Differential gene expression in peripheral blood T cells from patients with psoriasis, lichen planus, and atopic dermatitis

Identification of dynamic gene expression profiles during sequential vaccination with ChAdOx1/BNT162b2 using machine learning methods

To date, COVID-19 remains a serious global public health problem. Vaccination against SARS-CoV-2 has been adopted by many countries as an effective coping strategy. The strength of the body’s immune response in the face of viral infection correlates with the number of vaccinations and the duration of vaccination. In this study, we aimed to identify specific genes that may trigger and control the immune response to COVID-19 under different vaccination scenarios. A machine learning-based approach was designed to analyze the blood transcriptomes of 161 individuals who were classified into six groups according to the dose and timing of inoculations, including I-D0, I-D2-4, I-D7 (day 0, days 2–4, and day 7 after the first dose of ChAdOx1, respectively) and II-D0, II-D1-4, II-D7-10 (day 0, days 1–4, and days 7–10 after the second dose of BNT162b2, respectively). Each sample was represented by the expression levels of 26,364 genes. The first dose was ChAdOx1, whereas the second dose was mainly BNT162b2 (Only four individuals received a second dose of ChAdOx1). The groups were deemed as labels and genes were considered as features. Several machine learning algorithms were employed to analyze such classification problem. In detail, five feature ranking algorithms (Lasso, LightGBM, MCFS, mRMR, and PFI) were first applied to evaluate the importance of each gene feature, resulting in five feature lists. Then, the lists were put into incremental feature selection method with four classification algorithms to extract essential genes, classification rules and build optimal classifiers. The essential genes, namely, NRF2, RPRD1B, NEU3, SMC5, and TPX2, have been previously associated with immune response. This study also summarized expression rules that describe different vaccination scenarios to help determine the molecular mechanism of vaccine-induced antiviral immunity.

T cell co-stimulatory and co-inhibitory pathways in atopic dermatitis

The use of immune checkpoint inhibitors (ICIs) targeting the T cell inhibitory pathways has revolutionized cancer treatment. However, ICIs might induce progressive atopic dermatitis (AD) by affecting T cell reactivation. The critical role of T cells in AD pathogenesis is widely known. T cell co-signaling pathways regulate T cell activation, where co-signaling molecules are essential for determining the magnitude of the T cell response to antigens. Given the increasing use of ICIs in cancer treatment, a timely overview of the role of T cell co-signaling molecules in AD is required. In this review, we emphasize the importance of these molecules involved in AD pathogenesis. We also discuss the potential of targeting T cell co-signaling pathways to treat AD and present the unresolved issues and existing limitations. A better understanding of the T cell co-signaling pathways would aid investigation of the mechanism, prognosis evaluation, and treatment of AD.

Keratin 17 is Not Always a Marker of Proliferation of Keratinocytes in Skin Diseases

Purpose

Keratin 17 (K17) is an embryonic keratin and overexpression is seen in psoriasis, which is a hyperproliferation skin disease. Nonetheless, whether it is also highly expressed in other proliferative skin diseases remains unclear. The aim of this study is to explore the expression of K17 in cutaneous lichen planus (CLP), lichen simplex chronicus (LSC), and prurigo nodularis (PN).

Methods

A total of 20 skin samples from CLP lesions, 20 from LSC lesions, 20 from PN lesions, and 10 healthy adult skin tissues were obtained. Then, the expression of K17 was analyzed using immunohistochemistry on paraffin-embedded tissue sections. Furthermore, quantitative and semi-quantitative immunohistochemical scores of K17 were independently evaluated under a microscope by 2 dermatologists.

Results

Immunohistochemical analysis revealed that in normal skin, K17 was minimally expressed. Nevertheless, it was highly expressed in all epidermal layers in CLP lesions (P-value <0.01), and negatively expressed in LSC and PN lesions (all P-value >0.05). The average gray value of K17 in CLP was 151.153±13.985 (P-value <0.001), while the average values of K17 in LSC and PN were 178.720±12.001 and 181.316±8.920, respectively (all P-value >0.05).

Conclusion

K17 is potentially expressed in certain inflammatory skin diseases, including psoriasis and lichen planus. Besides, it is not always a marker of hyperproliferation of keratinocytes in skin diseases.

Challenge of Bovine Foot Skin Fibroblasts With Digital Dermatitis Treponemes Identifies Distinct Pathogenic Mechanisms

