Comparison of gene expression profiles in primary and immortalized human pterygium fibroblast cells

Research methods assessing sodium hypochlorite cytotoxicity: A scoping review

Sodium hypochlorite (NaOCl) cytotoxicity has been assessed using different methodologies, which has led to arbitrary interpretations. This scoping review aimed to discuss the different methodological protocols for assessing NaOCl cytotoxicity. A literature review performed in the PubMed and Embase databases up to July 2023 identified manuscripts reporting NaOCl cytotoxicity. The dataset identified 546 publications, further screened by 2 reviewers. Ninety studies were identified and mined methodologically to collect information on cell type, cytotoxicity assay, NaOCl dilution solutions, presence of fetal bovine serum (FBS), and NaOCl exposure time. The culture medium used in cytotoxicity assays contains buffering substances that neutralize the pH of NaOCl, thus reducing its cytotoxicity, an approach that may lead to bias when solutions with different pH are compared. For short exposure periods, as in simulations to evaluate the contact between irrigant and periapical tissue cells during chemo-mechanical preparation, NaOCl dilution should be performed with saline, which does not buffer the irrigant. For long exposure periods, as in simulations of irrigant extrusions, NaOCl should be diluted in the culture medium, to reproduce the expected buffering effect occurring in extrusions. The presence of FBS in culture medium can decrease NaOCl toxicity. There is no standardization of NaOCl cytotoxicity methodologies. This poses the risk of arriving at incorrect results and, therefore, pertinent tests must be refined.

TFOS Lifestyle Report: Impact of environmental conditions on the ocular surface

Environmental risk factors that have an impact on the ocular surface were reviewed and associations with age and sex, race/ethnicity, geographical area, seasonality, prevalence and possible interactions between risk factors are reviewed. Environmental factors can be (a) climate-related: temperature, humidity, wind speed, altitude, dew point, ultraviolet light, and allergen or (b) outdoor and indoor pollution: gases, particulate matter, and other sources of airborne pollutants. Temperature affects ocular surface homeostasis directly and indirectly, precipitating ocular surface diseases and/or symptoms, including trachoma. Humidity is negatively associated with dry eye disease. There is little data on wind speed and dewpoint. High altitude and ultraviolet light exposure are associated with pterygium, ocular surface degenerations and neoplastic disease. Pollution is associated with dry eye disease and conjunctivitis. Primary Sjögren syndrome is associated with exposure to chemical solvents. Living within a potential zone of active volcanic eruption is associated with eye irritation. Indoor pollution, "sick" building or house can also be associated with eye irritation. Most ocular surface conditions are multifactorial, and several environmental factors may contribute to specific diseases. A systematic review was conducted to answer the following research question: "What are the associations between outdoor environment pollution and signs or symptoms of dry eye disease in humans?" Dry eye disease is associated with air pollution (from NO2) and soil pollution (from chromium), but not from air pollution from CO or PM10. Future research should adequately account for confounders, follow up over time, and report results separately for ocular surface findings, including signs and symptoms.

Transglutaminase-2 is critical for corneal epithelial barrier function via positive regulation of Claudin-1

PURPOSE

Transglutaminase (TG)-2 is a ubiquitous multi-functional protein expressed in all living cells. The purpose of the current study was to investigate the role of TG-2 in corneal barrier function and its potential regulation of epithelial junctional proteins and transcription factors.

METHODS

Corneal barrier function to ions in TG-2-/- and TG-2+/+ mice was assessed by Ussing chamber assay. Hypo-osmolar water or FITC-dextran was applied on top of mouse eyes to evaluate the corneal barrier function to water and macromolecules. Western blots, qPCR and immunofluorescent staining were used to investigate the expression of tight junction proteins in TG-2-/- and TG-2+/+ mouse corneas, and also in TG-2 knockdown human corneal epithelial cells.

