vβ₃, thus contributing to the inflammatory milieu in PDR.

A 3-miRNA Risk Scoring Signature in Early Diabetic Retinopathy

PURPOSE

The aim of our study was to investigate a comprehensive profile of streptozotocin (STZ)-induced early diabetic retinopathy (DR) mice to identify a risk scoring signature based on micorRNAs (miRNAs) for early DR diagnosis.

METHODS

RNA sequencing was performed to obtain the gene expression profile of retinal pigment epithelium (RPE) in early STZ-induced mice. Differentially expressed genes (DEGs) were determined with log2|fold change (FC)| > 1 and p value < 0.05. Functional analysis was carried out based on gene ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis and the protein-protein interaction (PPI) network. We predicted the potential miRNAs via online tools and ROC curves were then conducted. Three potential miRNAs with AUC > 0.7 were explored via public datasets and a formula was further established to evaluate DR severity.

RESULTS

In total, 298 DEGs (200 up-regulating and 98 down-regulating) were obtained through RNA sequencing. Hsa-miR-26a-5p, hsa-miR-129-2-3p and hsa-miR-217 were three predicted miRNAs with AUC > 0.7, suggesting their potential to distinguish healthy controls from early DR. The formula of DR severity score = 19.257 - 0.004 × hsa-miR-217 + 5.09 × 10^-5 × hsa-miR-26a-5p - 0.003 × hsa-miR-129-2-3p was established based on regression analysis.

CONCLUSIONS

In the present study, we investigated the candidate genes and molecular mechanisms based on RPE sequencing in early DR mice models. Hsa-miR-26a-5p, hsa-miR-129-2-3p and hsa-miR-217 could work as biomarkers for early DR diagnosis and DR severity prediction, which was beneficial for DR early intervention and treatment.

Exosomal miRNA Profiling in Vitreous Humor in Proliferative Diabetic Retinopathy

MicroRNAs (miRNAs) are small noncoding RNAs which mediate some of the pathological mechanisms of diabetic retinopathy. The aim of this study was to identify differentially expressed miRNAs in the vitreal exosomes of proliferative diabetic retinopathy (PDR) patients and non-diabetic controls. Exosomes were extracted from the vitreous samples of 10 PDR patients and 10 controls. The expression of 372 miRNAs was determined using a quantitative polymerase chain reaction (qPCR) panel. We have demonstrated a significant dysregulation in 26 miRNAs. The most remarkable findings include a profound attenuation of the miR-125 family, as well as enhanced miR-21-5p expression in the diabetic samples. We also showed the downregulation of miR-204-5p and the upregulation of let-7g in PDR compared to the controls. This study identified miR-125 and miR-21 as potential targets for further functional analysis regarding their putative role in the pathogenesis of PDR.

IFI44L and C1QTNF5 as promising biomarkers of proliferative diabetic retinopathy

Proliferative diabetic retinopathy (PDR) is a world-wide leading cause of blindness among adults and may be associated with the influence of genetic factors. It is significant to search for genetic biomarkers of PDR. In our study, we collected genomic data about PDR from gene expression omnibus (GEO) database. Differentially expressed gene (DEG) analysis and weighted gene co-expression network analysis (WGCNA) were carried out. The gene module with the highest gene significance (GS) was defined as the key module. Hub genes were identified by Venn diagram. Then we verified the expression of hub genes in validation data sets and built a diagnostic model by least absolute shrinkage and selection operator (LASSO) regression. Enrichment analysis, including gene ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG), gene set enrichment analysis (GSEA) and construction of a protein-protein interaction (PPI) network were conducted. In GSE60436, we identified 466 DEGs. WGCNA established 14 gene modules, and the blue module (GS = 0.64), was the key module. Interferon (IFN)-induced protein 44-like (IFI44L) and complement C1q tumor necrosis factor-related protein 5 (C1QTNF5) were identified as hub genes. The expression of hub genes in GEO datasets was verified and a diagnostic model was constructed by LASSO as follows: index = IFI44L * 0.0432 + C1QTNF5 * 0.11246. IFI44L and C1QTNF5 might affect the disease progression of PDR by regulating metabolism-related and inflammatory pathways. IFI44L and C1QTNF5 may play important roles in the disease process of PDR, and a LASSO regression model suggested that the 2 genes could serve as promising biomarkers of PDR.

