Human tear proteome dataset in response to daily wear of water gradient contact lens using SWATH-MS approach.
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ABSTRACT:
SUBMITTER: Cheung JK
PROVIDER: S-EPMC8165404 | biostudies-literature |
REPOSITORIES: biostudies-literature
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Project description:The present study elucidated the pathogenesis of allergic symptoms (AS) related to contact lens (CL) wear by assaying CL care solutions in lens storage cases and tears from subjects with AS using molecular biology techniques. A total of 15 CL storage cases were collected from subjects with AS (n=9) and healthy, asymptomatic control CL wearers (n=6). Bacterial populations in CL care solutions and tears were assayed by culture and 16S rDNA sequencing. Histamine levels in tears were measured by high‑performance liquid chromatography. Western blot analysis was performed to identify the bacteria recognized by tear IgE from subjects with AS. No significant differences were found in the culture results between the subjects with AS and asymptomatic subjects. Histamine was detected in 2 subjects with AS. Meta‑16S rDNA sequencing identified a cluster of 4 subjects with AS that were distinguished from others by principal coordinate analysis. Detailed population analysis revealed that the abundance of Gram‑positive bacteria in the microbiomes of CL care solutions used by the subjects with AS were higher than those of asymptomatic subjects (42.24±9.47 vs. 16.85±22.76% abundance). Among these, Streptococcus was the dominant genus (12.1‑18.3% abundance). Tear microbiome analysis revealed that the abundance of Streptococcus in the subjects with AS was significantly higher than that in other subjects (19.02±5.50 vs. 3.08±3.35%, P<0.01). Western blot analysis demonstrated that the tear IgE in all subjects with AS reacted with Streptococcus (100%), but not with Staphylococcus. On the whole, these results provide novel insight into the pathogenesis of AS and identify Streptococcus as an important factor in AS associated with CL wear.
| S-EPMC7447315 | biostudies-literature
Project description:PurposeThis study investigated independent risk factors and causative organisms in microbial keratitis in daily disposable contact lens (CL)-wearers.MethodsA multisite prospective case-control study was undertaken. Cases were daily disposable CL-wearers attending Moorfields Eye Hospital with microbial keratitis and those reported through a one-year surveillance study in Australia and in New Zealand. A population-based telephone survey identified daily disposable CL-wearing controls. Subjects completed a questionnaire describing CL-wear history, hygiene and demographics. The sample used for risk factor analysis was weighted in proportion to the CL-wearing population at each location. Corneal scrape results were accessed. Independent risk factors were determined using multiple binary logistic regression. Causative organisms in different CL-wear modalities were compared using a chi-squared test.Results963 daily disposable CL-wearers were identified, from which 67 cases and 374 controls were sampled. Independent risk factors were; wearing CLs every day compared with less frequent use (OR 10.4x; 95% CI 2.9-56.4), any overnight wear (OR 1.8x; 95% CI 1.6-2.1), less frequent hand washing (OR 1.8x; 95% CI 1.6-2.0), and smoking (OR 1.3x; 95% CI 1.1-1.6). Certain daily disposable CLs (OR 0.2x; 95% CI 0.1-0.2) had protective effects. Environmental organisms were less frequently recovered with daily disposable CLs (20%), compared with other modalities (36%; p<0.02).ConclusionOvernight wear, increased exposure in daily wear, smoking and poor hand hygiene are significant risk factors for microbial keratitis with daily disposable CLs. Risk varied with daily disposable CL type. The profile of causative organisms is consistent with less severe disease.
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Project description:PurposeTo elucidate dysregulated proteins in keratoconus (KC) to provide a better understanding of the molecular mechanisms that lead to the development of the disease using sequential window acquisition of all theoretical mass spectra (SWATH-MS) as a protein quantification tool of the tear proteomic profile.MethodsProspective cross-sectional study that includes 25 keratoconic eyes and 25 healthy eyes. All participants underwent a clinical, tomographic, and aberrometric exam. Tear sample was collected using Schirmer strips and analyzed by liquid chromatography with tandem mass spectrometry. SWATH-MS was used as a quantification tool of the tear proteomic profile. The expression of the quantified proteins was compared between groups, and the biological and molecular functions of the dysregulated proteins as well as their functional relationships were studied by in silico analysis.ResultsA total of 203 proteins were quantified in tear samples of patients with KC and control participants, of which 18 showed differential expression between groups (P < 0.05). An increase in the expression of 7 proteins and a decrease in the expression of 11 proteins were observed. Protein-protein interactions and gene ontology analysis showed the involvement of these dysregulated proteins in structural, inflammatory-immune, iron homeostasis, oxidative stress, and extracellular matrix proteolysis processes.ConclusionsTear protein quantification has revealed the dysregulation of proteins involved in biological processes previously associated with KC. Among them, iron homeostasis should be highlighted as a relevant pathway in the KC pathophysiology, and it should be taken into account in the development of therapeutic targets to cope with tissue damage derived from iron accumulation and toxicity.
