- Open Access
Proteomic analysis of human vitreous humor
- Krishna R Murthy†1, 2, 3Email author,
- Renu Goel†1, 4,
- Yashwanth Subbannayya1,
- Harrys KC Jacob1,
- Praveen R Murthy3,
- Srikanth Srinivas Manda1, 5,
- Arun H Patil1,
- Rakesh Sharma6,
- Nandini A Sahasrabuddhe1,
- Arun Parashar7,
- Bipin G Nair2,
- Venkatarangaiah Krishna4,
- TS Keshava Prasad1, 2, 5,
- Harsha Gowda1 and
- Akhilesh Pandey8, 9
© Murthy et al.; licensee BioMed Central Ltd. 2014
- Received: 19 February 2014
- Accepted: 16 May 2014
- Published: 14 July 2014
The vitreous humor is a transparent, gelatinous mass whose main constituent is water. It plays an important role in providing metabolic nutrient requirements of the lens, coordinating eye growth and providing support to the retina. It is in close proximity to the retina and reflects many of the changes occurring in this tissue. The biochemical changes occurring in the vitreous could provide a better understanding about the pathophysiological processes that occur in vitreoretinopathy. In this study, we investigated the proteome of normal human vitreous humor using high resolution Fourier transform mass spectrometry.
The vitreous humor was subjected to multiple fractionation techniques followed by LC-MS/MS analysis. We identified 1,205 proteins, 682 of which have not been described previously in the vitreous humor. Most proteins were localized to the extracellular space (24%), cytoplasm (20%) or plasma membrane (14%). Classification based on molecular function showed that 27% had catalytic activity, 10% structural activity, 10% binding activity, 4% cell and 4% transporter activity. Categorization for biological processes showed 28% participate in metabolism, 20% in cell communication and 13% in cell growth. The data have been deposited to the ProteomeXchange with identifier PXD000957.
This large catalog of vitreous proteins should facilitate biomedical research into pathological conditions of the eye including diabetic retinopathy, retinal detachment and cataract.
- SCX chromatography
- OFFGEL electrophoresis
- Proteome discoverer
- Secreted proteins
- Protein biomarkers
- Body fluid proteomics
The vitreous is a highly hydrated gelatinous mass that fills the space between the lens and the retina. The vitreous is adherent to the retina diffusely though the adhesion is strongest at the anterior border of retina, the macula, the optic nerve head, over lattice degenerations and areas of scars. The major function of the vitreous is to allow light to reach the retina and maintain the shape of the eyeball. The formation of vitreous occurs in two phases. Primary vitreous is formed by the third or fourth week of gestation, when the neural ectoderm separates from the surface ectoderm. The space between the two is the future vitreous cavity. This space is bridged by fibrillar material which is thought to be collagenous in nature. By the time the fetus reaches the 10 mm stage, mesodermal cells enter the vitreous space via the fetal fissure and develop into hyaloid vessels which branch throughout the vitreous cavity . In the adventitia surrounding the vessels, there are mononuclear phagocytes and fibroblasts which are thought to later differentiate into hyalocytes. This cellular vitreous is the primary vitreous. Acellular structures begin to appear by end of the sixth week of gestation between the retina and the hyaloid vasculature. This secondary vitreous is essentially extracellular matrix consisting primarily of type 2 collagen . With the development of the secondary vitreous, the hyaloid vascular system regresses. Hyalocytes appear to be the most important cells and after birth, there is no new migration of these cells into the vitreous cortex. Thus, with an increase in globe size and vitreous cortex surface area, there is a decrease in the density of hyalocytes. Since the vitreous acts as a metabolic repository for the retina, hyalocytes and surrounding tissues , some of the proteins in vitreous humor could be contributed by these surrounding tissues. Its viscosity is two to four times greater than water, which gives it a gelatinous consistency . The human vitreous is composed of a complex network of cross-linked collagen fibres of types II, V, IX and XI of which type II is the most abundant. Non-collagenous structural proteins are less abundant as compared to collagen fibrils. Hyaluronic acid, a glycosaminoglycan is also found in abundance in the vitreous [5, 6]. A significant amount of prealbumin and transferrin in the vitreous has also been reported [7–9]. Of the soluble proteins that constitute the vitreous, sialic acid containing glycoproteins constitute the largest fraction .
It is well understood that the changes occurring in the retina are closely linked to biochemical changes occurring in the vitreous humor . Vitreous humor does not have any blood vessels but is nourished by vessels of the retina and the ciliary body. As the vitreous can be easily obtained during vitrectomy surgery, studying the changes occurring in the vitreous could provide valuable information about pathological changes occurring in the retina in disorders of the eye. Many researchers have studied the proteins of the normal vitreous using different techniques and some of them have also catalogued various proteins [12–16]. Nakanishi et al., have catalogued 51 proteins in the vitreous by Matrix assisted laser desorption ionization-time of flight (MALDI-TOF) mass spectrometry . Kim et al. employed immunoaffinity depletion followed by nano-liquid chromatography-Matrix assisted laser desorption ionization (LC-MALDI-MS/MS) resulting in the identification of 346 proteins from non-diabetic controls . In a subsequent study, Gao et al. identified 252 proteins from the vitreous employing sodium dodecyl sulphate polyacylamide gel electrophoresis (SDS-PAGE) analyzed by LC-MS/MS . Aretz et al have identified 1,111 distinct proteins by employing different protein prefractionation strategies such as liquid phase isoelectric focussing, 1D SDS gel electrophoresis and a combination of both .
Here, we identified 1,205 proteins of which 682 proteins have been detected in the vitreous humor for the first time. A comprehensive proteomic profiling of normal vitreous would serve as an invaluable template for future studies that focus on protein dynamics in vitreous in pathological conditions.
