Comparative analysis of the tear protein profile in herpes simplex virus type 1 epithelial keratitis

Applications of artificial intelligence and bioinformatics methodologies in the analysis of ocular biofluid markers: a scoping review

PURPOSE

This scoping review summarizes the applications of artificial intelligence (AI) and bioinformatics methodologies in analysis of ocular biofluid markers. The secondary objective was to explore supervised and unsupervised AI techniques and their predictive accuracies. We also evaluate the integration of bioinformatics with AI tools.

METHODS

This scoping review was conducted across five electronic databases including EMBASE, Medline, Cochrane Central Register of Controlled Trials, Cochrane Database of Systematic Reviews, and Web of Science from inception to July 14, 2021. Studies pertaining to biofluid marker analysis using AI or bioinformatics were included.

RESULTS

A total of 10,262 articles were retrieved from all databases and 177 studies met the inclusion criteria. The most commonly studied ocular diseases were diabetic eye diseases, with 50 papers (28%), while glaucoma was explored in 25 studies (14%), age-related macular degeneration in 20 (11%), dry eye disease in 10 (6%), and uveitis in 9 (5%). Supervised learning was used in 91 papers (51%), unsupervised AI in 83 (46%), and bioinformatics in 85 (48%). Ninety-eight papers (55%) used more than one class of AI (e.g. > 1 of supervised, unsupervised, bioinformatics, or statistical techniques), while 79 (45%) used only one. Supervised learning techniques were often used to predict disease status or prognosis, and demonstrated strong accuracy. Unsupervised AI algorithms were used to bolster the accuracy of other algorithms, identify molecularly distinct subgroups, or cluster cases into distinct subgroups that are useful for prediction of the disease course. Finally, bioinformatic tools were used to translate complex biomarker profiles or findings into interpretable data.

CONCLUSION

AI analysis of biofluid markers displayed diagnostic accuracy, provided insight into mechanisms of molecular etiologies, and had the ability to provide individualized targeted therapeutic treatment for patients. Given the progression of AI towards use in both research and the clinic, ophthalmologists should be broadly aware of the commonly used algorithms and their applications. Future research may be aimed at validating algorithms and integrating them in clinical practice.

Herpes simplex keratitis: A brief clinical overview

The aim of our minireview is to provide a brief overview of the diagnosis, clinical aspects, treatment options, management, and current literature available regarding herpes simplex keratitis (HSK). This type of corneal viral infection is caused by the herpes simplex virus (HSV), which can affect several tissues, including the cornea. One significant aspect of HSK is its potential to cause recurrent episodes of inflammation and damage to the cornea. After the initial infection, the HSV can establish a latent infection in the trigeminal ganglion, a nerve cluster near the eye. The virus may remain dormant for extended periods. Periodic reactivation of the virus can occur, leading to recurrent episodes of HSK. Factors triggering reactivation include stress, illness, immunosuppression, or trauma. Recurrent episodes can manifest in different clinical patterns, ranging from mild epithelial involvement to more severe stromal or endothelial disease. The severity and frequency of recurrences vary among individuals. Severe cases of HSK, especially those involving the stroma and leading to scarring, can result in vision impairment or even blindness in extreme cases. The cornea's clarity is crucial for good vision, and scarring can compromise this, potentially leading to visual impairment. The management of HSK involves not only treating acute episodes but also implementing long-term strategies to prevent recurrences and attempt repairs of corneal nerve endings via neurotization. Antiviral medications, such as oral Acyclovir or topical Ganciclovir, may be prescribed for prophylaxis. The immune response to the virus can contribute to corneal damage. Inflammation, caused by the body's attempt to control the infection, may inadvertently harm the corneal tissues. Clinicians should be informed about triggers and advised on measures to minimize the risk of reactivation. In summary, the recurrent nature of HSK underscores the importance of both acute and long-term management strategies to preserve corneal health and maintain optimal visual function.

