Applications of bioinformatics methods in ocular fundus diseases_Chinese Journal of Ocular Fundus Diseases

Authors：

Zhang Hui , Dong Lijie , Wang Qiong , Hong Yaru ,  Li Xiaorong

Tianjin Key Laboratory of Retinal Functions and Diseases, Tianjin International Joint Research and Development Centre of Ophthalmology and Vision Science, Eye Institute and School of Optometry, Tianjin Medical University Eye Hospital, Tianjin 300384, China;

Corresponding author：

Li Xiaorong, Email: xiaorli@163.com

Keywords：

Genomics; Transcriptome; Proteomics; Metabolomics; Retinal diseases; Review

DOI：

10.3760/cma.j.cn511434-20181203-00412

Video：

Export PDF Favorites Scan Get Citation

Abstract Full text Figures/Tables Video References Cited by

With the development of life sciences and informatics, bioinformatics is developing as an interdisciplinary subject. Its main application is the relationship between genes and proteins and their expression. With the help of genomics, proteomics, transcriptomics, and metabolomics, researchers introduce bioinformatics research methods into fundus disease research. A series of gratifying research results have been achieved including the screening of genetic susceptibility genes, the screening of diagnostic markers, and the exploration of pathogenesis. Genomics has the characteristics of high efficiency and accuracy. It has been used to detect new mutation sites in retinoblastoma and retinal pigment degeneration research, which helps to further improve the pathogenesis of retinal genetic diseases. Transcriptomics, proteomics, and metabolomics have high throughput characteristics. They are used to analyze changes in the expression profiles of RNA, proteins, and metabolites in intraocular fluid or isolated cells in disease states, which help to screen biomarkers and further elucidate the pathogenesis. With the advancement of technology, bioinformatics will provide new ideas for the study of ocular fundus diseases.

Citation： Zhang Hui, Dong Lijie, Wang Qiong, Hong Yaru, Li Xiaorong. Applications of bioinformatics methods in ocular fundus diseases. Chinese Journal of Ocular Fundus Diseases, 2020, 36(7): 570-575. doi: 10.3760/cma.j.cn511434-20181203-00412 Copy