A partial list of novel proteins identified in this study
Metalloproteinase inhibitor 1
Extracellular matrix structural constituent
Cell growth and/or maintenance
Extracellular matrix structural constituent
Chordin-like protein 1
Cell communication, Signal transduction
Molecular function unknown
Molecular function unknown
Hypothetical protein loc56005
Cell communication, Signal transduction
Growth factor activity
Protease inhibitor activity
Metabolism, Energy pathways
Molecular function unknown
Secreted frizzled-related protein 2
Cell communication, Signal transduction
Molecular function unknown
Defense/immunity protein activity
Protein-tyrosine phosphatase mitochondrial 1
Cell communication, Signal transduction
Protein tyrosine/serine/threonine phosphatase activity
Cell communication, Signal transduction
Calcium ion binding
Actin, cytoplasmic 1
Cell growth and/or maintenance
Structural constituent of cytoskeleton
Defense/immunity protein activity
Kinase regulator activity
A summary of some of the previously published proteomics studies on vitreous humor and the corresponding mass spectrometry platforms
Number of of proteins identified
Aretz S et al.,
SDS-PAGE, Liquid phase IEF
Simo et al., 
DIGE, Western blot
Gao et al. 
Kim et al. 
MS/MS, and LC-ESI-MS/MS
Ouchi et al. 
CapLC system with QTOF2
Wu et al., 
Yamane et al., 
Nakanishi et al. 
Known proteins in the vitreous humor
We identified several components of complement system including complement C1q subcomponent subunit A (C1QA), C1QB, C1QC, C1QL3, C1QTNF3, C1QTNF5, C1R, C1RL, C1S, C2, C3, C4A, C4B, C4BPA, C5, C6, C7, C8A, C8B, C8G, C9, CFB, CFD, CFH, CFHR1, CFHR2, CFHR3, CFI.
Activation of the complement pathways can initiate and accelerate thrombosis, apoptosis and leukostasis, all of which could be important steps in the development of diabetic retinopathy . Some of the complement factors are also associated with age-related macular degeneration (AMD). Raychaudhuri et al., have shown that compromised complement factor H (CFH) function contributes to pathogenesis of AMD . CFH risk allele reveals a polymorphism representing a tyrosine to histidine change at amino acid 402, which is associated with AMD . This region of CFH is crucial for binding of heparin and C-reactive protein . Ennis et al., have also shown that SNP in complement factor 1 is associated with risk of AMD .
Opticin (OPTC) is a member of the small leucine-rich repeat protein (SLRP) family. Opticin is expressed in the retina, skin, iris, vitreous humor, non-pigmented epithelium of the ciliary body, sclera, optic nerve, choroid, corneal epithelium, uveal tract and lens [25–27]. It is associated with age related macular degeneration and posterior column ataxia with retinitis pigmentosa, both of which are inherited eye diseases .
Retinol-binding protein 3 (RBP3) is a soluble single subunit glycoprotein that is synthesized and secreted by rod photoreceptor cells into the interphotoreceptor matrix [29–32]. It is believed to transport all trans retinol to the retinal pigment epithelium (RPE) and 11-cis retinal from the RPE to the bleached photoreceptors, thus playing an important role in the visual cycle . A mutation in the RBP3 gene (Asp1080Asn) has been linked to autosomal recessive retinitis pigmentosa . RBP3 is known to modulate the notch signal transduction by interacting with the phosphorylated intracellular domain of the notch receptor . It is surprising that molecules such as RBP3, which appears to function at the back of the retina farthest from the vitreous, could still be found in the vitreous. The possible explanation for this could be that even though the intravascular contents are prevented from directly reaching the vitreous by the presence of the blood ocular barrier, there is no evidence of an effective barrier for proteins in the intercellular and interstitial spaces of retina and surrounding tissues.
Serpin peptidase inhibitor, clade F, member 1 (SERPINF1) is a 50 kDa secreted glycoprotein and reported to be expressed in many tissue and vitreous [36, 37]. It belongs to a group of serine protease inhibitors with anti-angiogenic activities [38, 39]. SERPINF1 concentration is found to be significantly lower in the vitreous fluid of subjects with PDR [40–42].
Novel proteins identified in the vitreous humor
We compared our results with other high throughput studies on vitreous humour [13, 14, 16]. We have identified 523 proteins identified by other studies. In addition, we have identified 682 novel proteins not described in previous studies. Of the 682 novel proteins, we identified proteins such as S-Arrestin(SAG) and transforming growth factor-beta 2 (TGF-B2) which are involved in the pathophysiology of ocular diseases. S Arrestin, also known as S antigen(S-Ag) is a major photoreceptor protein. It is a member of the beta-arrestin protein family which participate in agonist-mediated desensitization of G-protein-coupled receptors. Arrestin preferentially binds light activated phosphorylated rhodopsin and prevents further signaling by direct competition with transducin, a visual G-protein . It is expressed in the retina and pineal gland. This protein is highly antigenic and has been implicated in experimental uveoretinitis. There is also recent evidence to suggest S-Ag specific T cells may be involved in the pathophysiology of Bechets disease, a chronic, relapsing, multisystem inflammatory disorder characterized by recurrent oral and genital ulcers, severe intraocular inflammation and skin lesions . Mutations in the S Arrestin gene is also associated with an autosomal recessive form of night blindness known as Oguchi disease [57–59].
