Identification of protein phosphatase 2C and confirmation of other protein phosphatases in the ocular lenses

Identification of potential biomarkers of myopia based on machine learning algorithms

PURPOSE

This study aims to identify potential myopia biomarkers using machine learning algorithms, enhancing myopia diagnosis and prognosis prediction.

METHODS

GSE112155 and GSE15163 datasets from the GEO database were analyzed. We used "limma" for differential expression analysis and "GO plot" and "clusterProfiler" for functional and pathway enrichment analyses. The LASSO and SVM-RFE algorithms were employed to screen myopia-related biomarkers, followed by ROC curve analysis for diagnostic performance evaluation. Single-gene GSEA enrichment analysis was executed using GSEA 4.1.0.

RESULTS

The functional analysis of differentially expressed genes indicated their role in carbohydrate generation and polysaccharide synthesis. We identified 23 differentially expressed genes associated with myopia, four of which were highly effective diagnostic biomarkers. Single gene GSEA results showed these genes control the ubiquitin-mediated protein hydrolysis pathway.

CONCLUSION

Our study identifies four key myopia biomarkers, providing a foundation for future clinical and experimental validation studies.

Heparan sulfate proteoglycans (HSPGs) of the ocular lens

Heparan sulfate proteoglycans (HSPGs) reside in most cells; on their surface, in the pericellular milieu and/or extracellular matrix. In the eye, HSPGs can orchestrate the activity of key signalling molecules found in the ocular environment that promote its development and homeostasis. To date, our understanding of the specific roles played by individual HSPG family members, and the heterogeneity of their associated sulfated HS chains, is in its infancy. The crystalline lens is a relatively simple and well characterised ocular tissue that provides an ideal stage to showcase and model the expression and unique roles of individual HSPGs. Individual HSPG core proteins are differentially localised to eye tissues in a temporal and spatial developmental- and cell-type specific manner, and their loss or functional disruption results in unique phenotypic outcomes for the lens, and other ocular tissues. More recent work has found that different HS sulfation enzymes are also presented in a cell- and tissue-specific manner, and that disruption of these different sulfation patterns affects specific HS-protein interactions. Not surprisingly, these sulfated HS chains have also been reported to be required for lens and eye development, with dysregulation of HS chain structure and function leading to pathogenesis and eye-related phenotypes. In the lens, HSPGs undergo significant and specific changes in expression and function that can drive pathology, or in some cases, promote tissue repair. As master signalling regulators, HSPGs may one day serve as valuable biomarkers, and even as putative targets for the development of novel therapeutics, not only for the eye but for many other systemic pathologies.

Identification of the WNK-SPAK/OSR1 signaling pathway in rodent and human lenses

PURPOSE

To identify whether the kinases that regulate the activity of cation chloride cotransporters (CCC) in other tissues are also expressed in rat and human lenses.

METHODS

The expression of with-no-lysine kinase (WNK 1, 3, 4), oxidative stress response kinase 1 (OSR1), and Ste20-like proline alanine rich kinase (SPAK) were determined at either the transcript or protein levels in the rat and human lenses by reverse-transcriptase PCR and/or Western blotting, respectively. Selected kinases were regionally and subcellularly characterized in rat and human lenses. The transparency, wet weight, and tissue morphology of lenses extracted from SPAK knock-out animals was compared with wild-type lenses.

RESULTS

WNK 1, 3, 4, SPAK, and OSR1 were identified at the transcript level in rat lenses and WNK1, 4, SPAK, and OSR1 expression confirmed at the protein level in both rat and human lenses. SPAK and OSR1 were found to associate with membranes as peripheral proteins and exhibited distinct subcellular and region-specific expression profiles throughout the lens. No significant difference in the wet weight of SPAK knock-out lenses was detected relative to wild-type lenses. However, SPAK knock-out lenses showed an increased susceptibility to opacification.