1.	刘爱华, 王礼明, 吕瀛娟, 等. 原发性开角型青光眼房水差异表达蛋白分析[J]. 中华实验眼科杂志, 2019, 37(10): 799-806. DOI: 10.3760/cma.j.issn.2095-0160.2019.10.007.Liu AH, Wang LM, Lyu YJ, et al. Analysis of different proteins in primary open angle glaucoma based on aqueous proteome[J]. Chin J Exp Ophthalmol, 2019, 37(10): 799-806. DOI: 10.3760/cma.j.issn.2095-0160.2019.10.007.
2.	王礼明, 东莉洁, 刘勋, 等. 急性原发性闭角型青光眼急性发作期房水蛋白质组学分析[J]. 中华眼科杂志, 2019, 55(9): 687-694. DOI: 10.3760/cma.j.issn.0412-4081.2019.09.011.Wang LM, Dong LJ, Liu X, et al. Proteomic analysis of aqueous humor in acute primary angle-closure glaucoma[J]. Chin J Ophthalmol, 2019, 55(9): 687-694. DOI: 10.3760/cma.j.issn.0412-4081.2019.09.011.
3.	温德佳, 任新军, 东莉洁, 等. 应用iTRAQ蛋白组技术筛选增生性糖尿病视网膜病变防治靶点的研究[J]. 中华眼科杂志, 2019, 55(10): 769-776. DOI: 10.3760/cma.j.issn.0412-4081.2019.10.008.Wen DJ, Ren XJ, Dong LJ, et al. New exploration of treatment target for proliferative diabetic retinopathy based on iTRAQ LC-MS/MS Proteomics[J]. Chin J Ophthalmol, 2019, 55(10): 769-776. DOI: 10.3760/cma.j.issn.0412-4081.2019.10.008.
4.	Li J, Lu Q, Lu P. Quantitative proteomics analysis of vitreous body from type 2 diabetic patients with proliferative diabetic retinopathy[J]. BMC Ophthalmol, 2018, 18(1): 151. DOI: 10.1186/s12886-018-0821-3.
5.	Zhang L, Du J, Justus S, et al. Reprogramming metabolism by targeting sirtuin 6 attenuates retinal degeneration[J]. J Clin Invest, 2016, 126(12): 4659-4673. DOI: 10.1172/jci86905.
6.	薄其玉, 东莉洁, 张琰, 等. 氧诱导视网膜病变小鼠模型微小RNA表达谱分析[J]. 中华眼底病杂志, 2015, 31(1): 77-82. DOI: 10.3760/cma.j.issn.1005-1015.2015.01.019.Bo QY, Dong LJ, Zhang Y, et al. MicroRNA expression profiling in a mouse model of oxygen-induced retinopathy[J]. Chin J Ocul Fundus Dis, 2015, 31(1): 77-82. DOI: 10.3760/cma.j.issn.1005-1015.2015.01.019.
7.	牛瑞, 东莉洁, 马腾, 等. 抗血管内皮生长因子药物治疗后视网膜血管内皮细胞基因表达谱的RNA-Seq分析[J]. 中华眼底病杂志, 2018, 34(3): 275-280. DOI: 10.3760/cma.j.issn.1005-1015.2018.03.016.Niu R, Dong LJ, Ma T, et al. RNA-Seq analysis of gene expression profiling in human retinal vascular endothelial cells after anti-vascular endothecial growth factor treatment[J]. Chin J Ocul Fundus Dis, 2018, 34(3): 275-280. DOI: 10.3760/cma.j.issn.1005-1015.2018.03.016.
8.	Ewens KG, Bhatti TR, Moran KA, et al. Phosphorylation of pRb: mechanism for RB pathway inactivation in MYCN-amplified retinoblastoma[J]. Cancer Med, 2017, 6(3): 619-630. DOI: 10.1002/cam4.1010.
9.	张哲, 刘巨平, 东莉洁, 等. 高糖状态下视网膜血管内皮细胞基因表达谱的RNA-Seq分析[J]. 中华眼底病杂志, 2018, 34(4): 377-381. DOI: 10.3760/cma.j.issn.1005-1015.2018.04.014.Zhang Z, Liu JP, Dong LJ, et al. RNA-Seq analysis of gene expression profiling in retinal vascular endothelial cells under high glucose condition[J]. Chin J Ocul Fundus Dis, 2018, 34(4): 377-381. DOI: 10.3760/cma.j.issn.1005-1015.2018.04.014.
10.	张丽娟, 张琰, 东莉洁, 等. MicroRNA在眼部的表达及其功能[J]. 中华眼科杂志, 2012, 48(12): 1136-1140. DOI: 10.3760/cma.j.issn.0412-4081.2012.12.023.Zhang LJ, Zhang J, Dong LJ, et al. MicroRNA expression and its function in eyes[J]. Chin J Ophthalmol, 2012, 48(12): 1136-1140. DOI: 10.3760/cma.j.issn.0412-4081.2012.12.023.
11.	Wang Z, Gerstein M, Snyder M. RNA-Seq: a revolutionary tool for transcriptomics[J]. Nat Rev Genet, 2009, 10(1): 57-63. DOI: 10.1038/nrg2484.
12.	Hawkins RD, Hon GC, Ren B. Next-generation genomics: an integrative approach[J]. Nat Rev Genet, 2010, 11(7): 476-486. DOI: 10.1038/nrg2795.
13.	Liang Q, Dharmat R, Owen L, et al. Single-nuclei RNA-seq on human retinal tissue provides improved transcriptome profiling[J]. Nat Commun, 2019, 10(1): 5743. DOI: 10.1038/s41467-019-12917-9.
14.	Benavente CA, Dyer MA. Genetics and epigenetics of human retinoblastoma[J]. Annu Rev Pathol, 2015, 10: 547-562. DOI: 10.1146/annurev-pathol-012414-040259.
15.	Felsher DW. Role of MYCN in retinoblastoma[J]. Lancet Oncol, 2013, 14(4): 270-271. DOI: 10.1016/s1470-2045(13)70070-6.
16.	Wu N, Jia D, Bates B, et al. A mouse model of MYCN-driven retinoblastoma reveals MYCN-independent tumor reemergence[J]. J Clin Invest, 2017, 127(3): 888-898. DOI: 10.1172/jci88508.
17.	Hauser S, Kogej M, Fechner G, et al. Cell-free serum DNA in patients with bladder cancer: results of a prospective multicenter study[J]. Anticancer Res, 2012, 32(8): 3119-3124. DOI: 10.1038/onc.2011.550.