RESULTS

Corneal explants from TG-2-/- mice had a lower trans-epithelial electrical resistance compared to TG-2+/+ mice. When challenged by hypo-osmolar water, the central corneal thickness of TG-2-/- mice increased faster, and these mice had a faster rise of fluorescence in the anterior chamber after ocular exposure to FITC-dextran, compared to TG-2+/+. Claudin-1 protein and transcript levels were reduced in the cornea of TG-2-/- mice and in TG-2 knockdown human corneal epithelial cells. Slug which previously reported suppressing Claudin-1 transcription, was increased at both protein and transcript level in TG-2 knockdown cells. TG-2 and Claudin-1 protein levels were unchanged in shRNA and shTG cells after MG132 treatment, while Slug accumulated in treated cells.

CONCLUSION

TG-2 may positively regulate Claudin-1 through repressing Slug at transcript level, and thus it is critical for normal corneal barrier function.

Characterization of the Cellular Microenvironment and Novel Specific Biomarkers in Pterygia Using RNA Sequencing

With a worldwide prevalence of ~12%, pterygium is a common degenerative and environmentally triggered ocular surface disorder characterized by wing-shaped growth of conjunctival tissue onto the cornea that can lead to blindness if left untreated. This study characterizes the transcriptional profile and the cellular microenvironment of conjunctival pterygia and identifies novel pterygia-specific biomarkers. Formalin-fixed and paraffin-embedded pterygia as well as healthy conjunctival specimens were analyzed using MACE RNA sequencing (n = 8 each) and immunohistochemistry (pterygia n = 7, control n = 3). According to the bioinformatic cell type enrichment analysis using xCell, the cellular microenvironment of pterygia was characterized by an enrichment of myofibroblasts, T-lymphocytes and various antigen-presenting cells, including dendritic cells and macrophages. Differentially expressed genes that were increased in pterygia compared to control tissue were mainly involved in autophagy (including DCN, TMBIM6), cellular response to stress (including TPT1, DDX5) as well as fibroblast proliferation and epithelial to mesenchymal transition (including CTNNB1, TGFBR1, and FN1). Immunohistochemical analysis confirmed a significantly increased FN1 stromal immunoreactivity in pterygia when compared to control tissue. In addition, a variety of factors involved in apoptosis were significantly downregulated in pterygia, including LCN2, CTSD, and NISCH. Furthermore, 450 pterygia-specific biomarkers were identified by including transcriptional data of different ocular surface pathologies serving as controls (training group), which were then validated using transcriptional data of cultured human pterygium cells. Among the most pterygia-specific factors were transcripts such as AHNAK, RTN4, TPT1, FSTL1, and SPARC. Immunohistochemical validation of SPARC revealed a significantly increased stromal immunoreactivity in pterygia when compared to controls, most notably in vessels and intravascular vessel wall-adherent mononuclear cells. Taken together, the present study provides new insights into the cellular microenvironment and the transcriptional profile of pterygia, identifies new and specific biomarkers and in addition to fibrosis-related genes, uncovers autophagy, stress response and apoptosis modulation as pterygium-associated processes. These findings expand our understanding of the pathophysiology of pterygia, provide new diagnostic tools, and may enable new targeted therapeutic options for this common and sight-threatening ocular surface disease.

Pterygium: an update on pathophysiology, clinical features, and management

Pterygium is a relatively common ocular surface disease. The clinical aspects and the treatment options have been studied since many years ago, but many uncertainties still exist. The core pathologic pathway and the role of heredity in the development of pterygium are still attractive fields for the researchers. The role of pterygium in corneal irregularities, in addition to the refractive properties of pterygium removal, has been increasingly recognized through numerous studies. The association between pterygium and ocular surface neoplasia is challenging the traditional beliefs regarding the safe profile of the disease. The need for a comprehensive clinical classification system has encouraged homogenization of trials and prediction of the recurrence rate of the pterygium following surgical removal. Evolving surgical methods have been associated with some complications, whose diagnosis and management are necessary for ophthalmic surgeons. According to the review, the main risk factor of pterygium progression remains to be the ultraviolet exposure. A major part of the clinical evaluation should consist of differentiating between typical and atypical pterygia, where the latter may be associated with the risk of ocular surface neoplasia. The effect of pterygium on astigmatism and the aberrations of the cornea may evoke the need for an early removal with a purpose of reducing secondary refractive error. Among the surgical methods, conjunctival or conjunctival-limbal autografting seems to be the first choice for ophthalmic surgeons because the recurrence rate following the procedure has been reported to be lower, compared with other procedures. The use of adjuvant options is supported in the literature, where intraoperative and postoperative mitomycin C has been the adjuvant treatment of choice. The efficacy and safety of anti–vascular endothelial growth factor agents and cyclosporine have been postulated; however, their exact role in the treatment of the pterygium requires further studies.