Viral MicroRNAs in Herpes Simplex Virus 1 Pathobiology

Simplexvirus humanalpha1 (Herpes simplex virus type 1 [HSV-1]) infects millions of people globally, manifesting as vesiculo-ulcerative lesions of the oral or genital mucosa. After primary infection, the virus establishes latency in the peripheral neurons and reactivates sporadically in response to various environmental and genetic factors. A unique feature of herpesviruses is their ability to encode tiny noncoding RNAs called microRNA (miRNAs). Simplexvirus humanalpha1 encodes eighteen miRNA precursors that generate twentyseven different mature miRNA sequences. Unique Simplexvirus humanalpha1 miRNAs repertoire is expressed in lytic and latent stages and exhibits expressional disparity in various cell types and model systems, suggesting their key pathological functions. This review will focus on elucidating the mechanisms underlying the regulation of host-virus interaction by HSV-1 encoded viral miRNAs. Numerous studies have demonstrated sequence- specific targeting of both viral and host transcripts by Simplexvirus humanalpha1 miRNAs. While these noncoding RNAs predominantly target viral genes involved in viral life cycle switch, they regulate host genes involved in antiviral immunity, thereby facilitating viral evasion and lifelong viral persistence inside the host. Expression of Simplexvirus humanalpha1 miRNAs has been associated with disease progression and resolution. Systemic circulation and stability of viral miRNAs compared to viral mRNAs can be harnessed to utilize their potential as diagnostic and prognostic markers. Moreover, functional inhibition of these enigmatic molecules may allow us to devise strategies that have therapeutic significance to contain Simplexvirus humanalpha1 infection.

Profiling tear film enzymes reveals major metabolic pathways involved in the homeostasis of the ocular surface

The ocular surface (OS) enzymes are of great interest due to their potential for novel ocular drug development. We aimed first to profile and classify the enzymes of the OS to describe major biological processes and pathways that are involved in the maintenance of homeostasis. Second, we aimed to compare the enzymatic profiles between the two most common tear collection methods, capillary tubes (CT) and Schirmer strips (ScS). A comprehensive tear proteomic dataset was generated by pooling all enzymes identified from nine tear proteomic analyses of healthy subjects using mass spectrometry. In these studies, tear fluid was collected using CT (n = 4), ScS (n = 4) or both collection methods (n = 1). Classification and functional analysis of the enzymes was performed using a combination of bioinformatic tools. The dataset generated identified 1010 enzymes. The most representative classes were hydrolases (EC 3) and transferases (EC 2). Phosphotransferases, esterases and peptidases were the most represented subclasses. A large portion of the identified enzymes was common to both collection methods (n = 499). More enzymes were specifically detected in the ScS-extracted proteome. The major pathways in which the identified enzymes participate are related to the immune system and protein, carbohydrate and lipid metabolism. Metabolic processes for nucleosides, cellular amides, sugars and sulfur compounds constituted the most enriched biological processes. Knowledge of these molecules highly susceptible to pharmacological manipulation might help to predict the metabolism of ophthalmic medications and develop novel prodrug strategies as well as new drug delivery systems. Combining such extensive knowledge of the OS enzymes with new analytical approaches and techniques might create new prospects for understanding, predicting and manipulating the metabolism of ocular pharmaceuticals. Our study reports new, essential data on OS enzymes while also comparing the enzyme profiles obtained via the two most popular methods of tear collection, capillary tubes and Schirmer strips.

Coronavirus disease 19 (COVID-19) and viral keratouveitis - unraveling the mystery

To demonstrate viral proteins/inflammatory cytokines in a patient with unilateral keratouveitis. Retrospective case report. A 70-year-old Asian-Indian male presented with acute onset of blurring of vision in the left eye (OS) of 2 days duration. He had was coronavirus disease 2019 (COVID-19)-positive 3 months earlier. He had undergone cataract surgery/retinal laser photocoagulation in both the eyes. The corrected distance visual acuity (CDVA) (Snellen) in the right eye (RE) (OD) and left eye (LE) (OS) was 20/20 and 20/80, respectively. OS showed decreased corneal sensation, Descemet's folds, mild stromal edema, and fine and pigmented keratic precipitates with anterior chamber 1+ flare and 1+ cells. Fundus evaluation showed scattered laser marks in the OD and temporal sectoral laser marks in OS. He was diagnosed with viral keratouveitis in OS. Tear samples were collected on Schirmer's strips and tear wash for mass spectrometry and cytokines, which had 368 and 451 viral proteins in the RE and LE, respectively, using nano liquid chromatography-mass spectrometry, which were more than controls. Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and varicella zoster virus proteins were detected. Cytokine analysis using flow cytometer analysis showed higher inflammation in OS as compared to OD. The patient was treated with oral acyclovir and topical steroids and resulted in resolution of his keratouveitis. SARS-CoV-2 proteins were present in the tear sample 3 months after COVID-19. The presence of viral proteins does not indicate causality.

Combined versus sequential penetrating keratoplasty and cataract surgery for herpes simplex keratitis: a retrospective study

Purpose

To compare the surgical outcomes of combined penetrating keratoplasty (PK) and cataract surgery with those of sequential surgery (cataract surgery after PK) for herpes simplex keratitis (HSK).