18.	Berry JL, Xu L, Murphree AL, et al. Potential of aqueous humor as a surrogate tumor biopsy for retinoblastoma[J]. JAMA Ophthalmol, 2017, 135(11): 1221-1230. DOI: 10.1001/jamaophthalmol.2017.4097.
19.	Liang Z, Gao KP, Wang YX, et al. RNA sequencing identified specific circulating miRNA biomarkers for early detection of diabetes retinopathy[J]. Am J Physiol Endocrinol Metab, 2018, 315(3): 374-385. DOI: 10.1152/ajpendo.00021.2018.
20.	Pan J, Liu S, Farkas M, et al. Serum molecular signature for proliferative diabetic retinopathy in Saudi patients with type 2 diabetes[J]. Mol Vis, 2016, 22: 636-645.
21.	Csősz É, Deák E, Kalló G, et al. Diabetic retinopathy: proteomic approaches to help the differential diagnosis and to understand the underlying molecular mechanisms[J]. J Proteomics, 2017, 150: 351-358. DOI: 10.1016/j.jprot.2016.06.034.
22.	牛瑞, 东莉洁, 杜雪利, 等. 卵泡抑素样蛋白1在增生型糖尿病视网膜病变进程中的潜在作用机制初步探讨[J]. 中华眼底病杂志, 2020, 36(3): 220-226. DOI: 10.3760/cma.j.cn511434-20190115-00024.Niu R, Dong LJ, Du XL, et al. A preliminary study on the potential mechanism of follicle inhibin-like protein 1 in the process of proliferative diabetic retinopathy[J]. Chin J Ocul Fundus Dis, 2020, 36(3): 220-226. DOI: 10.3760/cma.j.cn511434-20190115-00024.
23.	Csősz É, Boross P, Csutak A, et al. Quantitative analysis of proteins in the tear fluid of patients with diabetic retinopathy[J]. J Proteomics, 2012, 75(7): 2196-2204. DOI: 10.1016/j.jprot.2012.01.019.
24.	Tsybikov NN, Shovdra OL, Prutkina EV. The levels of endothelin, neuron-specific enolase, and their autoantibodies in the serum and tear fluid of patients with type 2 diabetes mellitus[J]. Vestn Oftalmol, 2010, 126(4): 14-16.
25.	Grigsby JG, Cardona SM, Pouw CE, et al. The role of microglia in diabetic retinopathy[J/OL]. J Ophthalmol, 2014, 2014: 705783[2014-08-31]. http://europepmc.org/article/MED/25258680. DOI: 10.1155/2014/705783.
26.	Vujosevic S, Micera A, Bini S, et al. Proteome analysis of retinal glia cells-related inflammatory cytokines in the aqueous humour of diabetic patients[J]. Acta Ophthalmol, 2016, 94(1): 56-64. DOI: 10.1111/aos.12812.
27.	Ben M'Barek K, Regent F, Monville C. Use of human pluripotent stem cells to study and treat retinopathies[J]. World J Stem Cells, 2015, 7(3): 596-604. DOI: 10.4252/wjsc.v7.i3.596.
28.	van Lookeren Campagne M, LeCouter J, Yaspan BL, et al. Mechanisms of age-related macular degeneration and therapeutic opportunities[J]. J Pathol, 2014, 232(2): 151-164. DOI: 10.1002/path.4266.
29.	Whitmore SS, Braun TA, Skeie JM, et al. Altered gene expression in dry age-related macular degeneration suggests early loss of choroidal endothelial cells[J]. Mol Vis, 2013, 19: 2274-2297.
30.	Ashikawa Y, Nishimura Y, Okabe S, et al. Potential protective function of the sterol regulatory element binding factor 1-fatty acid desaturase 1/2 axis in early-stage age-related macular degeneration[J/OL]. Heliyon, 2017, 3(3): 00266[2017-03-01]. https://linkinghub.elsevier.com/retrieve/pii/S2405-8440(16)31797-2. DOI: 10.1016/j.heliyon.2017.e00266.
31.	Seddon JM, McLeod DS, Bhutto IA, et al. Histopathological insights into choroidal vascular loss in clinically documented cases of age-related macular degeneration[J]. JAMA Ophthalmol, 2016, 134(11): 1272-1280. DOI: 10.1001/jamaophthalmol.2016.3519.
32.	Sohn EH, Flamme-Wiese MJ, Whitmore SS, et al. Loss of CD34 expression in aging human choriocapillaris endothelial cells[J/OL]. PLoS One, 2014, 9(1): 86538[2014-01-21]. http://europepmc.org/article/MED/24466138. DOI: 10.1371/journal.pone.0086538.
33.	Mullins RF, Johnson MN, Faidley EA, et al. Choriocapillaris vascular dropout related to density of drusen in human eyes with early age-related macular degeneration[J]. Invest Ophthalmol Vis Sci, 2011, 52(3): 1606-1612. DOI: 10.1167/iovs.10-6476.
34.	Songstad AE, Worthington KS, Chirco KR, et al. Connective tissue growth factor promotes efficient generation of human induced pluripotent stem cell-derived choroidal endothelium[J]. Stem Cells Transl Med, 2017, 6(6): 1533-1546. DOI: 10.1002/sctm.16-0399.
35.	Crabb JW, Miyagi M, Gu X, et al. Drusen proteome analysis: an approach to the etiology of age-related macular degeneration[J]. Proc Natl Acad Sci USA, 2002, 99(23): 14682-14687. DOI: 10.1073/pnas.222551899.
36.	Yuan X, Gu X, Crabb JS, et al. Quantitative proteomics: comparison of the macular Bruch membrane/choroid complex from age-related macular degeneration and normal eyes[J]. Mol Cell Proteomics, 2010, 9(6): 1031-1046. DOI: 10.1074/mcp.M900523-MCP200.