Hydrogen Sulfide Improves Angiogenesis by Regulating the Transcription of pri-miR-126 in Diabetic Endothelial Cells

Introduction: Diabetes mellitus results in high rates of cardiovascular disease, such as microcirculation disorder of the lower limbs, with angiogenesis impairment being the main factor. The endothelium functions as a barrier between blood and the vessel wall. Vascular endothelial cell dysfunction caused by hyperglycemia is the main factor leading to angiogenesis impairment. Hydrogen sulfide (H₂S) and miR-126-3p are known for their pro-angiogenesis effects; however, little is known about how H₂S regulates miR-126-3p to promote angiogenesis under high-glucose conditions. Objectives: The main objective of this research was to explore how H₂S regulates the miR-126-3p levels under high-glucose conditions. Methods: We evaluated the pro-angiogenesis effects of H₂S in the diabetic hindlimb of an ischemia mice model and in vivo Matrigel plugs. Two microRNA datasets were used to screen microRNAs regulated by both diabetes and H₂S. The mRNA and protein levels were detected through real-time PCR and Western blot, respectively. Immunofluorescent staining was also used to assess the capillary density and to evaluate the protein levels in vascular endothelial cells. Human umbilical vein endothelial cells (HUVECs) were used in in vitro experiments. A scratch wound-healing assay was applied to detect the migration ability of endothelial cells. Methylated DNA immunoprecipitation combined with real-time PCR was chosen to identify the DNA methylation level in the HUVECs. Results: Exogenous H₂S improved angiogenesis in diabetic mice. miR-126-3p was regulated by both diabetes and H₂S. Exogenous H₂S up-regulated the miR-126-3p level and recovered the migration rate of endothelial cells via down-regulating the DNMT1 protein level, which was increased by high glucose. Furthermore, DNMT1 upregulation in the HUVECs increased the methylation levels of the gene sequences upstream of miR-126-3p and then inhibited the transcription of primary-miR-126, thus decreasing the miR-126-3p level. CSE overexpression in the HUVECs rescued the miR-126-3p level, by decreasing the methylation level to improve migration. Conclusion: H₂S increases the miR-126-3p level through down-regulating the methylation level, by decreasing the DNMT1 protein level induced by high glucose, thus improving the angiogenesis originally impaired by high glucose.

The Correlation Between MicroRNAs and Diabetic Retinopathy

Micro ribonucleic acids (miRNAs), as a category of post-transcriptional gene inhibitors, have a wide range of biological functions, are involved in many pathological processes, and are attractive therapeutic targets. Considerable evidence in ophthalmology indicates that miRNAs play an important role in diabetic retinopathy (DR), especially in inflammation, oxidative stress, and neurodegeneration. Targeting specific miRNAs for the treatment of DR has attracted much attention. This is a review focusing on the pathophysiological roles of miRNAs in DR, diabetic macular edema, and proliferative DR complex multifactorial retinal diseases, with particular emphasis on how miRNAs regulate complex molecular pathways and underlying pathomechanisms. Moreover, the future development potential and application limitations of therapy that targets specific miRNAs for DR are discussed.

Plasma and urinary extracellular vesicle microRNAs and their related pathways in diabetic kidney disease

To explore extracellular vesicle microRNAs (EV miRNAs) and their target mRNAs in relation to diabetic kidney disease (DKD), we performed paired plasma and urinary EV small RNA sequencing (n = 18) in patients with type 2 diabetes and DKD (n = 5) and healthy subjects (n = 4) and metabolic network analyses using our own miRNA and public mRNA datasets. We found 13 common differentially expressed EV miRNAs in both fluids and 17 target mRNAs, including RRM2, NT5E, and UGDH. Because succinate dehydrogenase B was suggested to interact with proteins encoded by these three genes, we measured urinary succinate and adenosine in a validation study (n = 194). These two urinary metabolite concentrations were associated with DKD progression. In addition, renal expressions of NT5E and UGDH proteins were increased in db/db mice with DKD compared to control mice. In conclusion, we profiled DKD-related EV miRNAs in plasma and urine samples and found their relevant target pathways.

