Differentially expressed microRNAs in the aqueous humor of patients with exfoliation glaucoma or primary open-angle glaucoma
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Quigley, 1996, Number of people with glaucoma worldwide, Br. J. Ophthalmol, 80, 389, 10.1136/bjo.80.5.389
Thylefors, 1995, Global data on blindness, Bull. World Health Organ, 73, 115
Ritch, 1994, Exfoliation syndrome-the most common identifiable cause of open-angle glaucoma, J. Glaucoma, 3, 176, 10.1097/00061198-199400320-00018
Liu, 2013, Gene expression profile in human trabecular meshwork from patients with primary open-angle glaucoma, Invest. Ophthalmol. Vis. Sci, 54, 6382, 10.1167/iovs.13-12128
Mitchell, 1999, The relationship between glaucoma and pseudoexfoliation—The Blue Mountains Eye Study, Arch. Ophthalmol, 117, 1319, 10.1001/archopht.117.10.1319
Challa, 2009, Genetics of pseudoexfoliation syndrome, Curr. Opin. Ophthalmol, 20, 88, 10.1097/ICU.0b013e328320d86a
Leske, 2003, Factors for glaucoma progression and the effect of treatment: the early manifest glaucoma trial, Arch. Ophthalmol, 121, 48, 10.1001/archopht.121.1.48
The, 2000, The Advanced Glaucoma Intervention Study (AGIS): 7. The relationship between control of intraocular pressure and visual field deterioration, Am. J. Ophthalmol, 130, 429, 10.1016/S0002-9394(00)00538-9
Coca-Prados, 2007, New perspectives in aqueous humor secretion and in glaucoma: the ciliary body as a multifunctional neuroendocrine gland, Prog. Retin. Eye Res, 26, 239, 10.1016/j.preteyeres.2007.01.002
Goel, 2010, Aqueous humor dynamics: a review, Open Ophthalmol. J, 4, 52, 10.2174/1874364101004010052
Stamer, 2012, Current understanding of conventional outflow dysfunction in glaucoma, Curr. Opin. Ophthalmol, 23, 135, 10.1097/ICU.0b013e32834ff23e
Schlotzer-Schrehardt, 2006, Ocular and systemic pseudoexfoliation syndrome, Am. J. Ophthalmol, 141, 921, 10.1016/j.ajo.2006.01.047
Wang, 2014, Common and rare genetic risk factors for glaucoma, Cold Spring Harb. Perspect. Med, 4, a017244., 10.1101/cshperspect.a017244
Shastry, 2013, Emerging Concept of Genetic and Epigenetic Contribution to the Manifestation of Glaucoma
Liu, 2017, Major review: molecular genetics of primary open-angle glaucoma, Exp. Eye Res, 160, 62, 10.1016/j.exer.2017.05.002
Gonzalez, 2014, Role of microRNAs in the trabecular meshwork, J. Ocul. Pharmacol. Ther, 30, 128, 10.1089/jop.2013.0191
Jayaram, 2018, Investigation of microRNA expression in experimental glaucoma, Methods Mol. Biol, 1695, 287, 10.1007/978-1-4939-7407-8_19
Liu, 2016, A common variant in MIR182 is associated with primary open-angle glaucoma in the NEIGHBORHOOD consortium, Invest. Ophthalmol. Vis. Sci, 57, 3974, 10.1167/iovs.16-19688
Dunmire, 2013, MicroRNA in aqueous humor from patients with cataract, Exp. Eye Res, 108, 68, 10.1016/j.exer.2012.10.016
Wecker, 2016, MicroRNA profiling in aqueous humor of individual human eyes by next-generation sequencing, Invest. Ophthalmol. Vis. Sci, 57, 1706, 10.1167/iovs.15-17828
Tanaka, 2014, Profiles of extracellular miRNAs in the aqueous humor of glaucoma patients assessed with a microarray system, Sci. Rep, 4, 5089, 10.1038/srep05089
Lerner, 2017, Extracellular esicles mediate signaling between the aqueous humor producing and draining cells in the ocular system, PLoS One, 12, e0171153, 10.1371/journal.pone.0171153
De Guire, 2013, Circulating miRNAs as sensitive and specific biomarkers for the diagnosis and monitoring of human diseases: promises and challenges, Clin. Biochem, 46, 846, 10.1016/j.clinbiochem.2013.03.015