37.	Kim TW, Kang JW, Ahn J, et al. Proteomic analysis of the aqueous humor in age-related macular degeneration (AMD) patients[J]. J Proteome Res, 2012, 11(8): 4034-4043. DOI: 10.1021/pr300080s.
38.	Koss MJ, Hoffmann J, Nguyen N, et al. Proteomics of vitreous humor of patients with exudative age-related macular degeneration[J/OL]. PLoS One, 2014, 9(5): 96895[2014-05-14]. http://europepmc.org/article/MED/24828575. DOI: 10.1371/journal.pone.0096895.
39.	Nobl M, Reich M, Dacheva I, et al. Proteomics of vitreous in neovascular age-related macular degeneration[J]. Exp Eye Res, 2016, 146: 107-117. DOI: 10.1016/j.exer.2016.01.001.
40.	Laíns I, Gantner M, Murinello S, et al. Metabolomics in the study of retinal health and disease[J]. Prog Retin Eye Res, 2019, 69: 57-79. DOI: 10.1016/j.preteyeres.2018.11.002.
41.	Qin L, Mroczkowska SA, Ekart A, et al. Patients with early age-related macular degeneration exhibit signs of macro-and micro-vascular disease and abnormal blood glutathione levels[J]. Graefe’s Arch Clin Exp Ophthalmol, 2014, 252(1): 23-30. DOI: 10.1007/s00417-013-2418-0.
42.	Ates O, Azizi S, Alp HH, et al. Decreased serum paraoxonase 1 activity and increased serum homocysteine and malondialdehyde levels in age-related macular degeneration[J]. Tohoku J Exp Med, 2009, 217(1): 17-22. DOI: 10.1620/tjem.217.17.
43.	Bramall AN, Wright AF, Jacobson SG, et al. The genomic, biochemical, and cellular responses of the retina in inherited photoreceptor degenerations and prospects for the treatment of these disorders[J]. Annu Rev Neurosci, 2010, 33: 441-472. DOI: 10.1146/annurev-neuro-060909-153227.
44.	de Bruijn SE, Verbakel SK, de Vrieze E, et al. Homozygous variants in KIAA1549, encoding a ciliary protein, are associated with autosomal recessive retinitis pigmentosa[J]. J Med Genet, 2018, 55(10): 705-712. DOI: 10.1136/jmedgenet-2018-105364.
45.	Pomares E, Riera M, Permanyer J, et al. Comprehensive SNP-chip for retinitis pigmentosa-Leber congenital amaurosis diagnosis: new mutations and detection of mutational founder effects[J]. Eur J Hum Genet, 2010, 18(1): 118-124. DOI: 10.1038/ejhg.2009.114.
46.	Simpson DA, Clark GR, Alexander S, et al. Molecular diagnosis for heterogeneous genetic diseases with targeted high-throughput DNA sequencing applied to retinitis pigmentosa[J]. J Med Genet, 2011, 48(3): 145-151. DOI: 10.1136/jmg.2010.083568.
47.	Srilekha S, Arokiasamy T, Srikrupa NN, et al. Homozygosity Mapping in leber congenital amaurosis and autosomal recessive retinitis pigmentosa in South Indian families[J/OL]. PLoS One, 2015, 10(7): 0131679[2015-07-06]. http://europepmc.org/article/MED/26147992. DOI: 10.1371/journal.pone.0131679.
48.	Wang Y, Guo L, Cai SP, et al. Exome sequencing identifies compound heterozygous mutations in CYP4V2 in a pedigree with retinitis pigmentosa[J/OL]. PLoS One, 2012, 7(5): 33673[2012-05-31]. http://europepmc.org/article/MED/22693542. DOI: 10.1371/journal.pone.0033673.
49.	Huang H, Chen Y, Chen H, et al. Systematic evaluation of a targeted gene capture sequencing panel for molecular diagnosis of retinitis pigmentosa[J/OL]. PLoS One, 2018, 13(4): 0185237[2018-04-11]. http://europepmc.org/article/MED/29641573. DOI: 10.1371/journal.pone.0185237.
50.	Yang HJ, Ratnapriya R, Cogliati T, et al. Vision from next generation sequencing: multi-dimensional genome-wide analysis for producing gene regulatory networks underlying retinal development, aging and disease[J]. Prog Retin Eye Res, 2015, 46: 1-30. DOI: 10.1016/j.preteyeres.2015.01.005.
51.	Carrigan M, Duignan E, Malone CP, et al. Panel-based population next-generation sequencing for inherited retinal degenerations[J/OL]. Sci Rep, 2016, 6: 33248[2016-09-14]. http://europepmc.org/article/MED/27624628. DOI: 10.1038/srep33248.
52.	Uren PJ, Lee JT, Doroudchi MM, et al. A profile of transcriptomic changes in the rd10 mouse model of retinitis pigmentosa[J]. Mol Vis, 2014, 20: 1612-1628.
53.	Chen Y, Brooks MJ, Gieser L, et al. Transcriptome profiling of NIH3T3 cell lines expressing opsin and the P23H opsin mutant identifies candidate drugs for the treatment of retinitis pigmentosa[J]. Pharmacol Res, 2017, 115: 1-13. DOI: 10.1016/j.phrs.2016.10.031.

