Roxithromycin suppresses involucrin expression by modulation of activator protein-1 and nuclear factor-kappaB activities of keratinocytes

Deep Learning-based structure modelling illuminates structure and function in uncharted regions of β-solenoid fold space

Repeat proteins are common in all domains of life and exhibit a wide range of functions. One class of repeat protein contains solenoid folds where the repeating unit consists of β-strands separated by tight turns. β-solenoids have distinguishing structural features such as handedness, twist, oligomerisation state, coil shape and size which give rise to their diversity. Characterised β-solenoid repeat proteins are known to form regions in bacterial and viral virulence factors, antifreeze proteins and functional amyloids. For many of these proteins, the experimental structure has not been solved, as they are difficult to crystallise or model. Here we use various deep learning-based structure-modelling methods to discover novel predicted β-solenoids, perform structural database searches to mine further structural neighbours and relate their predicted structure to possible functions. We find both eukaryotic and prokaryotic adhesins, confirming a known functional linkage between adhesin function and the β-solenoid fold. We further identify exceptionally long, flat β-solenoid folds as possible structures of mucin tandem repeat regions and unprecedentedly small β-solenoid structures. Additionally, we characterise a novel β-solenoid coil shape, the FapC Greek key β-solenoid as well as plausible complexes between it and other proteins involved in Pseudomonas functional amyloid fibres.

Skewed inflammation is associated with aberrant interleukin-37 signaling pathway in atopic dermatitis

BACKGROUND

Atopic dermatitis (AD) is a severe global burden on physical, physiological, and mental health. The role of IL-37, a fundamental inhibitor of immunity, in AD was herein explored.

METHOD

Serum levels of IL-37 and T helper (Th) 2-related inflammatory mediators were quantified in subjects with or without AD. The expression of IL-37 receptors was determined by flow cytometry. Proteomics was employed to explore the serum protein profile and novel biomarkers. In vitro cell model, 3D-keratinocytes mimicking skin model, and the serum of subjects with or without AD were investigated to verify the proteomic results.

RESULTS

AD patients were found to present with higher levels of total and specific IgE as well as Th2 inflammatory mediators compared with healthy controls (HC). IL-37 level and its receptor IL18Rɑ expression in AD patients were significantly decreased, together with increased population of eosinophils, indicating that the signaling of IL37/IL18Rɑ was dampened. In addition, proteomic analysis revealed a significantly differential protein profile of AD patients compared with HC. IL-37 showed the strongest negative correlation with involucrin, a keratinizing epithelia protein. IL-37 was verified to suppress induced involucrin expression in in vitro skin cell models. AD patients show a significantly higher serum concentration of involucrin compared with HC. Together, our results demonstrated that IL-37 plays a regulatory role in AD. Its deficiency may lead to the aberrant involucrin expression in AD.

CONCLUSIONS

The dysregulation of serum protein and skin disruption in AD is related to the insufficiency of IL-37 and its attenuated anti-inflammatory signaling.

Identification, Validation, and Functional Annotations of Genome-Wide Profile Variation between Melanocytic Nevus and Malignant Melanoma

Cutaneous melanoma (CM) is known as an aggressive malignant cancer; some of which are directly derived from melanocytic nevi, which have been attracting growing attention from the last decades. This study focused on comprehensive identification, validation, and functional annotations of prognostic differentially expressed genes (DEGs) between melanocytic nevus and malignant melanoma in genome-wide profiles. DEGs were obtained using three chip datasets from GEO database to identify after standardization annotation. A total of 73 DEGs were identified as possible candidate prognostic biomarkers between melanocytic nevus and malignant melanoma. In addition, survival curves indicated that six hub genes, including FABP5, IVL, KRT6A, KRT15, KRT16, and TIMP2, were significant prognostic signatures for CM and of significant value to predict transformation from nevi to melanoma. Furthermore, immunohistochemistry staining was performed to validate differential expression levels and prognostic implications of six hub genes between CM tissue and nevus tissues from the First Affiliated Hospital of Soochow University cohort. It suggested that significantly elevated FABP5, IVL, KRT6A, KRT15, KRT16, and TIMP2 proteins expressed in the CM than in the nevus tissues. Functional enrichment and significant pathways of the six significant hub genes indicated that the mostly involved hallmarks include the P53 pathway, K-ras signaling, estrogen response late, and estrogen response early. In summary, this study identified significant DEGs participating in the process of malignant transformation from nevus to melanoma tissues based on comprehensive genomic profiles. Transcription profiles of FABP5, IVL, KRT6A, KRT15, KRT16, and TIMP2 provided clues of prognostic implications, which might help us evaluate malignant potential of nevus and underlying carcinogenesis progress from melanocytic nevus to melanoma.

Differential gene expression in disease: a comparison between high-throughput studies and the literature

BACKGROUND

Differential gene expression is important to understand the biological differences between healthy and diseased states. Two common sources of differential gene expression data are microarray studies and the biomedical literature.

METHODS

With the aid of text mining and gene expression analysis we have examined the comparative properties of these two sources of differential gene expression data.