Analysis of CRABP2 and FABP5 genes in primary and recurrent pterygium tissues

The etiology of pterygium remains unclear, but ultraviolet (UV) radiation is generally considered to be major risk factor. Pterygium has similarity features with many cancers, including inflammation, invasion, cell proliferation, anti-apoptosis, angiogenesis and recurrence after resection. Retinoic acid via cellular retinoic acid binding protein 2 (CRABP2) is involved in cell cycle arrest, apoptosis and differentiation, while it via fatty acid binding protein 5 (FABP5) is involved in survival, cell proliferation and angiogenesis, which pathway gets activated depends on the CRABP2/FABP5 ratio. Alterations of retinoid signaling were found in many cancer types. The deregulated retinoid signaling may also contribute to the development and/or recurrence of pterygium. The aim of our study was to determine mRNA and protein expressions of CRABP2 and FABP5 and ratio of CRABP2/FABP5 in primer and recurrent pterygium tissues. Pterygia tissues were collected from 30 eyes of 30 patients undergoing pterygium excision. CRABP2 and FABP5 mRNA and protein expression were assessed using Real-time PCR and Western blotting through examination of excised specimens from pterygium and conjunctiva tissues. The ratio of CRABP2/FABP5 gene expression was not altered when primary pterygium tissues compared normal conjunctival tissues (1.00-fold change). Whereas the ratio of CRABP2/ FABP5 gene expression was decreased when recurrent pterygium tissues compared normal conjunctival tissues (0.81-fold change). Understanding etiopathogenesis of pterygium may aid in the find of more promising treatments to prevent pterygium in earlier stages.

Carcinomas with Occult Metastasis Potential: Diagnosis/Prognosis Accuracy Improvement by Means of Force Spectroscopy

Accurate diagnosis of cancer stage is inevitable for the following prognosis in patients struggling with these lesions to promote their health and survival rate. Previous studies on survival rate statistics show, in some cases, failure in cancer stage surveys in which metastasis or recurrence of the disease was not accurately prognosed. Morphology study of cancer cells advances the understanding about cancer behavior and its progression, in which, in our previous study on invasive cancer cells, fewer formations of cytoskeleton components compared to their counterparts was observed. Here it is shown that carcinomas with an occult propensity of metastasis depict a number of poorly differentiated cells with decreased amounts of cytoskeleton components in a near-well differentiated population. Force spectroscopy in conjunction with fluorescence microscopy of lung cancer, liver hepatoma, and melanoma provides a general view of these cells' architecture, leading to the conclusion that the scarce abnormal-shaped cells with low formation of structural filaments convey the high risk of metastatic potential of the tumor. The results demonstrate that force spectroscopy complements conventional diagnostic approaches by an accurate cytoskeleton assessment and can improve the following prognosis in epithelial cancers with occult metastasis risk.

