Bioinformatics analysis of diabetic retinopathy using functional protein sequences

Rao, Allam Appa; Thota, Hanuman; Gumpeny, Ramachandra Sridhar; Akula, Annapurna; Changalasetty, Suresh Babu; Challa, Siva Reddy; Ravavarapu, Tejaswi; Akula, Siva Prasad; Divakar, C.; Srinivas, Kudipudi; Das, Undurti N.

doi:10.1016/j.mehy.2007.03.033

Cited by 12 publications

(9 citation statements)

References 63 publications

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“…NO can contribute to vasodilatation, increase local blood flow, and decrease vascular resistance in ocular circulation. Studies on humans and animal models have suggested that eNOS plays an essential role in retinal vascular function and disequilibrium in its production can lead to the development of DR [9–11]. The presence of eNOS polymorphisms might contribute to a decreased eNOS activity and a reduced NO level and has been reported to be a potential factor in the pathogenesis and development of DR.…”

Section: Introductionmentioning

confidence: 99%

Association between eNOS 4b/a Polymorphism and the Risk of Diabetic Retinopathy in Type 2 Diabetes Mellitus: A Meta-Analysis

Chen

Ren

et al. 2014

Journal of Diabetes Research

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Many studies have assessed the association between eNOS-4b/a polymorphism and the risk of diabetic retinopathy (DR) among type 2 diabetic subjects. However, the results are inconsistent. In order to derive a more precise estimation of the association, a meta-analysis was conducted. Fifteen studies with 3, 183 cases and 3, 410 controls were enrolled by searching the databases of Pubmed, Embase, China National Knowledge Infrastructure (CNKI), and Chinese Wanfang Database. Summary odds ratios (ORs) with 95% confidence intervals (CIs) were calculated. The main analysis indicated no significant association between eNOS-4b/a polymorphism and the risk of DR in overall population [allelic model: OR = 0.94 (0.79–1.11); additive model: OR = 0.91 (0.73–1.14); recessive model: OR = 1.01 (0.81–1.25); dominant model: OR = 0.91 (0.75–1.09)]. Subgroup analysis by ethnicity also indicated no significant association. In conclusion, the current meta-analysis did not observe any association between the polymorphism of eNOS 4b/a and the risk of DR among type 2 diabetic subjects. However, larger well-designed studies are required to confirm this finding.

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Section: Introductionmentioning

confidence: 99%

Association between eNOS 4b/a Polymorphism and the Risk of Diabetic Retinopathy in Type 2 Diabetes Mellitus: A Meta-Analysis

Chen

Ren

et al. 2014

Journal of Diabetes Research

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“…According to Hernandez C, et al, patients suffering with PDR showed intravitreous cortistatin levels low when compared to non-diabetic patients and higher cortistatin levels in vitreous fluid than in the plasma. No plasma and vitreous cortistatin concentrations relationship suggests a possible role in retinal homeostasis [23,24]. Generally increase in hyperglycemia increases the activity of aldose reductase which in turns set off a series of events which causes enhanced iNOS, VEGF, PIGF, and free radicals expression.…”

Section: Resultsmentioning

confidence: 99%

Identification of Protein Biomarkers for Diabetic Retinopathy using Sequence Mining Techniques

Devarapu¹,

Murali²,

Thota³

2018

J Proteomics Bioinform

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Bioinformatics and sequence mining are the application and development of data mining techniques to solve problems by comprehending biological data. Sequence analysis is the most primitive operation in sequence mining techniques. Modern sequence mining research is specialized in analyzing sequential patterns which are relevant and distinct from one another and utilizing retrieved sequences similarity and distance between different protein sequences can be analyzed. Diabetic retinopathy is the major cause of blindness in individuals mostly adults with diabetes and is it is the common problem of diabetes mellitus across the world. Various research analyses stated that there are many proteins which are found to take part in diabetic retinopathy. In this paper, we have evaluated certain proteins which are closely related with diabetic retinopathy with the help of multiple alignment tool viz. Clustal Omega and obtained a phylogenetic tree of 28 protein sequences gathered from National Center for Biotechnology Information (NCBI). In this work data mining technique called sequence mining plays a significant role in providing phylogram obtained with Neighbor-Joining algorithm. From the phylogenetic tree it was recognized that cortistatin, vitamin-D receptor and somatostatin proteins has close connection with diabetic retinopathy. Molecular docking studies have also been performed which is the most extensively used method for the calculation of protein-ligand interactions. In silico docking studies indicated that four inhibitory compounds i.e. Quercetin, Kaempferol, Naringenin and Melicitrin interact with aldose reductase which also found to have role in diabetic retinopathy. Outcomes infer that techniques intended to standardize cortistatin, vitamin-D receptor and somatostatin activities be of huge advantage and provide benefit in inhibiting diabetic retinopathy.

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“…The activity of eNOS is impaired in T2DM, 17 cardiovascular diseases, and hypertension, 15 while a disequilibrium in eNOS production is also implicated in DR onset. 13,[22][23][24] The eNOS gene is located on chromosome 7q35-36, is composed of 26 exons, and spans 21 kb. 25 The eNOS gene has numerous reported polymorphisms, which may affect NO bioavailability, exerting thus neutral, detrimental or protective effects in acute or chronic vascular diseases.…”

Section: Introductionmentioning

confidence: 99%

The association of T786C and G894T polymorphisms of eNOS gene with diabetic retinopathy in Greece

Gouliopoulos

Siasos

Oikonomou

et al. 2021

European Journal of Ophthalmology

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Purpose To investigate whether eNOS T786C (rs2070744) and G894T (rs1799983) gene polymorphisms are associated with diabetic retinopathy in Greek diabetic patients. Materials 271 patients with type-2 diabetes mellitus participated in our study; 130 suffered from diabetic retinopathy and 141 not. All the patients underwent a complete ophthalmological examination, while clinical and demographic data were assessed. Furthermore, they were genotyped for rs2070744 and rs1799983 single nucleotide polymorphisms of eNOS gene. Results Regarding the clinical and demographic data, no significant differences were detected between the studied groups, except for hemoglobin A1c levels and the frequency of insulin treatment (higher in patients with diabetic retinopathy). The frequency of rs1799983 GT genotype was significantly elevated in patients with diabetic retinopathy (55% vs. 40%, P = 0.011) and was associated with a 2-fold increased risk of developing retinopathy (OR 1.92, 95% CI 1.16–3.17). Furthermore, we demonstrated that the aforementioned genotype was significantly and independently associated with increased odds for retinopathy onset in diabetic subjects (OR 2.23, 95% CI 1.28–3.90, P = 0.005), regardless of the impact of other confounders. Conclusions We documented that rs1799983 GT genotype could be recognized as an independent risk factor of retinopathy in Greek patients with type-2 diabetes mellitus, while no role for rs2070744 polymorphism was identified. Further research in different ethnic groups will clarify the exact association of these polymorphisms with the risk for diabetic retinopathy development.

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Bioinformatics analysis of diabetic retinopathy using functional protein sequences

Cited by 12 publications

References 63 publications

Association between eNOS 4b/a Polymorphism and the Risk of Diabetic Retinopathy in Type 2 Diabetes Mellitus: A Meta-Analysis

Association between eNOS 4b/a Polymorphism and the Risk of Diabetic Retinopathy in Type 2 Diabetes Mellitus: A Meta-Analysis

Identification of Protein Biomarkers for Diabetic Retinopathy using Sequence Mining Techniques

The association of T786C and G894T polymorphisms of eNOS gene with diabetic retinopathy in Greece

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