Transforming growth factor-beta 2(TGF-B2) belongs to the TGFB family of cytokines. These proteins bind to their transmembrane receptors, which in turn activate their downstream effectors like SMAD proteins which are known to regulate cell proliferation, apoptosis and differentiation . Primary open angle glaucoma is a disease of the eye which is characterized by elevated intra ocular pressure due to increased resistance to the outflow of aqueous humor through the trabecular meshwork. TGF-B2 has been shown to be elevated in the aqueous humor of patients with primary open angle glaucoma. Its role in glaucoma is thought to be due to the increased production of extracellular matrix in the trabecular meshwork . A genetic defect in the gene that codes for this protein is associated with Peter's anomaly which is a congenital defect of the anterior chamber of the eye .
Gene ontology analysis
Our study provides a comprehensive proteomics profile of the human vitreous humor. Many of the pathologic changes occurring in the retina are likely to be reflected in the vitreous because of its close proximity to the retina and also because of the breakdown of the blood retinal barrier. Hence, a proteomic study of the vitreous in related retinal diseases such as diabetic retinopathy, retinal detachment and central or branch retinal vein occlusions would provide valuable insights about the pathophysiology of these diseases. The information from our study could serve as a baseline for future studies especially those aimed at identifying biomarkers for retinal disorders.
Vitreous sample collection
The vitreous samples for the proteomic analysis were obtained from five patients undergoing vitrectomy for macular hole, three patients with congenital cataract who underwent cataract surgery with intra-ocular lens implantation and primary posterior capsulotomy and two samples from patients with traumatic cataract with undisturbed vitreous and intact lens capsule but who also needed vitreous surgery due to zonular damage. All samples were collected by pars plana vitrectomy, were centrifuged at 13,000 rpm at 4°C for 15 minutes and archived at −80°C until further use. Informed consent was obtained from all the subjects and the research adhered to the tenets of Declaration of Helsinki. The study was approved by the Ethics committee “Science for Health” under the approval number 20080713/SFH-014/010. Pooled samples were concentrated by 3 kDa filter through low-adsorption membranes (Amicon, Milliore, Billerica, MA). Protein estimation was carried out for pooled concentrated sample using Lowry’s assay (BioRad Laboratories). A total of 4 mg protein was subjected to Agilent’s Multiple Affinity Removal System 14 (MARS 14) for depletion of abundant proteins. MARS 14 column is routinely used for depletion of abundant proteins in serum/plasma. This step allows us to deplete highly abundant albumin, IgG, transferrin, heptoglobin, IgM, IgA, fibrinogen, alpha antitrypsin, apolipoprotein A1, alpha 1 acid glycoprotein, alpha2 macroglobin, transthyretin, complement C3 and apolipoproteins. We had to optimize our procedures for depletion of abundant proteins from vitreous humor. For each depletion cycle, Agilent recommends 20 μl of serum that is approximately equivalent to 1 mg of total protein. During depletion of abundant proteins from vitreous, we also used 1 mg of protein for each depletion cycle. As we had 4 mg protein, we carried out 4 independent depletion cycles and pooled the flow through fractions. After passing the vitreous sample through MARS 14 column, 460 μg of protein was recovered in the flow through and the remaining 3.54 mg of protein accounted for the bound fraction. 60 μg of depleted vitreous sample was resolved on SDS-PAGE and subjected to in-gel digestion prior to mass spectrometry analysis. The remaining 400 μg of protein was reduced (5 mM DTT), alkylated (20 mM iodoacetamide) and digested using trypsin 1:20 w/w (Promega, Madison, WI) overnight at 37°C. The samples were acidified by adding 20% trifluoro acetic acid (TFA) to a final concentration of 0.1% and desalted using C18 macro-spin columns (Harvard apparatus, catalog no. 74-4101). 200 μg peptide digest was used for SCX fractionation as well as OFFGEL fractionation.
Sixty micrograms of depleted vitreous sample was resolved by SDS-PAGE and stained using colloidal Coomassie stain. The lane was excised into 16 pieces and destained with 40 mM ammonium bicarbonate in 50% acetonitrile (ACN). Trypsin digestion was carried out essentially as described previously [66, 67]. Briefly, reduction was carried out using 5 mM dithiothreitol (DTT, 60°C for 45 minutes) followed by alkylation using 20 mM iodoacetamide (room temperature for 10 min). Sequencing grade modified porcine trypsin (Promega, Madison, WI, US) in ammonium bicarbonate was added to the gel pieces at 4°C and incubated for 45 minutes. Excess trypsin was removed and the gel pieces were immersed in ammonium bicarbonate and incubated overnight at 37°C. The peptides were extracted from the gel bands using 0.4% formic acid in 3% ACN twice, once using 0.4% formic acid in 50% ACN and once using 100% ACN. The extracted peptides were dried using speedvac and stored at -80°C until LC-MS/MS analysis.
Strong cation exchange chromatography
The peptide digest equivalent to 200 μg was reconstituted with 10 mM potassium phosphate buffer containing 30% ACN, pH 2.7 (solvent A). SCX fractionation was carried out using Polysulfoethyl A column (PolyLC, Columbia, MD) (300 Å, 5 μm, 100 × 2.1 mm) using an Agilent 1200 HPLC system (Agilent Technologies, Santa Clara, USA) containing a binary pump, UV detector and a fraction collector [68, 69]. The peptides were eluted using a linear salt gradient (0 to 35%) of solvent B (10 mM potassium phosphate buffer containing 30% ACN, 350 mM KCl, pH 2.7) at a flow rate of 200 μl/min. The fractions were completely dried and reconstituted in 0.1% TFA. They were desalted using stage-tips and dried on speedvac.
The peptide digest equivalent to 200 μg in-solution digest was used for OFFGEL fractionation [70, 71]. Agilent 3100 OFFGEL fractionator (Agilent Technologies, Santa Clara, USA) was used for pI based separation of peptides. As per the protocol, peptides were separated using pH 3-10 Immobilized pH gradient (IPG) strip, 13 cm. The peptides were focused at 50 kVh with maximum current of 50 μA and maximum voltage set to 4000 V. Twelve fractions were collected and acidified to obtain a final concentration of 0.1% TFA prior to sample cleaning using stage-tip protocol .
