Corneal proteome and differentially expressed corneal proteins in highly myopic chicks using a label-free SWATH-MS quantification approach

Exploration of the pathophysiology of high myopia via proteomic profiling of human corneal stromal lenticules

This study aimed to investigate the underlying pathophysiology of high myopia by analyzing the proteome of human corneal stromal lenticule samples obtained through small incision lenticule extraction (SMILE). A total of thirty-two patients who underwent SMILE were included in the study. Label-free quantitative proteomic analysis was performed on corneal stromal lenticule samples, equally representing high myopia (n = 10) and low myopia (n = 10) groups. The identified and profiled lenticule proteomes were analyzed using in silico tools to explore biological characteristics of differentially expressed proteins (DEPs). Additionally, LASSO regression and random forest model were employed to identify key proteins associated with the pathophysiology of high myopia. The DEPs were found to be closely linked to immune activation, extracellular matrix, and cell adhesion-related pathways according to gene ontology analysis. Specifically, decreased expression of COL1A1 and increased expression of CDH11 were associated with the pathogenesis of high myopia and validated by western blotting (n = 6) and quantitative real time polymerase chain reaction (n = 6). Overall, this study provides evidence that COL1A1 and CDH11 may contribute to the pathophysiology of high myopia based on comparative proteomic profiling of human corneal stromal lenticules obtained through SMILE.

Corneal metabolic biomarkers for moderate and high myopia in human

This study aimed to identify the corneal metabolic biomarkers for moderate and high myopia in human. We enrolled 221 eyes from 221 subjects with myopia to perform the femtosecond laser small incision lenticule extraction (SMILE) surgery. Among these, 71 eyes of 71 subjects were enrolled in the low myopic group, 75 eyes of 75 subjects in the moderate myopic group and 75 eyes of 75 subjects in the high myopic group. The untargeted metabolomics analysis was performed to analyze the corneal tissues extracted during the SMILE surgery using an ultra-high-performance liquid chromatography (UHPLC) coupled to a quadrupole time-of-flight (Q-TOF) mass spectrometry (MS). The one-way analysis of variance (ANOVA) was used to identify the different metabolites among the three myopic groups, the orthogonal partial least-squares discriminant analysis (OPLS-DA) model was used to reveal the different metabolites between moderate myopia and low myopia, and between high myopia and low myopia. The Venn gram was used to find the overlapped metabolites of the three datasets of the different metabolites. The stepwise multiple linear regression analysis was used to determine the metabolic molecules associated with manifest refractive spherical equivalents (MRSE). The Receiver Operating Characteristics (ROC) analysis was performed to reveal the corneal biomarkers for moderate and high myopia. The hub biomarker was further selected by the networks among different metabolites created by the Cytoscape software. A total of 1594 metabolites were identified in myopic corneas. 321 metabolites were different among the three myopic groups, 106 metabolites were different between high myopic corneas and low myopic corneas, 104 metabolites were different between moderate myopic corneas and low myopic corneas, and 30 metabolic molecules overlapped among the three datasets. The multivariate linear regression analysis revealed the myopic degree was significantly influenced by the corneal levels of azelaic acid, arginine-proline (Arg-Pro), 1-stearoyl-2-myristoyl-sn-glycero-3-phosphocholine, and hypoxanthine. The ROC curve analysis showed that azelaic acid, Arg-Pro and hypoxanthine were effective in discriminating low myopia from moderate to high myopia with the area under the curve (AUC) values as 0.982, 0.991 and 0.982 for azelaic acid, Arg-Pro and hypoxanthine respectively. The network analysis suggested that Arg-Pro had the maximum connections among these three biomarkers. Thus, this study identified azelaic acid, Arg-Pro and hypoxanthine as corneal biomarkers to discriminate low myopia from moderate to high myopia, with Arg-Pro serving as the hub biomarker for moderate and high myopia.

Region-resolved multi-omics of the mouse eye

The eye is a complex organ consisting of multiple compartments with unique and specialized properties, and small disturbances in one eye region can result in impaired vision and blindness. Although there have been advancements in ocular research, the hierarchical molecular network in region-wide resolution, indicating the division of labor and crosstalk among different eye regions, is not yet comprehensively illuminated. Here, we present an atlas of region-resolved proteome and lipidome of mouse eye. Multiphoton microscopy-guided laser microdissection combined with in-depth label-free proteomics identifies 13,536 proteins across various mouse eye regions. Further integrative analysis of spectral imaging, label-free proteome, and imaging mass spectrometry of the lipidome and phosphoproteome reveals distinctive molecular features, including proteins and lipids of various anatomical mouse eye regions. These deposited datasets and our open proteome server integrating all information provide a valuable resource for future functional and mechanistic studies of mouse eye and ocular disease.