1. 刘爱华, 王礼明, 吕瀛娟, 等. 原发性开角型青光眼房水差异表达蛋白分析[J]. 中华实验眼科杂志, 2019, 37(10): 799-806. DOI: 10.3760/cma.j.issn.2095-0160.2019.10.007.Liu AH, Wang LM, Lyu YJ, et al. Analysis of different proteins in primary open angle glaucoma based on aqueous proteome[J]. Chin J Exp Ophthalmol, 2019, 37(10): 799-806. DOI: 10.3760/cma.j.issn.2095-0160.2019.10.007.
2. 王礼明, 东莉洁, 刘勋, 等. 急性原发性闭角型青光眼急性发作期房水蛋白质组学分析[J]. 中华眼科杂志, 2019, 55(9): 687-694. DOI: 10.3760/cma.j.issn.0412-4081.2019.09.011.Wang LM, Dong LJ, Liu X, et al. Proteomic analysis of aqueous humor in acute primary angle-closure glaucoma[J]. Chin J Ophthalmol, 2019, 55(9): 687-694. DOI: 10.3760/cma.j.issn.0412-4081.2019.09.011.
3. 温德佳, 任新军, 东莉洁, 等. 应用iTRAQ蛋白组技术筛选增生性糖尿病视网膜病变防治靶点的研究[J]. 中华眼科杂志, 2019, 55(10): 769-776. DOI: 10.3760/cma.j.issn.0412-4081.2019.10.008.Wen DJ, Ren XJ, Dong LJ, et al. New exploration of treatment target for proliferative diabetic retinopathy based on iTRAQ LC-MS/MS Proteomics[J]. Chin J Ophthalmol, 2019, 55(10): 769-776. DOI: 10.3760/cma.j.issn.0412-4081.2019.10.008.
4. Li J, Lu Q, Lu P. Quantitative proteomics analysis of vitreous body from type 2 diabetic patients with proliferative diabetic retinopathy[J]. BMC Ophthalmol, 2018, 18(1): 151. DOI: 10.1186/s12886-018-0821-3.
5. Zhang L, Du J, Justus S, et al. Reprogramming metabolism by targeting sirtuin 6 attenuates retinal degeneration[J]. J Clin Invest, 2016, 126(12): 4659-4673. DOI: 10.1172/jci86905.
6. 薄其玉, 东莉洁, 张琰, 等. 氧诱导视网膜病变小鼠模型微小RNA表达谱分析[J]. 中华眼底病杂志, 2015, 31(1): 77-82. DOI: 10.3760/cma.j.issn.1005-1015.2015.01.019.Bo QY, Dong LJ, Zhang Y, et al. MicroRNA expression profiling in a mouse model of oxygen-induced retinopathy[J]. Chin J Ocul Fundus Dis, 2015, 31(1): 77-82. DOI: 10.3760/cma.j.issn.1005-1015.2015.01.019.
7. 牛瑞, 东莉洁, 马腾, 等. 抗血管内皮生长因子药物治疗后视网膜血管内皮细胞基因表达谱的RNA-Seq分析[J]. 中华眼底病杂志, 2018, 34(3): 275-280. DOI: 10.3760/cma.j.issn.1005-1015.2018.03.016.Niu R, Dong LJ, Ma T, et al. RNA-Seq analysis of gene expression profiling in human retinal vascular endothelial cells after anti-vascular endothecial growth factor treatment[J]. Chin J Ocul Fundus Dis, 2018, 34(3): 275-280. DOI: 10.3760/cma.j.issn.1005-1015.2018.03.016.
8. Ewens KG, Bhatti TR, Moran KA, et al. Phosphorylation of pRb: mechanism for RB pathway inactivation in MYCN-amplified retinoblastoma[J]. Cancer Med, 2017, 6(3): 619-630. DOI: 10.1002/cam4.1010.
9. 张哲, 刘巨平, 东莉洁, 等. 高糖状态下视网膜血管内皮细胞基因表达谱的RNA-Seq分析[J]. 中华眼底病杂志, 2018, 34(4): 377-381. DOI: 10.3760/cma.j.issn.1005-1015.2018.04.014.Zhang Z, Liu JP, Dong LJ, et al. RNA-Seq analysis of gene expression profiling in retinal vascular endothelial cells under high glucose condition[J]. Chin J Ocul Fundus Dis, 2018, 34(4): 377-381. DOI: 10.3760/cma.j.issn.1005-1015.2018.04.014.
10. 张丽娟, 张琰, 东莉洁, 等. MicroRNA在眼部的表达及其功能[J]. 中华眼科杂志, 2012, 48(12): 1136-1140. DOI: 10.3760/cma.j.issn.0412-4081.2012.12.023.Zhang LJ, Zhang J, Dong LJ, et al. MicroRNA expression and its function in eyes[J]. Chin J Ophthalmol, 2012, 48(12): 1136-1140. DOI: 10.3760/cma.j.issn.0412-4081.2012.12.023.
11. Wang Z, Gerstein M, Snyder M. RNA-Seq: a revolutionary tool for transcriptomics[J]. Nat Rev Genet, 2009, 10(1): 57-63. DOI: 10.1038/nrg2484.
12. Hawkins RD, Hon GC, Ren B. Next-generation genomics: an integrative approach[J]. Nat Rev Genet, 2010, 11(7): 476-486. DOI: 10.1038/nrg2795.