LC-MS/MS analyses of the samples were carried out using high resolution Fourier transform mass spectrometer, LTQ-Orbitrap Velos (Thermo Electron, Bremen, Germany). The mass spectrometer was interfaced with a nano-LC system to a trap column (2 cm × 75 μm, C18 material 5 μm, 120 Å) and an analytical column (10 cm × 75 μm, C18 material 5 μm, 120 Å). Electrospray source was fitted with an 8 μm emitter tip (New Objective, Woburn, MA) and was applied a voltage of 2000 V. Peptide samples were loaded onto trap column in 3% solvent B (90% ACN in 0.1% formic acid) and washed for 5 minutes before peptide elution using a gradient of 3-35% solvent B for 60 minutes at a constant flow rate of 0.4 μl/min. Xcalibur 2.1 (Thermo Electron, Bremen, Germany) was used for data acquisition. The MS spectra were acquired in a data-dependent manner targeting the twenty most abundant ions in each survey scan in the range of m/z 350 to 1,800. Precursor ions selected for MS/MS fragmentation were dynamically excluded for 30s. Target ion quantity for FT full MS and MS2 were 5 × 105 and 2 × 105 respectively. Higher-energy collisional dissociation (HCD) was used for precursor fragmentation. MS and MS/MS data were acquired at a resolution of 60,000 and 15,000 at 400 m/z, respectively. Internal calibration was enabled using polydimethylcyclosiloxane (m/z, 445.1200025) ions and lock mass was used for accurate mass measurements.
Mass spectrometry data was processed using the Proteome Discoverer software (Version 220.127.116.11, Thermo Fisher Scientific, Bremen, Germany). Mascot, SEQUEST and X! Tandem search engines were employed to maximize the peptide identification. The mass spectrometry data was searched against NCBI RefSeq 59 human protein database containing 36,211 sequences with known contaminants. Carbamidomethylation of cysteine was used as the fixed modification and oxidation of methionine and protein N-terminal acetylation as variable modifications. Peptide mass and fragment mass tolerance were set as 20 ppm and 0.1 Da, respectively with 1 missed cleavage. Peptide identifications were filtered by setting 1% target false discovery rate (FDR). Subcellular localization, molecular function and biological process of identified proteins were analyzed using gene ontology (GO) compliant databases - Human Protein Reference Database (HPRD: http://www.hprd.org) and Human Proteinpedia [63, 73].
The raw data obtained from vitreous proteome are submitted to public data repositories. The peptide identifications and MS/MS spectra are available on Human Proteinpedia , (https://www.humanproteinpedia.org) as accession number HuPA_00682. The mass spectrometry proteomics data have been deposited to the ProteomeXchange Consortium  via the PRIDE partner repository with the dataset identifier PXD000957.
We thank the Department of Biotechnology (DBT) of the Government of India for research support to the Institute of Bioinformatics, Bangalore. Nandini A. Sahasrabuddhe and Harrys K.C. Jacob are recipients of Senior Research Fellowship from the Council for Scientific and Industrial Research (CSIR), India. Srikanth Srinivas Manda is a recipient of Senior Research Fellowship from University Grants Commission (UGC), India. Rakesh Sharma is a Research Associate supported by DBT. Harsha Gowda is a Wellcome Trust/DBT India Alliance Early Career Fellow. Dr. T. S. Keshava Prasad is the recipient of a research grant on “Development of Infrastructure and a Computational Framework for Analysis of Proteomic Data” from DBT.
- Jack RL: Ultrastructure of the hyaloid vascular system. Arch Ophthalmol. 1972, 87 (5): 555-567.View ArticlePubMedGoogle Scholar
- Linsenmayer TF, Gibney E, Little CD: Type II collagen in the early embryonic chick cornea and vitreous: immunoradiochemical evidence. Exp Eye Res. 1982, 34 (3): 371-379.View ArticlePubMedGoogle Scholar
- Walker F, Patrick RS: Constituent monosaccharides and hexosamine concentration of normal human vitreous humour. Exp Eye Res. 1967, 6 (3): 227-232.View ArticlePubMedGoogle Scholar
- Locke JC, Morton WR: Further studies of the viscosity of aspirated human vitreous fluid: with special reference to its use in retinal detachment surgery. Trans Am Ophthalmol Soc. 1965, 63: 129-145.PubMed CentralPubMedGoogle Scholar
- Scott JE: The chemical morphology of the vitreous. Eye. 1992, 6 (Pt 6): 553-555.View ArticlePubMedGoogle Scholar
- Bishop PN, Crossman MV, McLeod D, Ayad S: Extraction and characterization of the tissue forms of collagen types II and IX from bovine vitreous. Biochem J. 1994, 299 (Pt 2): 497-505.PubMed CentralView ArticlePubMedGoogle Scholar