CONCLUSIONS

Our results show that the WNK 1, 3, 4, OSR1, and SPAK signaling system known to play a role in regulating the phosphorylation status, and hence activity of the CCCs in other tissues, is also present in the rat and human lenses. The increased susceptibility of SPAK lenses to opacification suggests that disruption of this signaling pathway may compromise the ability of the lens to control its volume, and its ability to maintain its transparency.

Regulation of the innate immune response by threonine-phosphatase of Eyes absent

Innate immunity is stimulated not only by viral or bacterial components, but also by non-microbial danger signals (damage-associated molecular patterns). One of the damage-associated molecular patterns is chromosomal DNA that escapes degradation. In programmed cell death and erythropoiesis, DNA from dead cells or nuclei expelled from erythroblasts is digested by DNase II in the macrophages after they are engulfed. DNase II(-/-) (also known as Dnase2a(-/-)) mice suffer from severe anaemia or chronic arthritis due to interferon-beta (IFN-beta) and tumour necrosis factor-alpha (TNF-alpha) produced from the macrophages carrying undigested DNA in a Toll-like receptor (TLR)-independent mechanism. Here we show that Eyes absent 4 (EYA4), originally identified as a co-transcription factor, stimulates the expression of IFN-beta and CXCL10 in response to the undigested DNA of apoptotic cells. EYA4 enhanced the innate immune response against viruses (Newcastle disease virus and vesicular stomatitis virus), and could associate with signalling molecules (IPS-1 (also known as MAVS), STING (TMEM173) and NLRX1). Three groups have previously shown that EYA has phosphatase activity. We found that mouse EYA family members act as a phosphatase for both phosphotyrosine and phosphothreonine. The haloacid dehalogenase domain at the carboxy terminus contained the tyrosine-phosphatase, and the amino-terminal half carried the threonine-phosphatase. Mutations of the threonine-phosphatase, but not the tyrosine-phosphatase, abolished the ability of EYA4 to enhance the innate immune response, suggesting that EYA regulates the innate immune response by modulating the phosphorylation state of signal transducers for the intracellular pathogens.

Molecular basis of pregnancy-induced breast cancer protection

We have postulated that the lifetime protective effect of an early pregnancy against breast cancer is due to the complete differentiation of the mammary gland characterized by a specific genomic signature imprinted by the physiological process of pregnancy. In the present work, we show evidence that the breast tissue of postmenopausal parous women has had a shifting of stem cell 1 to stem cell 2 with a genomic signature different from similar structures derived from postmenopausal nulliparous women that have stem cell 1. Those genes that are significantly different are grouped in major categories on the basis of their putative functional significance. Among them are those gene transcripts related to immune surveillance, DNA repair, transcription, chromatin structure/activators/co-activators, growth factor and signal transduction pathway, transport and cell trafficking, cell proliferation, differentiation, cell adhesion, protein synthesis and cell metabolism. From these data, it was concluded that during pregnancy there are significant genomic changes that reflect profound alterations in the basic physiology of the mammary gland that explain the protective effect against carcinogenesis. The implication of this knowledge is that when the genomic signature of protection or refractoriness to carcinogenesis is acquired by the shifting of stem cell 1 to stem cell 2, the hormonal milieu induced by pregnancy or pregnancy-like conditions is no longer required. This is a novel concept that challenges the current knowledge that a chemopreventive agent needs to be given for a long period to suppress a metabolic pathway or abrogate the function of an organ.

Steroid (Glucocorticoid)-induced Cataract

Glucocorticoids (GC) have been widely used as a therapeutic drug for various diseases. However, there are many complications of GC therapy including cataracts. In a series of studies to elucidate the actions of GC using 15-day-old developing chick embryos, we found that GC produced hyperglycemia, hyperlipemia, osteoporosis, and cataractous lenses with a high incidence (>90%) within 48 h. Cataract formation is caused by oxidative stresses, probably derived from GC effects on the main target organ, the liver, and can be prevented by radical scavengers including ascorbic acid, and insulin. Ascorbic acid does not inhibit the inflammatory and immunosuppressive effects of GC. Therefore by analyzing and decreasing risk factors producing side effects, it will be possible to improve GC therapy without the loss of GC activity.