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Project description:Contact lens-induced papillary conjunctivitis (CLPC) continues to be a major cause of dropout during extended wear of contact lenses. This retrospective study explores risk factors for the development of CLPC during extended wear of silicone hydrogel lenses.Data from 205 subjects enrolled in the Longitudinal Analysis of Silicone Hydrogel Contact Lens study wearing lotrafilcon A silicone hydrogel lenses for up to 30 days of continuous wear were used to determine risk factors for CLPC in this secondary analysis of the main cohort. The main covariates of interest included substantial lens-associated bacterial bioburden and topographically determined lens base curve-to-cornea fitting relationships. Additional covariates of interest included history of adverse events, time of year, race, education level, gender, and other subject demographics. Statistical analyses included univariate logistic regression to assess the impact of potential risk factors on the binary CLPC outcome and Cox proportional hazards regression to describe the impact of those factors on time-to-CLPC diagnosis.Across 12 months of follow-up, 52 subjects (25%) experienced CLPC. No associations were found between the CLPC development and the presence of bacterial bioburden, lens-to-cornea fitting relationships, history of adverse events, gender, or race. Contact lens-induced papillary conjunctivitis development followed the same seasonal trends as the local peaks in environmental allergens.Lens fit and biodeposits, in the form of lens-associated bacterial bioburden, were not associated with the development of CLPC during extended wear with lotrafilcon A silicone hydrogel lenses.
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Project description:Proteins are major effectors and regulators of biological processes that can elicit multiple functions depending on their interaction with other proteins. The organization of proteins into macromolecular complexes and their quantitative distribution across these complexes is, therefore, of great biological and clinical significance. In this paper, we describe an integrated experimental and computational technique to quantify hundreds of protein complexes in a single operation. The method consists of size exclusion chromatography (SEC) to fractionate native protein complexes, SWATH/DIA mass spectrometry to precisely quantify the proteins in each SEC fraction, and the computational framework CCprofiler to detect and quantify protein complexes by error-controlled, complex-centric analysis using prior information from generic protein interaction maps. Our analysis of the HEK293 cell line proteome delineates 462 complexes composed of 2,127 protein subunits. The technique identifies novel sub-complexes and assembly intermediates of central regulatory complexes while assessing the quantitative subunit distribution across them. We make the toolset CCprofiler freely accessible and provide a web platform, SECexplorer, for custom exploration of the HEK293 proteome modularity.
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Project description:Purpose:To subjectively evaluate the in vivo tear film stability of three daily disposable contact lenses (DDCLs) using placido ring reflection at lens wear times of 5 mins and 8 and 12 hrs. Patients and Methods:This prospective, randomized, observer-masked, 3-way crossover study evaluated 28 subjects with good tear film stability. In vivo tear film stability was assessed for three DDCLs (nelfilcon A, etafilcon A, omafilcon A) on three different days over 12 hrs of lens wear. Time to first distortion by non-invasive keratography drying-up time (NIK-DUTf) was assessed by reviewing the captured videos. Lens wettability was also graded subjectively by three investigators using a scale from 0 (no visible distortions) to 3 (distortions in more than one-third of the ring reflection zone). Medians were analyzed statistically. Results:Mean NIKDUTf at 8 hrs was longer for nelfilcon A and shorter for etafilcon A and omafilcon A, but the differences were not significant. NIK-DUTf did not differ significantly among nelfilcon A, etafilcon A and omafilcon A DDCLs at all visits (p=0.36). Subjective wettability grades after 5 mins, 8 hrs, and 12 hrs differed significantly for etafilcon A (P <0.01) and omafilcon A (p < 0.01), but not for nelfilcon A (p = 0.05), DDCLs. Conclusion:Grading was sufficiently sensitive to differentiate the wettability performances of the three lens materials. Nelfilcon A maintained wettability over the wearing period, whereas etafilcon A material showed faster dewetting at 8 and 12 hrs than at 5 mins after lens insertion.