- Ramakrishnan S, Sulochana KN, Parikh S, Punitham R: Transthyretin (prealbumin) in eye structures and variation of vitreous-transthyretin in diseases. Indian J Ophthalmol. 1999, 47 (1): 31-34.PubMedGoogle Scholar
- Eichenbaum JW, Zheng W: Distribution of lead and transthyretin in human eyes. J Toxicol Clin Toxicol. 2000, 38 (4): 377-381.View ArticlePubMedGoogle Scholar
- Clausen R, Weller M, Wiedemann P, Heimann K, Hilgers RD, Zilles K: An immunochemical quantitative analysis of the protein pattern in physiologic and pathologic vitreous. Graefes Arch Clin Exp Ophthalmol. 1991, 229 (2): 186-190.View ArticlePubMedGoogle Scholar
- Jacobson B: Identification of sialyl and galactosyl transferase activities in calf vitreous hyalocytes. Curr Eye Res. 1984, 3 (8): 1033-1041.View ArticlePubMedGoogle Scholar
- Yoshimura T, Sonoda KH, Sugahara M, Mochizuki Y, Enaida H, Oshima Y, Ueno A, Hata Y, Yoshida H, Ishibashi T: Comprehensive analysis of inflammatory immune mediators in vitreoretinal diseases. PLoS One. 2009, 4 (12): e8158-PubMed CentralView ArticlePubMedGoogle Scholar
- Nakanishi T, Koyama R, Ikeda T, Shimizu A: Catalogue of soluble proteins in the human vitreous humor: comparison between diabetic retinopathy and macular hole. J Chromatogr B Analyt Technol Biomed Life Sci. 2002, 776 (1): 89-100.View ArticlePubMedGoogle Scholar
- Kim T, Kim SJ, Kim K, Kang UB, Lee C, Park KS, Yu HG, Kim Y: Profiling of vitreous proteomes from proliferative diabetic retinopathy and nondiabetic patients. Proteomics. 2007, 7 (22): 4203-4215.View ArticlePubMedGoogle Scholar
- Gao BB, Chen X, Timothy N, Aiello LP, Feener EP: Characterization of the vitreous proteome in diabetes without diabetic retinopathy and diabetes with proliferative diabetic retinopathy. J Proteome Res. 2008, 7 (6): 2516-2525.View ArticlePubMedGoogle Scholar
- Ouchi M, West K, Crabb JW, Kinoshita S, Kamei M: Proteomic analysis of vitreous from diabetic macular edema. Exp Eye Res. 2005, 81 (2): 176-182.View ArticlePubMedGoogle Scholar
- Aretz S, Krohne TU, Kammerer K, Warnken U, Hotz-Wagenblatt A, Bergmann M, Stanzel BV, Kemph T, Holz FG, Schnolzer M, Kopitz J: In-depth mass spectrometric mapping of the human vitreous proteome. Proteome Sci. 2013, 11 (1): 22-PubMed CentralView ArticlePubMedGoogle Scholar
- Simo R, Higuera M, Garcia Ramirez M, Canals F, Garcia-Arumi J, Hernandez C: Elevation of apolipoprotein A-1 and apolipoprotein H levels in the vitreous fluid and overexpression in the retina of diabetic patients. Arch Ophthalmol. 2008, 126 (8): 1076-1081.View ArticlePubMedGoogle Scholar
- Wu CW, Sauter JL, Johnson PK, Chen CD, Olsen TW: Identification and localization of major soluble proteins in human ocular tissue. Am J Ophthalmol. 2004, 137 (4): 655-661.PubMedGoogle Scholar
- Yamane K, Minamoto A, Yamashita H, Takamura H, Miyamoto-Myoken Y, Yoshizato K, Nabetani T, Tsugita A, Mishima HK: Proteome analysis of human vitreous proteins. Mol Cell Proteomics. 2003, 2 (11): 1177-1187.View ArticlePubMedGoogle Scholar
- Zhang J, Gerhardinger C, Lorenzi M: Early complement activation and decreased levels of glycosylphosphatidylinositol-anchored complement inhibitors in human and experimental diabetic retinopathy. Diabetes. 2002, 51 (12): 3499-3504.View ArticlePubMedGoogle Scholar
- Raychaudhuri S, Iartchouk O, Chin K, Tan PL, Tai AK, Ripke S, Gowrisankar S, Vemuri S, Montgomery K, Yu Y, Reynolds R, Zack DJ, Campochiaro B, Campochiaro P, Katsanis N, Daly MJ, Seddon JM: A rare penetrant mutation in CFH confers high risk of age-related macular degeneration. Nat Genet. 2011, 43 (12): 1232-1236.PubMed CentralView ArticlePubMedGoogle Scholar
- Klein RJ, Zeiss C, Chew EY, Tsai JY, Sackler RS, Haynes C, Henning AK, SanGiovanni JP, Mane SM, Mayne ST, Bracken MB, Ferris FL, Ott J, Barnstable C, Hoh J: Complement factor H polymorphism in age-related macular degeneration. Science. 2005, 308 (5720): 385-389.PubMed CentralView ArticlePubMedGoogle Scholar
- Rodriguez de Cordoba S, Esparza-Gordillo J, Goicoechea de Jorge E, Lopez-Trascasa M, Sanchez-Corral P: The human complement factor H: functional roles, genetic variations and disease associations. Mol Immunol. 2004, 41 (4): 355-367.View ArticlePubMedGoogle Scholar
- Ennis S, Gibson J, Cree AJ, Collins A, Lotery AJ: Support for the involvement of complement factor I in age-related macular degeneration. Eur J Hum Genet. 2010, 18 (1): 15-16.PubMed CentralView ArticlePubMedGoogle Scholar