13. Liang Q, Dharmat R, Owen L, et al. Single-nuclei RNA-seq on human retinal tissue provides improved transcriptome profiling[J]. Nat Commun, 2019, 10(1): 5743. DOI: 10.1038/s41467-019-12917-9.
14. Benavente CA, Dyer MA. Genetics and epigenetics of human retinoblastoma[J]. Annu Rev Pathol, 2015, 10: 547-562. DOI: 10.1146/annurev-pathol-012414-040259.
15. Felsher DW. Role of MYCN in retinoblastoma[J]. Lancet Oncol, 2013, 14(4): 270-271. DOI: 10.1016/s1470-2045(13)70070-6.
16. Wu N, Jia D, Bates B, et al. A mouse model of MYCN-driven retinoblastoma reveals MYCN-independent tumor reemergence[J]. J Clin Invest, 2017, 127(3): 888-898. DOI: 10.1172/jci88508.
17. Hauser S, Kogej M, Fechner G, et al. Cell-free serum DNA in patients with bladder cancer: results of a prospective multicenter study[J]. Anticancer Res, 2012, 32(8): 3119-3124. DOI: 10.1038/onc.2011.550.
18. Berry JL, Xu L, Murphree AL, et al. Potential of aqueous humor as a surrogate tumor biopsy for retinoblastoma[J]. JAMA Ophthalmol, 2017, 135(11): 1221-1230. DOI: 10.1001/jamaophthalmol.2017.4097.
19. Liang Z, Gao KP, Wang YX, et al. RNA sequencing identified specific circulating miRNA biomarkers for early detection of diabetes retinopathy[J]. Am J Physiol Endocrinol Metab, 2018, 315(3): 374-385. DOI: 10.1152/ajpendo.00021.2018.
20. Pan J, Liu S, Farkas M, et al. Serum molecular signature for proliferative diabetic retinopathy in Saudi patients with type 2 diabetes[J]. Mol Vis, 2016, 22: 636-645.
21. Csősz É, Deák E, Kalló G, et al. Diabetic retinopathy: proteomic approaches to help the differential diagnosis and to understand the underlying molecular mechanisms[J]. J Proteomics, 2017, 150: 351-358. DOI: 10.1016/j.jprot.2016.06.034.
22. 牛瑞, 东莉洁, 杜雪利, 等. 卵泡抑素样蛋白1在增生型糖尿病视网膜病变进程中的潜在作用机制初步探讨[J]. 中华眼底病杂志, 2020, 36(3): 220-226. DOI: 10.3760/cma.j.cn511434-20190115-00024.Niu R, Dong LJ, Du XL, et al. A preliminary study on the potential mechanism of follicle inhibin-like protein 1 in the process of proliferative diabetic retinopathy[J]. Chin J Ocul Fundus Dis, 2020, 36(3): 220-226. DOI: 10.3760/cma.j.cn511434-20190115-00024.
23. Csősz É, Boross P, Csutak A, et al. Quantitative analysis of proteins in the tear fluid of patients with diabetic retinopathy[J]. J Proteomics, 2012, 75(7): 2196-2204. DOI: 10.1016/j.jprot.2012.01.019.
24. Tsybikov NN, Shovdra OL, Prutkina EV. The levels of endothelin, neuron-specific enolase, and their autoantibodies in the serum and tear fluid of patients with type 2 diabetes mellitus[J]. Vestn Oftalmol, 2010, 126(4): 14-16.
25. Grigsby JG, Cardona SM, Pouw CE, et al. The role of microglia in diabetic retinopathy[J/OL]. J Ophthalmol, 2014, 2014: 705783[2014-08-31]. http://europepmc.org/article/MED/25258680. DOI: 10.1155/2014/705783.
26. Vujosevic S, Micera A, Bini S, et al. Proteome analysis of retinal glia cells-related inflammatory cytokines in the aqueous humour of diabetic patients[J]. Acta Ophthalmol, 2016, 94(1): 56-64. DOI: 10.1111/aos.12812.
27. Ben M'Barek K, Regent F, Monville C. Use of human pluripotent stem cells to study and treat retinopathies[J]. World J Stem Cells, 2015, 7(3): 596-604. DOI: 10.4252/wjsc.v7.i3.596.
28. van Lookeren Campagne M, LeCouter J, Yaspan BL, et al. Mechanisms of age-related macular degeneration and therapeutic opportunities[J]. J Pathol, 2014, 232(2): 151-164. DOI: 10.1002/path.4266.