Circ_NNT suppresses the apoptosis and inflammation in glucose-induced human retinal pigment epithelium by regulating miR-320b/TIMP3 axis in diabetic retinopathy

BACKGROUND

Diabetic retinopathy (DR) is a frequent complication of diabetes. Recent reports have showed that circular RNAs (circRNAs) play important roles in DR progression. Herein, the aim of this study was to explore the role and molecular mechanism of circ_NNT in DR process.

METHODS

Human retinal pigment epithelial cells ARPE-19 were treated with high glucose (HG) in experimental group. The expression of circ_NNT, miR-320b, and TIMP3 (TIMP Metallopeptidase Inhibitor 3) were determined using quantitative real-time polymerase chain reaction and Western blot. In vitro experiments were conducted by 5-ethynyl-2'-deoxyuridine (EdU) assay, MTT assay, flow cytometry, Western blot, and ELISA. The binding interaction was confirmed using dual-luciferase reporter and pull-down assays.

RESULTS

HG stimulation led to a decrease of circ_NNT and TIMP3 expression, and an increase of miR-320b expression in ARPE-19 cells. Functionally, circ_NNT up-regulation reversed HG-evoked apoptosis and inflammation in ARPE-19 cells. Mechanistically, circ_NNT acted as a sponge for miR-320b to elevate TIMP3 expression. Further rescue experiments showed that miR-320b elevation attenuated the protective effects of circ_NNT on HG-induced ARPE-19 cells. Moreover, inhibition of miR-320b protected ARPE-19 cells against HG-evoked apoptosis and inflammation, which were abolished by TIMP3 knockdown.

CONCLUSION

Circ_NNT protected ARPE-19 cells against HG-evoked apoptosis and inflammation via elevating TIMP3 through sequestering miR-320b, indicating that up-regulation of circ_NNT might contribute to the inhibition of DR process.

Oscillatory Behaviors of microRNA Networks: Emerging Roles in Retinal Development

A broad repertoire of transcription factors and other genes display oscillatory patterns of expression, typically ranging from 30 min to 24 h. These oscillations are associated with a variety of biological processes, including the circadian cycle, somite segmentation, cell cycle, and metabolism. These rhythmic behaviors are often prompted by transcriptional feedback loops in which transcriptional activities are inhibited by their corresponding gene target products. Oscillatory transcriptional patterns have been proposed as a mechanism to drive biological clocks, the molecular machinery that transforms temporal information into accurate spatial patterning during development. Notably, several microRNAs (miRNAs) -small non-coding RNA molecules-have been recently shown to both exhibit rhythmic expression patterns and regulate oscillatory activities. Here, we discuss some of these new findings in the context of the developing retina. We propose that miRNA oscillations are a powerful mechanism to coordinate signaling pathways and gene expression, and that addressing the dynamic interplay between miRNA expression and their target genes could be key for a more complete understanding of many developmental processes.

Decreased Levels of miR-126 and miR-132 in Plasma and Vitreous Humor of Non-Proliferative Diabetic Retinopathy Among Subjects with Type-2 Diabetes Mellitus

PURPOSE

Diabetic retinopathy (DR), the leading cause of blindness among working adults, is an urgent public health problem as diabetes mellitus (DM) is increasing at an alarming rate. Hyperglycemia-induced endothelial dysfunction is the principal contributing factor leading to the development of microangiopathy. Altered levels of microRNA (miR), the negative regulator of protein-coding genes, have been observed and considered to be markers for DR. Present study aimed to find out whether miR levels in plasma could be effective biomarkers to differentiate between type 2 diabetes mellitus (T2DM) with non-proliferative retinopathy (NPDR) from T2DM with no-DR (DNR).

METHODS

We recruited 50 T2DM subjects comprising 31 NPDR and 19 DNR individuals. Surrogate markers of systemic oxidative stress and vascular endothelial growth factor (VEGF) were measured in plasma. Levels of miR-126 and miR-132 were determined in plasma and vitreous fluid using real-time PCR.

RESULTS

We observed that levels of miR-126 and miR-132 were decreased in NPDR subjects in comparison to DNR. Plasma levels of miRs were inversely correlated with secreted levels of VEGF and oxidative stress marker. The levels of these miRs showed discriminating ability between NPDR and DNR.