Methods

The medical records of consecutive patients diagnosed with HSK who underwent combined or sequential PK and cataract surgery in active and stable stages between June 2015 and June 2022 were reviewed retrospectively. Complications, graft survival, endothelial cell density (ECD), and final BCVA were compared and analyzed between both surgical methods in each stage.

Results

A total of 171 eyes of 171 patients were enrolled, including active stage (69 combined, 46 sequential) and stable stage (34 combined, 22 sequential). The average follow up was 24.2 ± 15.8 months (range, 3 months - 48 months). The final BCVA had obvious improvement and the postoperative ECD was not different in combined and sequential groups of each stage. In sequential group of active stage, 66.7% of persistent epithelial defects and 50% of HSK recurrence occurred within 3 months after cataract surgery; nevertheless, compared to that in sequential group, capsular rupture (p = 0.021), persistent epithelial defects (p = 0.027), and HSK recurrence (p = 0.035) occurred more frequently in combined group, leading to a lower graft survival rate (p = 0.045); at the last visit, 46.4 and 67.4% of grafts remained clear in combined and sequential groups, respectively. By contrary, 82.4 and 50.0% of grafts remained clear in stable stages of combined and sequential groups at the last visit, respectively, and a higher graft survival rate was observed in combined group (p = 0.030).

Conclusion

Although the postoperative ECD is not different between two surgical groups in each stage, sequential surgery in active stage of HSK seems to have advantages in less complications and higher graft survival rate, whereas combined surgery in stable stage has a better outcome than that in sequential surgery.

Tear proteomic analysis of young glasses, orthokeratology, and soft contact lens wearers

Contact lens-related ocular surface complications occur more often in teenagers and young adults. The purpose of this study was to determine changes in tear proteome of young patients wearing glasses (GL), orthokeratology lenses (OK), and soft contact lenses (SCL). Twenty-two young subjects (10-26 years of age) who were established GL, OK, and SCL wearers were recruited. Proteomic data were collected using a data-independent acquisition-parallel accumulation serial fragmentation workflow. In total, 3406 protein groups were identified, the highest number of proteins identified in Schirmer strip tears to date. Eight protein groups showed higher abundance, and 11 protein groups showed lower abundance in the SCL group compared to the OK group. In addition, the abundance of 82 proteins significantly differed in children compared to young adult GL wearers, among which 67 proteins were higher, and 15 proteins were lower in children. These 82 proteins were involved in inflammation, immune, and glycoprotein metabolic biological processes. In summary, this work identified over 3000 proteins in Schirmer Strip tears. The results indicated that tear proteomes were altered by orthokeratology and soft contact wear and age, which warrants further larger-scale study on the ocular surface responses of teenagers and young adults separately to contact lens wear. SIGNIFICANCE: In this work, we examined the tear proteomes of young patients wearing glasses, orthokeratology lenses, and soft contact lenses using a data-independent acquisition-parallel accumulation serial fragmentation (diaPASEF) workflow and identified 3406 protein groups in Schirmer strip tears. Nineteen protein groups showed significant abundance changes between orthokeratology and soft contact lens wearers. Moreover, eighty-two protein groups significantly differed in abundance in children and young adult glasses wearers. As a pilot study, this work provides a deep coverage of tear proteome and suggests the need to investigate ocular responses to contact lens wear separately for children and young adults.

Characterization of human tear proteome reveals differentially abundance proteins in thyroid-associated ophthalmopathy

Background

Thyroid-associated ophthalmopathy (TAO) is a common orbital inflammatory disease, but the abnormal expression of proteins in tears of TAO patients has not been systematically studied. The purpose of this study is to compare and analyze the total tear protein profile of TAO patients and to provide protein cues for TAO pathogenesis.

Methods

Tear samples were isolated from 30 TAO patients with obvious ocular surface damage and 30 healthy control subjects. Tear samples from 30 individuals were mixed and divided into three sample pools. Easy nano-scale LC-MS/MS based on labeling-free quantitative technology was utilized to profile tear proteome.

Results

Here, electrospray ionization mass spectra and SDS-PAGE results confirmed the good parallelisms among samples. A total of 313 proteins were obtained from six tear pools, among them, 103 differential abundance proteins (DAPs) were identified, including 99 up-regulated DAPs (including APOA1, HV103, IGH, and Transferrin variant) and four down-regulated DAPs (including FABA, VCC1, NUCB2, and E-cadherin) in the TAO group compared with the control group. GO analysis showed that up-regulated DAPs were mainly enriched in lipid metabolism and platelet molecular function, and down-regulated DAPs were involved in binding, cell junction, and cellular process. KEGG results indicated that DAPs were involved in 117 kinds of signal transduction pathways, among which the immune-related pathway of complement and coagulation cascades had the greatest relevance.