Gene expression in immortalized versus primary isolated cardiac endothelial cells

Endothelial cells take pivotal roles in the heart and the vascular system and their differentiation, subspecification and function is determined by gene expression. A stable, in vitro cardiac endothelial cell line could provide high cell numbers as needed for many epigenetic analyses and facilitate the understanding of molecular mechanisms involved in endothelial cell biology. To test their suitability for transcriptomic or epigenetic studies, we compared the transcriptome of cultured immortalized mouse cardiac endothelial cells (MCEC) to primary cardiac endothelial cells (pEC). Whole transcriptome comparison of MCEC and pEC showed a correlation of 0.75–0.77. Interestingly, correlation of gene expression declined in endothelial cell-typical genes. In MCEC, we found a broad downregulation of genes that are highly expressed in pEC, including well-described markers of endothelial cell differentiation. Accordingly, systematic analysis revealed a downregulation of genes associated with typical endothelial cell functions in MCEC, while genes related to mitotic cell cycle were upregulated when compared to pEC. In conclusion, the findings from this study suggest that primary cardiac endothelial cells should preferably be used for genome-wide transcriptome or epigenome studies. The suitability of in vitro cell lines for experiments investigating single genes or signaling pathways should be carefully validated before use.

Microphysiological System Design: Simplicity Is Elegance

Design parameters for microphysiological systems (MPS) are driven by the need for new tools to answer questions focusing on human physiology in a robust and reliable manner. Within this perspective, engineering benchmarks and principles are identified to guide the construction of new devices in the MPS field, with emphasis placed on the design principles common to all tissues, as well as those unique to a subset of tissues. Leading organ replica technologies that recapitulate various functions of the brain, heart, intestine, and lung are highlighted as examples that meet the identified benchmarks and standards, with current barriers for large scale production and commercialization discussed. To reach their full potential and achieve widespread use, MPS will have to be recognized officially by government agencies, and toward this end, considerations of MPS as a potential regulatory tool are presented.

Effects of Calcium Hypochlorite and Octenidine Hydrochloride on L929 And Human Periodontal Ligament Cells

Abstract The aim of this study was to assess cytotoxicity and cell migration of calcium hypochlorite [Ca(OCl)2] and octenidine hydrochloride - OCT (Octenisept®, Schülke & Mayr, Norderstedt, Germany) in L929 and human periodontal ligament (hPDL) cells. The cells were exposed to different doses of different solutions: 2.5% and 5% Ca(OCl)2, 0.1% OCT, 2.5% NaOCl and 2% CHX for 10 min. Cell viability was assessed by methyl-thiazol-tetrazolium (MTT) and neutral red (NR) assays, and cell migration was determined by wound-healing assay. Statistical analysis was performed by two-way ANOVA and Bonferroni tests (α=0.05). The MTT and NR assays revealed that 0.1% OCT was less cytotoxic in hPDL cells (p<0.05), followed by 2% CHX and 2.5% Ca(OCl)2 (p<0.05). There was no significant difference between 2.5% NaOCl and 5% Ca(OCl)2 (p>0.05), but these solutions showed greater cytotoxicity than the others. The result was the same for L929 cells, except that there was no significant difference between 2% CHX and 2.5% Ca(OCl)2 (p>0.05). Wound-healing assay in L929 and hPDL cells showed that cell migration of 0.1% OCT, 2% CHX and 2.5% Ca(OCl)2 groups was higher than 5% Ca(OCl)2 and 2.5% NaOCl groups at 24 h (p<0.05). In conclusion, 0.1% OCT had lower cytotoxicity in tested cell lines than CHX, Ca(OCl)2 and NaOCl. Cell migration was higher for 0.1% OCT, 2% CHX and 2.5% Ca(OCl)2. Therefore, in terms of cytotoxicity, OCT and Ca(OCl)2 have the potential to be used as root canal irrigants.

Toll-like receptor 2-mediated NF-kappa B pathway activation in ocular surface epithelial cells

BACKGROUND

Gram-positive bacteria stimulate Toll-like receptor (TLR) 2 and then activate the pro-inflammatory nuclear factor-kappa B (NF-κB) pathway. As the human ocular surface is heavily colonised by gram-positive cocci bacteria, a balance of activation/repression of NF-κB target genes is essential to avoid uncontrolled infection or autoimmune-related inflammation. It is advantageous to test NF-κB targeting molecules in an ocular surface culture system that allows assessment of temporal NF-κB activation in a longitudinal fashion without destruction of cells. Such initial testing under standardised conditions should reduce the number of molecules that progress to further evaluation in animal models. This study aims to establish an in-vitro cell culture system to assess NF-κB activation in the context of ocular surface cells.