Mitchell, 2008, Circulating microRNAs as stable blood-based markers for cancer detection, Proc. Natl. Acad. Sci. U.S.A, 105, 10513, 10.1073/pnas.0804549105
Jayaram, 2017, Comparison of microRNA expression in aqueous humor of normal and primary open-angle glaucoma patients using PCR arrays: a pilot study, Invest. Ophthalmol. Vis. Sci, 58, 2884, 10.1167/iovs.17-21844
Drewry, 2016, miRNA profile in three different normal human ocular tissues by miRNA-Seq, Invest. Ophthalmol. Vis. Sci, 57, 3731, 10.1167/iovs.16-19155
Hsu, 2014, miRTarBase update 2014: an information resource for experimentally validated miRNA-target interactions, Nucleic Acids Res, 42, D78, 10.1093/nar/gkt1266
Izzotti, 2010, Proteome alterations in primary open angle glaucoma aqueous humor, J. Proteome Res, 9, 4831, 10.1021/pr1005372
Uechi, 2014, Proteomic view of basement membranes from human retinal blood vessels, inner limiting membranes, and lens capsules, J. Proteome Res, 13, 3693, 10.1021/pr5002065
Goel, 2013, Characterizing the normal proteome of human ciliary body, Clin. Proteomics, 10, 9, 10.1186/1559-0275-10-9
Golubnitschaja, 2007, Disease proteomics reveals altered basic gene expression regulation in leukocytes of normal-tension and primary open-angle glaucoma patients, Proteomics Clin. Appl, 1, 1316, 10.1002/prca.200700150
Bagnis, 2012, Aqueous humor oxidative stress proteomic levels in primary open angle glaucoma, Exp. Eye Res, 103, 55, 10.1016/j.exer.2012.07.011
Sacca, 2012, New proteins as vascular biomarkers in primary open angle glaucomatous aqueous humor, Invest. Ophthalmol. Vis. Sci, 53, 4242, 10.1167/iovs.11-8902
Mestdagh, 2014, Evaluation of quantitative miRNA expression platforms in the microRNA quality control (miRQC) study, Nat. Methods, 11, 809, 10.1038/nmeth.3014
Kolbert, 2013, Multi-platform analysis of microRNA expression measurements in RNA from fresh frozen and FFPE tissues, PLoS One, 8, e52517, 10.1371/journal.pone.0052517
Fuchshofer, 2012, The role of TGF-beta in the pathogenesis of primary open-angle glaucoma, Cell Tissue Res, 347, 279, 10.1007/s00441-011-1274-7
Sun, 2013, Diverse functions of miR-125 family in different cell contexts, J. Hematol. Oncol, 6, 6, 10.1186/1756-8722-6-6
Bleazard, 2015, Bias in microRNA functional enrichment analysis, Bioinformatics, 31, 1592, 10.1093/bioinformatics/btv023
Godard, 2015, Pathway analysis from lists of microRNAs: common pitfalls and alternative strategy, Nucleic Acids Res, 43, 3490, 10.1093/nar/gkv249
Last, 2011, Elastic modulus determination of normal and glaucomatous human trabecular meshwork, Invest. Ophthalmol. Vis. Sci, 52, 2147, 10.1167/iovs.10-6342
Kuchtey, 2010, Multiplex cytokine analysis reveals elevated concentration of interleukin-8 in glaucomatous aqueous humor, Invest. Ophthalmol. Vis. Sci, 51, 6441, 10.1167/iovs.10-5216
Aung, 2017, Genetic association study of exfoliation syndrome identifies a protective rare variant at LOXL1 and five new susceptibility loci, Nat. Genet, 49, 993, 10.1038/ng.3875
Hauser, 2015, Genetic variants and cellular stressors associated with exfoliation syndrome modulate promoter activity of a lncRNA within the LOXL1 locus, Hum. Mol. Genet, 24, 6552, 10.1093/hmg/ddv347
Li, 2015, A common variant near TGFBR3 is associated with primary open angle glaucoma, Hum. Mol. Genet, 24, 3880, 10.1093/hmg/ddv128