Advances in biomedical study of the myopia-related signaling pathways and mechanisms

Myopia has become one of the most critical health problems in the world with the increasing time spent indoors and increasing close work. Pathological myopia may have multiple complications, such as myopic macular degeneration, retinal detachment, cataracts, open-angle glaucoma, and severe cases that can cause blindness. Mounting evidence suggests that the cause of myopia can be attributed to the complex interaction of environmental exposure and genetic susceptibility. An increasing number of researchers have focused on the genetic pathogenesis of myopia in recent years. Scleral remodeling and excessive axial elongating induced retina thinning and even retinal detachment are myopia's most important pathological manifestations. The related signaling pathways are indispensable in myopia occurrence and development, such as dopamine, nitric oxide, TGF-β, HIF-1α, etc. We review the current major and recent progress of biomedicine on myopia-related signaling pathways and mechanisms.

Preparation of Hard Tissues Like Bone or Cartilage for Shotgun Mass Spectrometry Analysis of the Proteome

Proteomic analyses of intervertebral discs (IVDs) reveal information for understanding the fundamentals of biological processes and pathogenesis but also provide insights for novel pharmaceutical development. Sensitive mass spectrometry techniques and bioinformatics have advanced the detection and identification of proteins from any sample. Due to the challenges of catastrophic sample-loss artifacts during hard-tissue extraction, however, many researchers have omitted the cartilage endplates of IVDs for protein extraction, analyzing only the cellular components of the annulus fibrosus and/or nucleus pulposus. The full proteomic picture of IVDs is compromised without extracting proteins from intact IVDs. Here, we describe a novel preparation method using snap-freeze grinding, which allows for mechanical disruption and customized chemical lysis of hard tissues such as bone or cartilage. This method replaces the time-consuming and insufficient conventional tissue homogenization methods. Sample loss and contamination could be minimized during proteolysis by using an in-solution protein digestion and desalting procedure. We demonstrate excellent proteome coverage with intact mouse IVDs by analyzing samples in a hybrid quadrupole time-of-flight tandem mass spectrometer. © 2021 Wiley Periodicals LLC.

Novel Corneal Protein Biomarker Candidates Reveal Iron Metabolic Disturbance in High Myopia Eyes

Myopia is a major public health concern with increasing global prevalence and is the leading cause of vision loss and complications. The potential role of the cornea, a substantial component of refractive power and the protective fortress of the eye, has been underestimated in the development of myopia. Our study acquired corneal stroma tissues from myopic patients undergoing femtosecond laser-assisted small incision lenticule extraction (SMILE) surgery and investigated the differential expression of circulating proteins between subjects with low and high myopia by means of high-throughput proteomic approaches—the quantitative tandem mass tag (TMT) labeling method and parallel reaction monitoring (PRM) validation. Across all corneal stroma tissue samples, a total of 2,455 proteins were identified qualitatively and quantitatively, 103 of which were differentially expressed between those with low and high myopia. The differentially abundant proteins (DAPs) between the groups of stroma samples mostly demonstrated catalytic activity and molecular function regulator and transporter activity and participated in metabolic processes, biological regulation, response to stimulus, and so forth. Pathway enrichment showed that mineral absorption, ferroptosis, and HIF-1 signaling pathways were activated in the human myopic cornea. Furthermore, TMT analysis and PRM validation revealed that the expression of ferritin light chain (FTL, P02792) and ferritin heavy chain (FTH1, P02794) was negatively associated with myopia development, while the expression of serotransferrin (TF, P02787) was positively related to myopia status. Overall, our results indicated that subjects with low and high myopia could have different proteomic profiles or signatures in the cornea. These findings revealed disturbances in iron metabolism and corneal oxidative stress in the more myopic eyes. Iron metabolic proteins could serve as an essential modulator in the pathogenesis of myopia.

Integrating Clinical Data and Tear Proteomics to Assess Efficacy, Ocular Surface Status, and Biomarker Response After Orthokeratology Lens Wear

Purpose

This study evaluated the efficacy and ocular surface status of Breath-O Correct, novel orthokeratology (OK) lenses, worn overnight for 3 months. Lens-induced changes in the tear proteome were evaluated.

Methods

Thirty-one subjects, aged 19 to 26 years with refractive error from -1.00 to -5.00 D, were randomly assigned 1:1 to the treatment or control group. Refraction, visual acuity, corneal integrity, biomechanics and endothelial health, ocular surface changes, and subjective symptoms were assessed at the baseline, one-month, and three-month visits. The tear proteome was characterized over time using sequential window acquisition of all theoretical ion spectra mass spectrometry.

Results

Lenses improved uncorrected visual acuity and reduced spherical powers with similar efficacy to other OK lenses. Significant reductions (P < 0.05) in corneal hysteresis (11.12 ± 1.12 to 10.38 ± 1.36 mm Hg) and corneal resistance factor (11.06 ± 1.32 to 9.90 ± 1.45 mm Hg) were observed in the treatment group after one month of lens wear, whereas other assessed factors remained unchanged. Thirteen and eight differentially expressed proteins were found after one month and three months of lens wear, respectively. Two proteins (proline-rich protein 27 and immunoglobulin V regions) were differentially expressed at both visits.

Conclusions

Over a three-month period, Breath-O Correct lenses were overall safe, well tolerated, efficacious in refractive power reduction, and comparable with other OK lenses. Furthermore, their use caused only minor noninflammatory protein expression changes in the tear proteome.

Translational Relevance

This study investigated the safety of orthokeratology contact lenses on the ocular surface in molecular aspects and standard clinical parameters.