METHODS

NF-κB activity was evaluated through a secretory alkaline phosphatase reporter assay (SEAP). Immunoblots and immunofluorescence were used to examine IκBα phosphorylation and p65/p50 nuclear localization. Monocyte chemoattractant protein-1 (MCP-1) transcripts were evaluated by real time PCR and protein levels were measured by ELISA.

RESULTS

NF-κB activity in HCE-T cells treated with TLR2 activator Pam3CSK4 was higher than control cells at both 6 and 24 h. Pam3CSK4-stimulated NF-κB activation was inhibited by IκK inhibitors, Wedelolactone and BMS-345541. In Pam3CSK4 treated cells, active NF-κB subunits p50 and p65 increased in cell nuclear fractions as early as 1.5 h. Although the level of total IκB-α remained constant, phospho-IκB-α increased with treatment over time. In the culture media of Pam3CSK4-stimulated cells, MCP-1 protein level was increased, which was suppressed in the presence of IκK inhibitors.

CONCLUSION

NF-κB pathway can be activated by the TLR2 ligand and inhibited by IκK inhibitors in the ocular surface cell culture system. This cell culture system may be used to evaluate TLR-related innate defences in ocular surface diseases.

Cytotoxicity and Bioactivity of Calcium Silicate Cements Combined with Niobium Oxide in Different Cell Lines

Abstract The aim of this study was to evaluate the cytotoxicity and bioactivity of calcium silicate-based cements combined with niobium oxide (Nb2O5) micro and nanoparticles, comparing the response in different cell lines. This evaluation used four cell lines: two primary cultures (human dental pulp cells - hDPCs and human dental follicle cells - hDFCs) and two immortalized cultures (human osteoblast-like cells - Saos-2 and mouse periodontal ligament cells - mPDL). The tested materials were: White Portland Cement (PC), mineral trioxide aggregate (MTA), white Portland cement combined with microparticles (PC/Nb2O5µ) or nanoparticles (PC/Nb2O5n) of niobium oxide (Nb2O5). Cytotoxicity was evaluated by the methylthiazolyldiphenyl-tetrazolium bromide (MTT) and trypan blue exclusion assays and bioactivity by alkaline phosphatase (ALP) enzyme activity. Results were analyzed by ANOVA and Tukey test (a=0.05). PC/Nb2O5n presented similar or higher cell viability than PC/Nb2O5µ in all cell lines. Moreover, the materials presented similar or higher cell viability than MTA. Saos-2 exhibited high ALP activity, highlighting PC/Nb2O5µ material at 7 days of exposure. In conclusion, calcium silicate cements combined with micro and nanoparticles of Nb2O5 presented cytocompatibility and bioactivity, demonstrating the potential of Nb2O5 as an alternative radiopacifier agent for these cements. The different cell lines had similar response to cytotoxicity evaluation of calcium silicate cements. However, bioactivity was more accurately detected in human osteoblast-like cell line, Saos-2.

In vitro secretomics study of pterygium-derived fibroblasts by iTRAQ-based quantitative proteomics strategy