- Reardon AJ, Le Goff M, Briggs MD, McLeod D, Sheehan JK, Thornton DJ, Bishop PN: Identification in vitreous and molecular cloning of opticin, a novel member of the family of leucine-rich repeat proteins of the extracellular matrix. J Biol Chem. 2000, 275 (3): 2123-2129.View ArticlePubMedGoogle Scholar
- Ramesh S, Bonshek RE, Bishop PN: Immunolocalisation of opticin in the human eye. Br J Ophthalmol. 2004, 88 (5): 697-702.PubMed CentralView ArticlePubMedGoogle Scholar
- Friedman JS, Faucher M, Hiscott P, Biron VL, Malenfant M, Turcotte P, Raymond V, Walter MA: Protein localization in the human eye and genetic screen of opticin. Hum Mol Genet. 2002, 11 (11): 1333-1342.View ArticlePubMedGoogle Scholar
- Friedman JS, Ducharme R, Raymond V, Walter MA: Isolation of a novel iris-specific and leucine-rich repeat protein (oculoglycan) using differential selection. Invest Ophthalmol Vis Sci. 2000, 41 (8): 2059-2066.PubMedGoogle Scholar
- Liou GI, Ma DP, Yang YW, Geng L, Zhu C, Baehr W: Human interstitial retinoid-binding protein. Gene structure and primary structure. J Biol Chem. 1989, 264 (14): 8200-8206.PubMedGoogle Scholar
- Taniguchi T, Adler AJ, Mizuochi T, Kochibe N, Kobata A: The structures of the asparagine-linked sugar chains of bovine interphotoreceptor retinol-binding protein. Occurrence of fucosylated hybrid-type oligosaccharides. J Biol Chem. 1986, 261 (4): 1730-1736.PubMedGoogle Scholar
- Hollyfield JG, Fliesler SJ, Rayborn ME, Bridges CD: Rod photoreceptors in the human retina synthesize and secrete interstitial retinol-binding protein. Prog Clin Biol Res. 1985, 190: 141-149.PubMedGoogle Scholar
- Barnstable CJ, Tombran-Tink J: Neuroprotective and antiangiogenic actions of PEDF in the eye: molecular targets and therapeutic potential. Prog Retin Eye Res. 2004, 23 (5): 561-577.View ArticlePubMedGoogle Scholar
- Pepperberg DR, Okajima TL, Wiggert B, Ripps H, Crouch RK, Chader GJ: Interphotoreceptor retinoid-binding protein (IRBP). Molecular biology and physiological role in the visual cycle of rhodopsin. Mol Neurobiol. 1993, 7 (1): 61-85.View ArticlePubMedGoogle Scholar
- Den Hollander AI, McGee TL, Ziviello C, Banfi S, Dryja TP, Gonzalez-Fernandez F, Ghosh D, Berson EL: A homozygous missense mutation in the IRBP gene (RBP3) associated with autosomal recessive retinitis pigmentosa. Invest Ophthalmol Vis Sci. 2009, 50 (4): 1864-1872.PubMed CentralView ArticlePubMedGoogle Scholar
- Foltz DR, Nye JS: Hyperphosphorylation and association with RBP of the intracellular domain of Notch1. Biochem Biophys Res Commun. 2001, 286 (3): 484-492.View ArticlePubMedGoogle Scholar
- Ortego J, Escribano J, Becerra SP, Coca-Prados M: Gene expression of the neurotrophic pigment epithelium-derived factor in the human ciliary epithelium. Synthesis and secretion into the aqueous humor. Invest Ophthalmol Vis Sci. 1996, 37 (13): 2759-2767.PubMedGoogle Scholar
- Meyer C, Notari L, Becerra SP: Mapping the type I collagen-binding site on pigment epithelium-derived factor. Implications for its antiangiogenic activity. J Biol Chem. 2002, 277 (47): 45400-45407.View ArticlePubMedGoogle Scholar
- Fan W, Crawford R, Xiao Y: The ratio of VEGF/PEDF expression in bone marrow mesenchymal stem cells regulates neovascularization. Differentiation. 2011, 81 (3): 181-191.View ArticlePubMedGoogle Scholar
- Park K, Jin J, Hu Y, Zhou K, Ma JX: Overexpression of pigment epithelium-derived factor inhibits retinal inflammation and neovascularization. Am J Pathol. 2011, 178 (2): 688-698.PubMed CentralView ArticlePubMedGoogle Scholar
- Garcia-Ramirez M, Canals F, Hernandez C, Colome N, Ferrer C, Carrasco E, Garcia-Arumi J, Simo R: Proteomic analysis of human vitreous fluid by fluorescence-based difference gel electrophoresis (DIGE): a new strategy for identifying potential candidates in the pathogenesis of proliferative diabetic retinopathy. Diabetologia. 2007, 50 (6): 1294-1303.View ArticlePubMedGoogle Scholar
- Noma H, Funatsu H, Mimura T, Eguchi S, Shimada K, Hori S: Vitreous levels of pigment epithelium-derived factor and vascular endothelial growth factor in macular edema with central retinal vein occlusion. Curr Eye Res. 2011, 36 (3): 256-263.View ArticlePubMedGoogle Scholar
- Konson A, Pradeep S, D'Acunto CW, Seger R: Pigment epithelium-derived factor and its phosphomimetic mutant induce JNK-dependent apoptosis and p38-mediated migration arrest. J Biol Chem. 2011, 286 (5): 3540-3551.PubMed CentralView ArticlePubMedGoogle Scholar
- Khanna AK, Meher S, Prakash S, Tiwary SK, Singh U, Srivastava A, Dixit VK: Comparison of Ranson, Glasgow, MOSS, SIRS, BISAP, Apache-II, CTSI scores, IL-6, CRP and Procalcitonin in predicting severity, organ failure, pancreatic necrosis and mortality in acute pancratitis. HPB Surg. 2013, 2013: 367581-PubMed CentralView ArticlePubMedGoogle Scholar