RESULTS

The literature shows a preference for reporting genes associated to higher fold changes in microarray data, rather than genes that are simply significantly differentially expressed. Thus, the resemblance between the literature and microarray data increases when the fold-change threshold for microarray data is increased. Moreover, the literature has a reporting preference for differentially expressed genes that (1) are overexpressed rather than underexpressed; (2) are overexpressed in multiple diseases; and (3) are popular in the biomedical literature at large. Additionally, the degree to which diseases are similar depends on whether microarray data or the literature is used to compare them. Finally, vaguely-qualified reports of differential expression magnitudes in the literature have only small correlation with microarray fold-change data.

CONCLUSIONS

Reporting biases of differential gene expression in the literature can be affecting our appreciation of disease biology and of the degree of similarity that actually exists between different diseases.

Roxithromycin suppresses airway remodeling and modulates the expression of caveolin-1 and phospho-p42/p44MAPK in asthmatic rats

Roxithromycin (RXM) expresses anti-asthmatic effects that are separate from its antibiotic activity, but its effects on airway remodeling are still unknown. Here, we evaluated the effects of RXM on airway remodeling and the expression of caveolin-1 and phospho-p42/p44mitogen-activated protein kinase (phospho-p42/p44MAPK) in chronic asthmatic rats. The chronic asthma was induced by ovalbumin/Al(OH)3 sensitization and ovalbumin challenge, RXM (30mg/kg) or dexamethasone (0.5mg/kg) was given before airway challenge initiation. We measured the thickness of bronchial wall and bronchial smooth muscle cell layer to indicate airway remodeling, and caveolin-1 and phospho-p42/p44MAPK expression in lung tissue and airway smooth muscle were detected by immunohistochemistry and western blot analysis, respectively. The results demonstrated that RXM treatment decreased the thickness of bronchial wall and bronchial smooth muscle cell layer, and also downregulated the phospho-p42/p44MAPK expression and upregulated the caveolin-1 expression. The above effects of RXM were similar to dexamethasone. Our results suggested that pretreatment with RXM could suppress airway remodeling and regulate the expression of caveolin-1 and phospho-p42/p44MAPK in chronic asthmatic rats.

Tetracyclines modulate protease-activated receptor 2-mediated proinflammatory reactions in epidermal keratinocytes

In addition to their antibiotic effects, tetracyclines have anti-inflammatory action that is often beneficial in the control of inflammatory skin disorders. In this study, we examined the effects of tetracycline (TET) and two of its derivatives, doxycycline (DOX) and minocycline (MIN), on the production of interleukin-8 (IL-8) elicited by the activation of protease-activated receptor 2 (PAR2) in normal human epidermal keratinocytes (NHEK). In NHEK, the production of IL-8 stimulated by an agonist peptide of PAR2, SLIGKIV-NH(2), at 100 microM was significantly reduced by TET, DOX, or MIN at 5 and 10 microM, concentrations that are noncytotoxic. The tumor necrosis factor alpha (TNF-alpha)-induced production of IL-8 was synergistically augmented by SLIGKIV-NH(2), and that synergistic increase in the production of IL-8 was suppressed by 100 nM PAR2-specific small interfering RNA. It was also suppressed by TET, DOX, or MIN but not by the 14-membered-ring macrolide antibiotics erythromycin, roxithromycin, and clarithromycin, which also have anti-inflammatory activities, at 10 microM. These results suggest that tetracyclines attenuate the PAR2-IL-8 axis in keratinocytes and thereby effectively modulate proinflammatory responses in the skin.

Immunomodulatory effects of erythromycin and its derivatives on human T-lymphocyte in vitro

To elucidate the immunomodulatory mechanisms of macrolides, we investigated here the effects of erythromycin (EM) and its derivatives, 1 and 2, which show no antibacterial activity, on the proliferation and the activation of the transcription factor nuclear factor-kappaB (NF-kappaB) in Jurkat T cells. MTT assay revealed that EM, 1 and 2 could inhibit T lymphocyte proliferation markedly. Flow cytometry and TUNEL analysis showed EM (30 microg/mL-100 microg/mL) and 1 (3 microg/mL-30 microg/mL) could induce T lymphocyte apoptosis, 2 (3 microg/mL-30 microg/mL) induced a cell cycle arrest in G(2)/M. RT-PCR and Western blotting analysis conformed that EM and its two derivatives could inhibit the expressions of NF-kappaB mRNA and protein. Taken together, these data suggest EM and its derivatives, 1 and 2, have immunomodulatory effect, presumably via an interaction with the NF-kappaB expression, inhibiting the proliferation of T lymphocyte, implicating an approach for the development of new drugs for treating inflammatory diseases.

Effect of 14-membered-ring macrolides on production of interleukin-8 mediated by protease-activated receptor 2 in human keratinocytes

The production of interleukin-8 induced by the activation of protease-activated receptor 2 and its synergism with interleukin-1beta were modulated by 14-membered-ring macrolides, namely, roxithromycin, erythromycin, and clarithromycin, in cultured normal human epidermal keratinocytes. Those macrolides may attenuate the protease-activated receptor 2-interleukin-8 axis and thereby modulate proinflammatory responses in the skin.