29. Whitmore SS, Braun TA, Skeie JM, et al. Altered gene expression in dry age-related macular degeneration suggests early loss of choroidal endothelial cells[J]. Mol Vis, 2013, 19: 2274-2297.
30. Ashikawa Y, Nishimura Y, Okabe S, et al. Potential protective function of the sterol regulatory element binding factor 1-fatty acid desaturase 1/2 axis in early-stage age-related macular degeneration[J/OL]. Heliyon, 2017, 3(3): 00266[2017-03-01]. https://linkinghub.elsevier.com/retrieve/pii/S2405-8440(16)31797-2. DOI: 10.1016/j.heliyon.2017.e00266.
31. Seddon JM, McLeod DS, Bhutto IA, et al. Histopathological insights into choroidal vascular loss in clinically documented cases of age-related macular degeneration[J]. JAMA Ophthalmol, 2016, 134(11): 1272-1280. DOI: 10.1001/jamaophthalmol.2016.3519.
32. Sohn EH, Flamme-Wiese MJ, Whitmore SS, et al. Loss of CD34 expression in aging human choriocapillaris endothelial cells[J/OL]. PLoS One, 2014, 9(1): 86538[2014-01-21]. http://europepmc.org/article/MED/24466138. DOI: 10.1371/journal.pone.0086538.
33. Mullins RF, Johnson MN, Faidley EA, et al. Choriocapillaris vascular dropout related to density of drusen in human eyes with early age-related macular degeneration[J]. Invest Ophthalmol Vis Sci, 2011, 52(3): 1606-1612. DOI: 10.1167/iovs.10-6476.
34. Songstad AE, Worthington KS, Chirco KR, et al. Connective tissue growth factor promotes efficient generation of human induced pluripotent stem cell-derived choroidal endothelium[J]. Stem Cells Transl Med, 2017, 6(6): 1533-1546. DOI: 10.1002/sctm.16-0399.
35. Crabb JW, Miyagi M, Gu X, et al. Drusen proteome analysis: an approach to the etiology of age-related macular degeneration[J]. Proc Natl Acad Sci USA, 2002, 99(23): 14682-14687. DOI: 10.1073/pnas.222551899.
36. Yuan X, Gu X, Crabb JS, et al. Quantitative proteomics: comparison of the macular Bruch membrane/choroid complex from age-related macular degeneration and normal eyes[J]. Mol Cell Proteomics, 2010, 9(6): 1031-1046. DOI: 10.1074/mcp.M900523-MCP200.
37. Kim TW, Kang JW, Ahn J, et al. Proteomic analysis of the aqueous humor in age-related macular degeneration (AMD) patients[J]. J Proteome Res, 2012, 11(8): 4034-4043. DOI: 10.1021/pr300080s.
38. Koss MJ, Hoffmann J, Nguyen N, et al. Proteomics of vitreous humor of patients with exudative age-related macular degeneration[J/OL]. PLoS One, 2014, 9(5): 96895[2014-05-14]. http://europepmc.org/article/MED/24828575. DOI: 10.1371/journal.pone.0096895.
39. Nobl M, Reich M, Dacheva I, et al. Proteomics of vitreous in neovascular age-related macular degeneration[J]. Exp Eye Res, 2016, 146: 107-117. DOI: 10.1016/j.exer.2016.01.001.
40. Laíns I, Gantner M, Murinello S, et al. Metabolomics in the study of retinal health and disease[J]. Prog Retin Eye Res, 2019, 69: 57-79. DOI: 10.1016/j.preteyeres.2018.11.002.
41. Qin L, Mroczkowska SA, Ekart A, et al. Patients with early age-related macular degeneration exhibit signs of macro-and micro-vascular disease and abnormal blood glutathione levels[J]. Graefe’s Arch Clin Exp Ophthalmol, 2014, 252(1): 23-30. DOI: 10.1007/s00417-013-2418-0.