- Ucmak D, Akkurt M, Toprak G, Yesilova Y, Turan E, Yıldız I: Determination of dermatology life quality index, and serum C-reactive protein and plasma interleukin-6 levels in patients with chronic urticaria. Postepy Dermatol Alergol. 2013, 30 (3): 146-151.PubMed CentralView ArticlePubMedGoogle Scholar
- Clemmons DR: Role of insulin-like growth factor binding proteins in controlling IGF actions. Mol Cell Endocrinol. 1998, 140 (1–2): 19-24.View ArticlePubMedGoogle Scholar
- Clemmons DR: Insulin-like growth factor binding proteins and their role in controlling IGF actions. Cytokine Growth Factor Rev. 1997, 8 (1): 45-62.View ArticlePubMedGoogle Scholar
- Clemmons DR, Busby W, Clarke JB, Parker A, Duan C, Nam TJ: Modifications of insulin-like growth factor binding proteins and their role in controlling IGF actions. Endocr J. 1998, 45 (Suppl): S1-S8.View ArticlePubMedGoogle Scholar
- Ceda GP, Fielder PJ, Henzel WJ, Louie A, Donovan SM, Hoffman AR, Rosenfeld RG: Differential effects of insulin-like growth factor (IGF)-I and IGF-II on the expression of IGF binding proteins (IGFBPs) in a rat neuroblastoma cell line: isolation and characterization of two forms of IGFBP-4. Endocrinology. 1991, 128 (6): 2815-2824.View ArticlePubMedGoogle Scholar
- Shimasaki S, Gao L, Shimonaka M, Ling N: Isolation and molecular cloning of insulin-like growth factor-binding protein-6. Mol Endocrinol. 1991, 5 (7): 938-948.View ArticlePubMedGoogle Scholar
- Li Z, Picard F: Modulation of IGFBP2 mRNA expression in white adipose tissue upon aging and obesity. Horm Metab Res. 2010, 42 (11): 787-791.View ArticlePubMedGoogle Scholar
- Koyama N, Zhang J, Huqun , Miyazawa H, Tanaka T, Su X, Hagiwara K: Identification of IGFBP-6 as an effector of the tumor suppressor activity of SEMA3B. Oncogene. 2008, 27 (51): 6581-6589.View ArticlePubMedGoogle Scholar
- Ehrenborg E, Zazzi H, Lagercrantz S, Granqvist M, Hillerbrand U, Allander SV, Larsson C, Luthman H: Characterization and chromosomal localization of the human insulin-like growth factor-binding protein 6 gene. Mamm Genome. 1999, 10 (4): 376-380.View ArticlePubMedGoogle Scholar
- Neumann GM, Marinaro JA, Bach LA: Identification of O-glycosylation sites and partial characterization of carbohydrate structure and disulfide linkages of human insulin-like growth factor binding protein 6. Biochemistry. 1998, 37 (18): 6572-6585.View ArticlePubMedGoogle Scholar
- Migita T, Narita T, Asaka R, Miyagi E, Nagano H, Nomura K, Matsuura M, Satoh Y, Okumura S, Nakagawa K, Seimiya H, Ishikawa Y: Role of insulin-like growth factor binding protein 2 in lung adenocarcinoma: IGF-independent antiapoptotic effect via caspase-3. Am J Pathol. 2010, 176 (4): 1756-1766.PubMed CentralView ArticlePubMedGoogle Scholar
- Zhuang T, Chen Q, Cho MK, Vishnivetskiy SA, Iverson TM, Gurevich VV, Sanders CR: Involvement of distinct arrestin-1 elements in binding to different functional forms of rhodopsin. Proc Natl Acad Sci U S A. 2013, 110 (3): 942-947.PubMed CentralView ArticlePubMedGoogle Scholar
- Zhao C, Yang P, He H, Lin X, Li B, Zhou H, Huang X, Kijlstra A: S-antigen specific T helper type 1 response is present in Behcet's disease. Mol Vis. 2008, 14: 1456-1464.PubMed CentralPubMedGoogle Scholar
- Huang L, Li W, Tang W, Zhu X, Ou-Yang P, Lu G: A Chinese family with Oguchi’s disease due to compound heterozygosity including a novel deletion in the arrestin gene. Mol Vis. 2012, 18: 528-536.PubMed CentralPubMedGoogle Scholar
- Fujinami K, Tsunoda K, Nakamura M, Oguchi Y, Miyake Y: Oguchi disease with unusual findings associated with a heterozygous mutation in the SAG gene. Arch Ophthalmol. 2011, 129 (10): 1375-1376.View ArticlePubMedGoogle Scholar
- Fuchs S, Nakazawa M, Maw M, Tamai M, Oguchi Y, Gal A: A homozygous 1-base pair deletion in the arrestin gene is a frequent cause of Oguchi disease in Japanese. Nat Genet. 1995, 10 (3): 360-362.View ArticlePubMedGoogle Scholar
- Shi Y, Massagué J: Mechanisms of TGF-beta signaling from cell membrane to the nucleus. Cell. 2003, 113 (6): 685-700.View ArticlePubMedGoogle Scholar
- Wordinger RJ, Fleenor DL, Hellberg PE, Pang IH, Tovar TO, Zode GS, Fuller JA, Clark AF: Effects of TGF-beta2, BMP-4, and gremlin in the trabecular meshwork: implications for glaucoma. Invest Ophthalmol Vis Sci. 2007, 48 (3): 1191-1200.View ArticlePubMedGoogle Scholar