Aung, 2015, A common variant mapping to CACNA1A is associated with susceptibility to exfoliation syndrome, Nat. Genet, 47, 387, 10.1038/ng.3226
Armstrong, 2015, MicroRNA molecular profiling from matched tumor and bio-fluids in bladder cancer, Mol. Cancer, 14, 194, 10.1186/s12943-015-0466-2
Robinson, 2010, A scaling normalization method for differential expression analysis of RNA-seq data, Genome Biol, 11, R25, 10.1186/gb-2010-11-3-r25
Team, 2015
Huber, 2015, Orchestrating high-throughput genomic analysis with Bioconductor, Nat. Methods, 12, 115, 10.1038/nmeth.3252
Ritchie, 2015, limma powers differential expression analyses for RNA-sequencing and microarray studies, Nucleic Acids Res, 43, e47, 10.1093/nar/gkv007
Phipson, 2016, Robust hyperparameter estimation protects against hypervariable genes and improves power to detect differential expression, Ann. Appl. Stat, 10, 946, 10.1214/16-AOAS920
Law, 2014, voom: precision weights unlock linear model analysis tools for RNA-seq read counts, Genome Biol, 15, R29., 10.1186/gb-2014-15-2-r29
Ritchie, 2007, A comparison of background correction methods for two-colour microarrays, Bioinformatics, 23, 2700, 10.1093/bioinformatics/btm412
Liu, 2015, Why weight? Modelling sample and observational level variability improves power in RNA-seq analyses, Nucleic Acids Res, 43, e97, 10.1093/nar/gkv412
Vaes, 2014, Statistical analysis of differential gene expression relative to a fold change threshold on NanoString data of mouse odorant receptor genes, BMC Bioinformatics, 15, 39, 10.1186/1471-2105-15-39
Ploner, 2015
Zhang, 2005, WebGestalt: an integrated system for exploring gene sets in various biological contexts, Nucleic Acids Res, 33, W741, 10.1093/nar/gki475
Wang, 2013, WEB-based GEne SeT AnaLysis Toolkit (WebGestalt): update 2013, Nucleic Acids Res, 41, W77, 10.1093/nar/gkt439
Benjamini, 1995, Controlling the false discovery rate: a practical and powerful approach to multiple testing, J. Roy. Stat. Soc. B Met, 57, 289, 10.1111/j.2517-6161.1995.tb02031.x
Tenenbaum, 2017
Rider, 2016, ExtraPEG: a polyethylene glycol-based method for enrichment of extracellular vesicles, Sci. Rep, 6, 23978, 10.1038/srep23978
Helwa, 2017, A comparative study of serum exosome isolation using differential ultracentrifugation and three commercial reagents, PLoS One, 12, e0170628, 10.1371/journal.pone.0170628
Klingeborn, 2017, Roles of exosomes in the normal and diseased eye, Prog. Retin. Eye. Res, 59, 158, 10.1016/j.preteyeres.2017.04.004
Han, 2011, Elasticity-dependent modulation of TGF-beta responses in human trabecular meshwork cells, Invest. Ophthalmol. Vis. Sci, 52, 2889, 10.1167/iovs.10-6640
Huang, 2008, Differential roles of phosphatidylinositol 3-kinase/akt pathway in retinal ganglion cell survival in rats with or without acute ocular hypertension, Neuroscience, 153, 214, 10.1016/j.neuroscience.2008.02.007
Nickells, 2008, Involvement of the Bcl2 gene family in the signaling and control of retinal ganglion cell death, Prog. Brain Res, 173, 423, 10.1016/S0079-6123(08)01129-1
Liu, 2005, The effect of C3 transgene expression on actin and cellular adhesions in cultured human trabecular meshwork cells and on outflow facility in organ cultured monkey eyes, Mol. Vis, 11, 1112
Wiggs, 2012, Common variants at 9p21 and 8q22 are associated with increased susceptibility to optic nerve degeneration in glaucoma, PLoS Genet, 8, e1002654., 10.1371/journal.pgen.1002654
Pasquale, 2013, Estrogen pathway polymorphisms in relation to primary open angle glaucoma: an analysis accounting for gender from the United States, Mol. Vis, 19, 1471