42. Ates O, Azizi S, Alp HH, et al. Decreased serum paraoxonase 1 activity and increased serum homocysteine and malondialdehyde levels in age-related macular degeneration[J]. Tohoku J Exp Med, 2009, 217(1): 17-22. DOI: 10.1620/tjem.217.17.
43. Bramall AN, Wright AF, Jacobson SG, et al. The genomic, biochemical, and cellular responses of the retina in inherited photoreceptor degenerations and prospects for the treatment of these disorders[J]. Annu Rev Neurosci, 2010, 33: 441-472. DOI: 10.1146/annurev-neuro-060909-153227.
44. de Bruijn SE, Verbakel SK, de Vrieze E, et al. Homozygous variants in KIAA1549, encoding a ciliary protein, are associated with autosomal recessive retinitis pigmentosa[J]. J Med Genet, 2018, 55(10): 705-712. DOI: 10.1136/jmedgenet-2018-105364.
45. Pomares E, Riera M, Permanyer J, et al. Comprehensive SNP-chip for retinitis pigmentosa-Leber congenital amaurosis diagnosis: new mutations and detection of mutational founder effects[J]. Eur J Hum Genet, 2010, 18(1): 118-124. DOI: 10.1038/ejhg.2009.114.
46. Simpson DA, Clark GR, Alexander S, et al. Molecular diagnosis for heterogeneous genetic diseases with targeted high-throughput DNA sequencing applied to retinitis pigmentosa[J]. J Med Genet, 2011, 48(3): 145-151. DOI: 10.1136/jmg.2010.083568.
47. Srilekha S, Arokiasamy T, Srikrupa NN, et al. Homozygosity Mapping in leber congenital amaurosis and autosomal recessive retinitis pigmentosa in South Indian families[J/OL]. PLoS One, 2015, 10(7): 0131679[2015-07-06]. http://europepmc.org/article/MED/26147992. DOI: 10.1371/journal.pone.0131679.
48. Wang Y, Guo L, Cai SP, et al. Exome sequencing identifies compound heterozygous mutations in CYP4V2 in a pedigree with retinitis pigmentosa[J/OL]. PLoS One, 2012, 7(5): 33673[2012-05-31]. http://europepmc.org/article/MED/22693542. DOI: 10.1371/journal.pone.0033673.
49. Huang H, Chen Y, Chen H, et al. Systematic evaluation of a targeted gene capture sequencing panel for molecular diagnosis of retinitis pigmentosa[J/OL]. PLoS One, 2018, 13(4): 0185237[2018-04-11]. http://europepmc.org/article/MED/29641573. DOI: 10.1371/journal.pone.0185237.
50. Yang HJ, Ratnapriya R, Cogliati T, et al. Vision from next generation sequencing: multi-dimensional genome-wide analysis for producing gene regulatory networks underlying retinal development, aging and disease[J]. Prog Retin Eye Res, 2015, 46: 1-30. DOI: 10.1016/j.preteyeres.2015.01.005.
51. Carrigan M, Duignan E, Malone CP, et al. Panel-based population next-generation sequencing for inherited retinal degenerations[J/OL]. Sci Rep, 2016, 6: 33248[2016-09-14]. http://europepmc.org/article/MED/27624628. DOI: 10.1038/srep33248.
52. Uren PJ, Lee JT, Doroudchi MM, et al. A profile of transcriptomic changes in the rd10 mouse model of retinitis pigmentosa[J]. Mol Vis, 2014, 20: 1612-1628.
53. Chen Y, Brooks MJ, Gieser L, et al. Transcriptome profiling of NIH3T3 cell lines expressing opsin and the P23H opsin mutant identifies candidate drugs for the treatment of retinitis pigmentosa[J]. Pharmacol Res, 2017, 115: 1-13. DOI: 10.1016/j.phrs.2016.10.031.

Previous Article
Effects of intravitreal injection of anti-vascular endothelial growth factor drugs on retinal blood circulation

Chinese Journal of Ocular Fundus Diseases

Applications of bioinformatics methods in ocular fundus diseases

Abstract Full text Figures/Tables Video References Cited by

Previous Article

Format

Content