Pterygium is a triangular shaped ocular fibrous surface lesion growing from conjunctiva towards central cornea, causing ocular irritation, astigmatism, and visual disturbance. The condition is characterized by epithelial proliferation, fibrovascular growth, chronic inflammation, and prominent extracellular matrix remodeling. Studies have suggested that aberrant extracellular proteins secreted by fibroblasts lead to abnormal matrix production and tissue invasion contributing to the development of the disease. In this study, secreted proteins collected from paired pterygium and conjunctival fibroblasts in vitro were identified and quantified by LC-MS iTRAQ-based analysis, in which 433 proteins common to all samples were identified. Among these proteins, 48.0% (208) were classified as classically secreted proteins, 17.1% (74) were exported out of the cells via non-classical secretion pathways, and 31.2% (135) were exosome proteins. A minority (3.7%) was not previously known to be secreted, or might be contaminants. 31 and 27 proteins were found up- or down-regulated in the conditioned media of pterygium fibroblasts relative to the media of control cells, respectively. Molecular function analysis showed that these proteins either belonged to catalytic proteins, structural molecules or were involved with receptor activities and protein binding. Further pathway analysis revealed that these proteins were involved in ECM-receptor interaction, focal adhesion, cancer-related, p53 signaling, complement and coagulation, and TGF-beta signaling pathways. These molecules identified may serve as extracellular ligands to activate intracellular pathways, possibly serving as potential therapeutic targets.

The species translation challenge-a systems biology perspective on human and rat bronchial epithelial cells

The biological responses to external cues such as drugs, chemicals, viruses and hormones, is an essential question in biomedicine and in the field of toxicology, and cannot be easily studied in humans. Thus, biomedical research has continuously relied on animal models for studying the impact of these compounds and attempted to 'translate' the results to humans. In this context, the SBV IMPROVER (Systems Biology Verification for Industrial Methodology for PROcess VErification in Research) collaborative initiative, which uses crowd-sourcing techniques to address fundamental questions in systems biology, invited scientists to deploy their own computational methodologies to make predictions on species translatability. A multi-layer systems biology dataset was generated that was comprised of phosphoproteomics, transcriptomics and cytokine data derived from normal human (NHBE) and rat (NRBE) bronchial epithelial cells exposed in parallel to more than 50 different stimuli under identical conditions. The present manuscript describes in detail the experimental settings, generation, processing and quality control analysis of the multi-layer omics dataset accessible in public repositories for further intra- and inter-species translation studies.

Evaluation of global differential gene and protein expression in primary Pterygium: S100A8 and S100A9 as possible drivers of a signaling network

Purpose

Pterygium is a wing shaped fibrovascular growth on the ocular surface, characterized by fibrosis, angiogenesis, extracellular matrix remodeling, and inflammatory infiltrates. Epidemiologic studies have linked pterygium formation to various chronic inflammatory conditions, such as ultraviolet radiation, sawdust exposure, and dry eye disease. The purpose of this study is to identify proteins that are differentially expressed in primary pterygium by using a combination of gene microarray and proteomic platforms.

Methods

Paired pterygium and uninvolved conjunctiva tissues of four patients were evaluated for differences in global gene transcript levels using a genechip microarray. Proteins extracted from another four pairs of tissues were quantified by iTRAQ approach. Western blot and immunofluorescent staining on additional patients were used to validate dysregulated protein expression obtained from microarray and proteomics data. In addition, primary conjunctival fibroblasts were treated with recombinant S100A8, S100A9 or both. Transcript level changes of a panel of potential target genes were evaluated by real time-PCR.

Results

The following were up-regulated at both protein and transcript levels S100 A8 and A9, aldehyde dehydrogenase 3 family, member1 (ALDH3A1) and vimentin (VIM). Conversely, serpin peptidase inhibitor clade A member 1 (SERPINA1) and transferrin (TF) were down-regulated. Upon adding S100A8, S100A9 or both, the inflammatory chemokine CXCL1, matrix proteins vimentin, biglycan, and gelsolin, as well as annexin-A2, thymosin-β4, chymase (CMA1), member of Ras oncogene family RAB10 and SERPINA1 were found to be up-regulated.

Conclusions

We identified 3 up-regulated and 2 down-regulated proteins by using a stringent approach comparing microarray and proteomic data. On stimulating cells with S100A8/9, a repertoire of key genes found to be up-regulated in pterygium tissue, were induced in these cells. S100A8/9 may be an upstream trigger for inflammation and other disease pathways in pterygium.