CONCLUSION

Circulating miRs 126 and 132 in plasma or vitreous may serve as biomarkers for early diabetic retinopathy risk prediction, provided validated in a larger cohort and other forms of retinal vasculopathy or retinopathy in the future.

Relationship between elevated microRNAs and growth factors levels in the vitreous of patients with proliferative diabetic retinopathy

AIM

The aim of this study was to identify differentially expressed microRNAs (miRNAs) in the vitreous of patients with proliferative diabetic retinopathy (PDR) and correlate some of them with growth factors.

METHODS

Vitreous samples were collected from 5 PDR eyes and 5 control eyes, and then miRNAs were assayed with next-generation sequencing (NGS). Three differentially expressed miRNAs were validated in vitreous of another cohort using reverse transcriptase quantitative polymerase chain reaction (RT-qPCR).

RESULTS

Transforming growth factor β (TGF-β) and vascular endothelial growth factor (VEGF) signaling pathway were excavated out through bioinformatic analysis of deregulated miRNAs. The expression of hsa-miR-24-3p, hsa-miR-197-3p and hsa-miR-3184-3p, VEGF-A and TGF-β were confirmed to be significantly higher in the vitreous of PDR eyes than controls(P < 0.05). Furthermore, Pearson's correlation analysis showed significantly positive correlations between these elevated miRNAs and growth factors (P < 0.05).

CONCLUSIONS

Elevated vitreous levels of hsa-miR-24-3p, hsa-miR-197-3p, hsa-miR-3184-3p in PDR patients may play roles in pathophysiology of PDR, the target mRNAs of which significantly enriched in VEGF and TGF-β signaling pathways. Positive correlations between elevated vitreous levels of the three miRNAs and VEGF-A, TGF-β in PDR patients could provide a novel research direction for PDR.

MicroRNA and diabetic retinopathy-biomarkers and novel therapeutics

Diabetic retinopathy (DR) accounts for ~80% of legal blindness in persons aged 20-74 years and is associated with enormous social and health burdens. Current therapies are invasive, non-curative, and in-effective in 15-25% of DR patients. This review outlines the potential utility of microRNAs (miRNAs) as biomarkers and potential therapy for diabetic retinopathy. miRNAs are small noncoding forms of RNA that may play a role in the pathogenesis of DR by altering the level of expression of genes via single nucleotide polymorphism and regulatory loops. A majority of miRNAs are intracellular and specific intracellular microRNAs have been associated with cellular changes associated with DR. Some microRNAs are extracellular and called circulatory microRNAs. Circulatory miRNAs have been found to be differentially expressed in serum and bodily fluid in patients with diabetes mellitus (DM) with and without retinopathy. Some miRNAs have been associated with the severity of DR, and future studies may reveal whether circulatory miRNAs could serve as novel reliable biomarkers to detect or predict retinopathy progression. Therapeutic strategies can be developed utilizing the natural miRNA/long noncoding RNA (lncRNA) regulatory loops. miRNAs and lncRNAs are two major families of the non-protein-coding transcripts. They are regulatory molecules for fundamental cellular processes via a variety of mechanisms, and their expression and function are tightly regulated. The recent evidence indicates a cross-talk between miRNAs and lncRNAs. Therefore, dysregulation of miRNAs and lncRNAs is critical to human disease pathogenesis, such as diabetic retinopathy. miRNAs are long-distance communicators and reprogramming agents, and they embody an entirely novel paradigm in cellular and tissue signaling and interaction. By targeting specific miRNAs, whole pathways implicated in the pathogenesis of DR may potentially be altered. Understanding the endogenous roles of miRNAs in the pathogenesis of diabetic retinopathy could lead to novel diagnostic and therapeutic approaches to managing this frequently blinding retinal condition.

MicroRNA-93-5p participates in type 2 diabetic retinopathy through targeting Sirt1

OBJECTIVE

To investigate the role of miR-93-5p in rats with type 2 diabetic retinopathy (DR) through targeting Sirt1.