Conclusion

In conclusion, label-free LC-MS/MS is an effective strategy for profiling tear proteins component. Our study provides proteins and pathways altered in TAO and provides protein cues for further study on the precise mechanism of TAO pathogenesis.

The role of Herpes Simplex Virus type 1 in oral diseases in children

Relevance. Herpes virus infections are the most common and poorly controllable viral infections. There are many difficulties in herpetic lesion verification and treatment in dental practice.

Purpose. The study aimed to present the results of a foreign publication investigation on the role of herpes simplex virus type 1 in the development of oral diseases in children.

Material and methods. Foreign scientific articles about the oral HSV-1 infections published from 2018 to 2022 formed the basis for the study. The study searched the publications on PubMed and Google Scholar bases.

Results. The article presents the newest data on the prevalence, clinical characteristics and diagnosis of oral HSV infection in children. Primary herpetic gingivostomatitis (PHGS), chronic recurrent herpetic gingivostomatitis, chronic recurrent herpes labialis are the main clinical presentations of herpes infection diagnosed in a dental practice. Primary herpetic gingivostomatitis is very common in children aged six months to fve years and occurs in newborns from 2 to 43 days of life. Modern virology success can improve diagnosis and treatment of oral herpetic lesions.

Conclusion. Primary herpetic gingivostomatitis is an acute infectious disease that requires the joint attention of a general practitioner and a dentist to ensure comprehensive treatment.

Ocular Surface Infection Mediated Molecular Stress Responses: A Review

Infection mediated ocular surface stress responses are activated as early defense mechanisms in response to host cell damage. Integrated stress responses initiate the host response to different types of infections and modulate the transcription of key genes and translation of proteins. The crosstalk between host and pathogen results in profound alterations in cellular and molecular homeostasis triggering specific stress responses in the infected tissues. The amplitude and variations of such responses are partly responsible for the disease severity and clinical sequelae. Understanding the etiology and pathogenesis of ocular infections is important for early diagnosis and effective treatment. This review considers the molecular status of infection mediated ocular surface stress responses which may shed light on the importance of the host stress-signaling pathways. In this review, we collated literature on the molecular studies of all ocular surface infections and summarize the results from such studies systematically. Identification of important mediators involved in the crosstalk between the stress response and activation of diverse signaling molecules in host ocular surface infection may provide novel molecular targets for maintaining the cellular homeostasis during infection. These targets can be then explored and validated for diagnostic and therapeutic purposes.

Proteomic Analysis of Tears and Conjunctival Cells Collected with Schirmer Strips Using timsTOF Pro: Preanalytical Considerations

This study aimed to investigate the human proteome profile of samples collected from whole (W) Schirmer strips (ScS) and their two parts—the bulb (B) and the rest of the strip (R)—with a comprehensive proteomic approach using a trapped ion mobility mass spectrometer, the timsTOF Pro. Eight ScS were collected from two healthy subjects at four different visits to be separated into three batches, i.e., 4W, 4B, and 4R. In total, 1582 proteins were identified in the W, B, and R batches. Among all identified proteins, binding proteins (43.4%) and those with catalytic activity (42.2%) constituted more than 80% of the molecular functions. The most represented biological processes were cellular processes (31.2%), metabolic processes (20.8%), and biological regulation (13.1%). Enzymes were the most represented protein class (41%), consisting mainly of hydrolases (47.5%), oxidoreductases (22.1%), and transferases (16.7%). The bulb (B), which is in contact with the conjunctiva, might collect both tear and cell proteins and therefore promote the identification of more proteins. Processing B and R separately before mass spectrometry (MS) analysis, combined with the high data acquisition speed and the addition of ion-mobility-based separation in the timsTOF Pro, can bring a new dimension to biomarker investigations of a limited sample such as tear fluid.

Looking deeper into ocular surface health: an introduction to clinical tear proteomics analysis

Ocular surface diseases are becoming more prevalent worldwide. Reasons for this include the ongoing population ageing and increasing use of digital displays, although ophthalmologists have a wide selection of tools, which can be implemented in the evaluation of the ocular surface health, methods, which enable the in-depth study of biological functions are gaining more interest. These new approaches are needed, since the individual responses to ocular surface diseases and treatments can vary from person to person, and the correlations between clinical signs and symptoms are often low. Modern mass spectrometry (MS) methods can produce information on hundreds of tear proteins, which in turn can provide valuable information on the biological effects occurring on the ocular surface. In this review article, we will provide an overview of the different aspects, which are part of a successful tear proteomics study design and equip readers with a better understanding of the methods most suited for their MS-based tear proteomics study in the field of ophthalmology and ocular surface.