- David D, Cardoso J, Marques B, Marques R, Silva ED, Santos H, Boavida MG: Molecular characterization of a familial translocation implicates disruption of HDAC9 and possible position effect on TGFbeta2 in the pathogenesis of Peters’ anomaly. Genomics. 2003, 81 (5): 489-503.View ArticlePubMedGoogle Scholar
- Mathivanan S, Ahmed M, Ahn NG, Alexandre H, Amanchy R, Andrews PC, Bader JS, Balgley BM, Bantscheff M, Bennett KL, Bjorling E, Blagoev B, Bose R, Brahmachari SK, Burlingame AS, Bustelo XR, Cagney G, Cantin GT, Cardasis HL, Celis JE, Chaerkady R, Chu F, Cole PA, Costello CE, Cotter RJ, Crockett D, DeLany JP, De Marzo AM, DeSouza LV, Deutsch EW, et al: Human Proteinpedia enables sharing of human protein data. Nat Biotechnol. 2008, 26 (2): 164-167.View ArticlePubMedGoogle Scholar
- Mishra GR, Suresh M, Kumaran K, Kannabiran N, Suresh S, Bala P, Shivakumar K, Anuradha N, Reddy R, Raghavan TM, Menon S, Hanumanthu G, Gupta M, Upendran S, Gupta S, Mahesh M, Jacob B, Mathew P, Chatterjee P, Arun KS, Sharma S, Chandrika KN, Deshpande N, Palvankar K, Raghavnath R, Krishnakanth R, Karathia H, Rekha B, Nayak R, Vishnupriya G, et al: Human protein reference database–2006 update. Nucleic Acids Res. 2006, 34 (Database issue): D411-D414.PubMed CentralView ArticlePubMedGoogle Scholar
- Goel R, Harsha HC, Pandey A, Prasad TS: Human Protein Reference Database and Human Proteinpedia as resources for phosphoproteome analysis. Mol Biosyst. 2012, 8 (2): 453-463.PubMed CentralView ArticlePubMedGoogle Scholar
- Harsha HC, Molina H, Pandey A: Quantitative proteomics using stable isotope labeling with amino acids in cell culture. Nat Protoc. 2008, 3 (3): 505-516.View ArticlePubMedGoogle Scholar
- Goel R, Murthy KR, Srikanth SM, Pinto SM, Bhattacharjee M, Kelkar DS, Madugundu AK, Dey G, Mohan SS, Venkatarangaiah K, Prasad TSK, Chakravarti S, Harsha HC, Pandey A: Characterizing the normal proteome of human ciliary body. Clin Proteomics. 2013, 10 (1): 9-PubMed CentralView ArticlePubMedGoogle Scholar
- Chaerkady R, Harsha HC, Nalli A, Gucek M, Vivekanandan P, Akhtar J, Cole RN, Simmers J, Schulick RD, Singh S, Torbenson M, Pandey A, Thuluvath PJ: A quantitative proteomic approach for identification of potential biomarkers in hepatocellular carcinoma. J Proteome Res. 2008, 7 (10): 4289-4298.PubMed CentralView ArticlePubMedGoogle Scholar
- Yang Y, Chaerkady R, Kandasamy K, Huang TC, Selvan LD, Dwivedi SB, Kent OA, Mendell JT, Pandey A: Identifying targets of miR-143 using a SILAC-based proteomic approach. Mol Biosyst. 2010, 6 (10): 1873-1882.View ArticlePubMedGoogle Scholar
- Barbhuiya MA, Sahasrabuddhe NA, Pinto SM, Mutjusamy B, Singh TD, Nanjappa V, Keerthikumar S, Delanghe B, Harsha HC, Chaerkady R, Jalaj V, Gupta S, Srivastav BR, Tiwari PK, Pandey A: Comprehensive proteomic analysis of human bile. Proteomics. 2011, 11 (23): 4443-4453.View ArticlePubMedGoogle Scholar
- Kelkar DS, Kumar D, Kumar P, Muthusamy B, Yadav AK, Srivastava P, Marimuthu A, Anand S, Sundaram H, Kingsbury R, Harsha HC, Nair B, Prasad TS, Chauhan DS, Katoch K, Katoch VM, Kumar P, Chaerkady R, Ramachandran S, Dash D, Pandey A: Proteogenomic analysis of Mycobacterium tuberculosis by high resolution mass spectrometry. Mol Cell Proteomics. 2011, 10 (12): M111.011627-doi: 10.1074/mcp.M111.011445. Epub 2011 Oct 3,PubMed CentralView ArticlePubMedGoogle Scholar
- Rappsilber J, Mann M, Ishihama Y: Protocol for micro-purification, enrichment, pre-fractionation and storage of peptides for proteomics using StageTips. Nat Protoc. 2007, 2 (8): 1896-1906.View ArticlePubMedGoogle Scholar
- Keshava Prasad TS, Goel R, Kandasamy K, Keerthikumar S, Kumar S, Mathivanan S, Telikicherla D, Raju R, Shafreen B, Venugopal A, Balakrishnan L, Marimuthu A, Banerjee S, Somanathan DS, Sebastian A, Rani S, Ray S, Harrys Kishore CJ, Kanth S, Ahmed M, Kashyap MK, Mohmood R, Ramachandra YL, Krishna V, Rahiman BA, Mohan S, Ranganathan P, Ramabadran S, Chaerkady R, Pandey A: Human Protein Reference Database--2009 update. Nucleic Acids Res. 2009, 37 (Database issue): D767-D772.PubMed CentralView ArticlePubMedGoogle Scholar
- Vizcaíno JA, Deutsch EW, Wang R, Csordas A, Reisinger F, Ríos D, Dianes JA, Sun Z, Farrah T, Bandeira N, Binz PA, Xenarios I, Eisenacher M, Mayer G, Gatto L, Campos A, Chalkley RJ, Kraus HJ, Albar JP, Martinez-Bartolomé S, Apweiler R, Omenn GS, Martens L, Jones AR, Hermjakob H: ProteomeXchange provides globally co-ordinated proteomics data submission and dissemination. Nature Biotechnol. 2014, 30 (3): 223-226.View ArticleGoogle Scholar
This article is published under license to BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly credited. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.