| S-EPMC7053817 | biostudies-literature
Project description:PurposeMicrobial contamination of contact lenses is associated with corneal infection and inflammation. This study determined the microbiological, clinical, and demographic factors that are associated with bacterial contamination of a silicone hydrogel contact lens when worn for continuous wear (CW).MethodsTwo hundred five healthy subjects were enrolled in the Longitudinal Analysis of Silicone Hydrogel Contact Lens Study and were fitted with lotrafilcon A lenses for monthly CW and followed for 1 year. Lenses were aseptically removed after 1 week and 4 months of wear and cultured using an agar sandwich technique. Lids and conjunctiva were routinely cultured at baseline and after 1 week and 4 months of CW. Lenses and ocular sites were considered to have substantial microbial bioburden when they harbored pathogenic organisms or high levels of commensal organisms. Univariate and multivariate logistic regression analyses were conducted to examine whether substantial conjunctival or lid bioburden, subject demographics, lens-wearing history, symptoms, and biomicroscopic signs were associated with lens bioburden.ResultsAbout one third (32.4%) of subjects had substantial bacterial bioburden in either eye across multiple visits. Over half (53.2%) and about one tenth (11.7%) of subjects had substantial lid and conjunctival bioburden, respectively, and 11.2% discontinued because of discomfort. The adjusted odds ratios (and 95% confidence intervals) for presence of substantial lens bioburden were 2.49 (1.17-5.30), 4.24 (1.45-12.40), and 4.11 (1.17-14.46) for substantial lid bioburden, substantial conjunctival bioburden, and lens discomfort, respectively.ConclusionsBacterial contamination of silicone hydrogel contact lenses is common during CW. Substantial lens bioburden is associated with discomfort precluding successful CW. The presence of substantial lid and conjunctival bioburden is associated with a 2.5-fold and more than fourfold greater risk of substantial lens bioburden and is likely the major route of contamination.
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Project description:Data independent acquisition (DIA) has emerged as a promising mass spectrometry based approach, combining the advantages of shotgun and targeted proteomics. Here we applied a DIA approach (termed SWATH) to monitor the dynamics of the Drosophila melanogaster embryonic proteome upon heat-shock treatment. Embryos were incubated for 0.5, 1 or 3 h at 37 °C to induce heat-shock or maintained at 25 °C. The present dataset contains SWATH files acquired on a Sciex Triple-TOF 6600. A spectral library built in-house was used to analyse these data and led to the quantification of more than 2500 proteins at every timepoint. The files presented here are permanent digital maps and can be reanalysed to search for new questions. The data have been deposited with the ProteomeXchange Consortium with the dataset identifier PRIDE: PXD004753.
| S-EPMC5123040 | biostudies-literature
Project description:ObjectivesThis study used a rat contact lens (CL) model to test if high- versus low-Dk lens wear caused changes in (1) conjunctival Langerhans cell (LC) number or location; (2) Bcl-2 expression; and (3) infection risk.MethodsFemale, Lewis rats wore a high- or low-Dk CL continuously for 2 weeks. Afterward, corneas were harvested and processed for ADPase activity to identify LCs, for immunostaining and for real time-polymerase chain reaction. Contact lens-wearing rats also were challenged with Pseudomonas aeruginosa by placing a bacterial-soaked CL on the eye followed by topical delivery of bacteria. After 48 hrs, slit lamp examination and real time-polymerase chain reaction were used to evaluate the corneal response.ResultsConjunctival LC were significantly increased after low- versus high-Dk CL wear (P<0.0001). In contrast, conjunctival LC in non-lens wearing rats was not significantly different from the high-Dk lens wearing group. Bcl-2 mRNA levels were significantly decreased in low- versus high-Dk CL wearing rats, while Bax, FasL, caspase 3, and caspase 9 levels were unchanged. Immunostaining for Bcl-2 showed fewer positively stained epithelial cells in the low- versus high-Dk lens wearing group. After bacterial challenge, 30% of low- versus none of the high-Dk CL wearing corneas became infected and showed increased mRNA levels for several proinflammatory cytokines/chemokines, inducible nitric oxide synthase and matrix metalloproteinase-9.ConclusionLow- versus high-Dk or non-CL wear led to an increased number of conjunctival LC, decreased Bcl-2 levels, and increased the risk of bacterial infection.
| S-EPMC4274951 | biostudies-literature
Project description:Embryogenesis is one of the most important processes in the life of an animal. During this dynamic process, progressive cell division and cellular differentiation are accompanied by significant changes in protein expression at the level of the proteome. However, very few studies to date have described the dynamics of the proteome during the early development of an embryo in any organism. In this dataset, we monitor changes in protein expression across a timecourse of more than 20 h of Drosophila melanogaster embryonic development. Mass-spectrometry data were produced using a SWATH acquisition mode on a Sciex Triple-TOF 6600. A spectral library built in-house was used to analyse these data and more than 1950 proteins were quantified at each embryonic timepoint. The files presented here are a permanent digital map and can be reanalysed to test against new hypotheses. The data have been deposited with the ProteomeXchange Consortium with the dataset identifier PRIDE: PXD0031078.
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