METHODS

The targeting correlation between miR-93-5p and Sirt1 was validated by dual-luciferase reporter gene assay. Type 2 diabetes mellitus (T2DM) rat models were received intravitreal injection of antagomir NC (negative control), miR-93-5p antagomir, miR-93-5p agomir and/or recombinant Sirt1, followed by observation of pathological changes in retina via HE staining. Besides, retinal vascular permeability was determined by fluorescein isothiocyanate-bovine serum albumin (FITC-BSA), while the retinal vasculature was observed through retinal trypsin digestion. Expression of miR-93-5p and Sirt1 was measured by qRT-PCR and Western blotting, while the levels of VEGF, proinflammatory cytokines and anti-oxidative indicators were determined using corresponding kits.

RESULTS

MiR-93-5p could target Sirt1 as analyzed by the luciferase reporter gene assay. Rats in the T2DM group presented the up-regulation of miR-93-5p and down-regulation of Sirt1 in the retina, and miR-93-5p inhibition could up-regulate Sirt1 expression in the T2DM rats. Recombinant Sirt1 decreased retinal vascular permeability and acellular capillaries with improved pathological changes in retina from T2DM rats, which was abolished by miR-93-5p agomir. Moreover, miR-93-5p inhibition or Sirt1 overexpression decreased the levels of VEGF and proinflammatory cytokines while enhancing the activity of anti-oxidative indicators. However, indicators above had no significant differences between T2DM group and T2DM + agomir + Sirt1 group.

CONCLUSION

MiR-93-5p, via targeting Sirt1, could affect the vascular permeability and acellular capillaries and mitigate the inflammation and oxidative stress in the retinas, which may play a critical role in DR.

Recent Highlights of Research on miRNAs as Early Potential Biomarkers for Cardiovascular Complications of Type 2 Diabetes Mellitus

Type 2 diabetes mellitus (T2DM) and its complications pose a serious threat to the life and health of patients around the world. The most dangerous complications of this disease are vascular complications. Microvascular complications of T2DM include retinopathy, nephropathy, and neuropathy. In turn, macrovascular complications include coronary artery disease, peripheral artery disease, and cerebrovascular disease. The currently used diagnostic methods do not ensure detection of the disease at an early stage, and they also do not predict the risk of developing specific complications. MicroRNAs (miRNAs) are small, endogenous, noncoding molecules that are involved in key processes, such as cell proliferation, differentiation, and apoptosis. Recent research has assigned them an important role as potential biomarkers for detecting complications related to diabetes. We suggest that utilizing miRNAs can be a routine approach for early diagnosis and prognosis of diseases and may enable the development of better therapeutic approaches. In this paper, we conduct a review of the latest reports demonstrating the usefulness of miRNAs as biomarkers in the vascular complications of T2DM.

Integrative Computational Approach Revealed Crucial Genes Associated With Different Stages of Diabetic Retinopathy

The increased incidence of diabetic retinopathy (DR) and the legacy effect associated with it has raised a great concern toward the need to find early diagnostic and treatment strategies. Identifying alterations in genes and microRNAs (miRNAs) is one of the most critical steps toward understanding the mechanisms by which a disease progresses, and this can be further used in finding potential diagnostic and prognostic biomarkers and treatment methods. We selected different datasets to identify altered genes and miRNAs. The integrative analysis was employed to find potential candidate genes (differentially expressed and aberrantly methylated genes that are also the target of altered miRNAs) and early genes (genes showing altered expression and methylation pattern during early stage of DR) for DR. We constructed a protein-protein interaction (PPI) network to find hub genes (potential candidate genes showing a greater number of interactions) and modules. Gene ontologies and pathways associated with the identified genes were analyzed to determine their role in DR progression. A total of 271 upregulated-hypomethylated genes, 84 downregulated-hypermethylated genes, 11 upregulated miRNA, and 30 downregulated miRNA specific to DR were identified. 40 potential candidate genes and 9 early genes were also identified. PPI network analysis revealed 7 hub genes (number of interactions >5) and 1 module (score = 5.67). Gene ontology and pathway analysis predicted enrichment of genes in oxidoreductase activity, binding to extracellular matrix, immune responses, leukocyte migration, cell adhesion, PI3K-Akt signaling pathway, ECM receptor interaction, etc., and thus their association with DR pathogenesis. In conclusion, we identified 7 hub genes and 9 early genes that could act as a potential prognostic, diagnostic, or therapeutic target for DR, and a few early genes could also play a role in metabolic memory phenomena.