Babizhayev, 1989, Fibronectin detection in drainage outflow system of human eyes in ageing and progression of open-angle glaucoma, Mech. Ageing Dev, 47, 145, 10.1016/0047-6374(89)90017-1
Tezel, 2000, Immunostaining of heat shock proteins in the retina and optic nerve head of normal and glaucomatous eyes, Arch. Ophthalmol, 118, 511, 10.1001/archopht.118.4.511
Zhou, 2010, Single nucleotide polymorphisms of metabolic syndrome-related genes in primary open angle glaucoma, Int. J. Ophthalmol, 3, 36
Konstas, 1990, Immunogold localisation of laminin in normal and exfoliative iris, Br. J. Ophthalmol, 74, 450, 10.1136/bjo.74.8.450
Beit-Yannai, 2007, Does the aqueous humor have a role in mitogen-activated protein kinase (MAPK) intracellular signaling in glaucoma?, Med. Hypotheses, 68, 299, 10.1016/j.mehy.2006.05.067
Kumar, 2013, Tissue plasminogen activator in trabecular meshwork attenuates steroid induced outflow resistance in mice, PLoS One, 8, e72447, 10.1371/journal.pone.0072447
Ronkko, 2007, Matrix metalloproteinases and their inhibitors in the chamber angle of normal eyes and patients with primary open-angle glaucoma and exfoliation glaucoma, Graefes Arch. Clin. Exp. Ophthalmol, 245, 697, 10.1007/s00417-006-0440-1
Schlotzer-Schrehardt, 2003, Matrix metalloproteinases and their inhibitors in aqueous humor of patients with pseudoexfoliation syndrome/glaucoma and primary open-angle glaucoma, Invest. Ophthalmol. Vis. Sci, 44, 1117, 10.1167/iovs.02-0365
Rezaie, 2002, Adult-onset primary open-angle glaucoma caused by mutations in optineurin, Science, 295, 1077, 10.1126/science.1066901
Itakura, 2015, Glaucomatous MYOC mutations activate the IL-1/NF-κB inflammatory stress response and the glaucoma marker SELE in trabecular meshwork cells, Mol. Vis, 21, 1071
Zenkel, 2007, Impaired cytoprotective mechanisms in eyes with pseudoexfoliation syndrome/glaucoma, Invest. Ophthalmol. Vis. Sci, 48, 5558, 10.1167/iovs.07-0750
Keller, 2013, Ankyrin repeat and suppressor of cytokine signaling box containing protein-10 is associated with ubiquitin-mediated degradation pathways in trabecular meshwork cells, Mol. Vis, 19, 1639
Nagabhushana, 2010, Regulation of endocytic trafficking of transferrin receptor by optineurin and its impairment by a glaucoma-associated mutant, BMC Cell Biol, 11, 4, 10.1186/1471-2121-11-4
Koliakos, 2001, Transforming and insulin-like growth factors in the aqueous humour of patients with exfoliation syndrome, Graefes Arch. Clin. Exp. Ophthalmol, 239, 482, 10.1007/s004170100287
Sethi, 2011, Transforming growth factor-beta induces extracellular matrix protein cross-linking lysyl oxidase (LOX) genes in human trabecular meshwork cells, Invest. Ophthalmol. Vis. Sci, 52, 5240, 10.1167/iovs.11-7287
Burdon, 2011, Genome-wide association study identifies susceptibility loci for open angle glaucoma at TMCO1 and CDKN2B-AS1, Nat. Genet, 43, 574, 10.1038/ng.824
Fan, 2010, Association of polymorphisms of tumor necrosis factor and tumor protein p53 with primary open-angle glaucoma, Invest. Ophthalmol. Vis. Sci, 51, 4110, 10.1167/iovs.09-4974
Skarie, 2008, The primary open-angle glaucoma gene WDR36 functions in ribosomal RNA processing and interacts with the p53 stress-response pathway, Hum. Mol. Genet, 17, 2474, 10.1093/hmg/ddn147
Kang, 2014, Vascular tone pathway polymorphisms in relation to primary open-angle glaucoma, Eye (London), 28, 662, 10.1038/eye.2014.42