Bovine digital dermatitis (BDD) is a common infectious disease of digital skin in cattle and an important cause of lameness worldwide, with limited treatment options. It is of increasing global concern for both animal welfare and food security, imposing a large economic burden on cattle farming industries each year. A polytreponemal etiology has been consistently identified, with three key phylogroups implicated globally: Treponema medium, Treponema phagedenis, and Treponema pedis. Pathogenic mechanisms which might enable targeted treatment/therapeutic development are poorly defined. This study used RNA sequencing to determine global differential mRNA expression in primary bovine foot skin fibroblasts following challenge with three representative BDD treponemes and a commensal treponeme, Treponema ruminis. A pro-inflammatory response was elicited by the BDD treponemes, mediated through IL-8/IL-17 signaling. Unexpectedly, the three BDD treponemes elicited distinct mechanisms of pathogenesis. T. phagedenis and T. pedis increased abundance of mRNA transcripts associated with apoptosis, while T. medium and T. pedis increased transcripts involved in actin rearrangement and loss of cell adhesion, likely promoting tissue invasion. The upregulation of antimicrobial peptide precursor, DEFB123, by T. phagedenis spirochaetes may present a microbial ecological advantage to all treponemes within BDD infected tissue, explaining their dominance within lesions. A commensal, T. ruminis, significantly dysregulated over three times the number of host mRNA transcripts compared to BDD treponemes, implying BDD treponemes, akin to the syphilis pathogen (Treponema pallidum), have evolved as "stealth pathogens" which avoid triggering substantial host immune/inflammatory responses to enable persistence and tissue invasion. Immunohistochemistry demonstrated increased IL-6, IL-8, RND1, and CFB protein expression in BDD lesions, confirming in vitro fibroblast observations and highlighting the system's value in modeling BDD pathogenesis. Several unique shared gene targets were identified, particularly RGS16, GRO1, MAFF, and ZC3H12A. The three key BDD Treponema phylogroups elicited both distinct and shared pathogenic mechanisms in bovine foot skin; upregulating inflammation whilst simultaneously suppressing adaptive immunity. The novel gene targets identified here should enable future vaccine/therapeutic approaches.

Possible Relation between Vitamin D and Interleukin-17 in the Pathogenesis of Lichen Planus

BACKGROUND

Lichen planus (LP) is a chronic autoimmune inflammatory mucocutaneous disease. Interleukin (IL)-17 is the signature cytokine of T-helper 17 cells, involved in the aetiology of many autoimmune and inflammatory disorders. Vitamin D has an immune-regulatory role and suppresses IL-17 production via direct transcriptional inhibition of IL-17 gene expression.

OBJECTIVE

To explore the relationship of IL-17 and vitamin D levels with LP, and the possible inter-relationship between IL-17 and vitamin D.

METHODS

The study enrolled 30 patients with LP and 30 healthy controls. Blood samples and skin biopsies were taken from all participants for evaluation of serum vitamin D, and serum and tissue IL-17 levels using enzyme-linked immunosorbent assay (ELISA).

RESULTS

Patients had significantly higher serum and tissue IL-17 (p < 0.001 for both), as well as significantly lower serum vitamin D levels and more deficient patterns of vitamin D status than controls (p < 0.001 for both). In the patient group, there was a statistically significant positive correlation between extent of the disease and serum IL-17. There was no direct statistical correlation between IL-17 levels and serum vitamin D in either patients or controls.

CONCLUSION

This study confirms a previously suggested role of IL-17 in the pathogenesis of LP and suggests its relation to the extent and severity of the disease. We also found an association between vitamin D deficiency and LP. However, a direct relationship between IL-17 and vitamin D deficiency could not be clarified.

Cross-sectional study reveals thatHLA-C*07:02 is a potential biomarker of early onset/lesion severityof psoriasis

Psoriasis is a common chronic autoimmune skin disease, with T cells playing a predominant role in its pathogenesis.Here, we aimed to investigate the relation of T cell repertoires (TCR) and major histocompatibility complex (MHC) in psoriatic patients to further understand mechanisms in disease pathogenesis.We conducted a cross-sectional study involving 9 pairs of monozygotic twins with inconsistent psoriasis and examined the TCR diversity and MHC haplotype ofthe individuals using multiple-PCR and high-throughput sequencing. Additionally, 665 psoriatic patients were applied to validate the relation of human leukocyte antigen (HLA)-class I allele HLA-C*07:02 and early onset or lesion severity of psoriasis.The immune diversity was lower in psoriatic patients compared with unaffected individuals within the twin pairs, although the difference was not significant.The clonotypes of TCR significantly decreased in psoriatic patients with high PASI score and early onset. HLA-C*07:02, a haplotype associated with psoriasis, was positively correlated with the diversity of the TCRV gene. Moreover, HLA-C*07:02 clustered in patients with high PASI and early onset. In the replication stage, we found that the PASI and onset age in psoriasis with HLA-C*07:02 were significantly different from those without HLA-C*07:02 and without HLA-C*06:02. Our observations indicate that HLA-C*07:02 is positively correlated with the diversity of TCRV gene in psoriasis, and maybe a potential biomarker of early onset/severe lesions of psoriasis.

Review-Current Concepts in Inflammatory Skin Diseases Evolved by Transcriptome Analysis: In-Depth Analysis of Atopic Dermatitis and Psoriasis

During the last decades, high-throughput assessment of gene expression in patient tissues using microarray technology or RNA-Seq took center stage in clinical research. Insights into the diversity and frequency of transcripts in healthy and diseased conditions provide valuable information on the cellular status in the respective tissues. Growing with the technique, the bioinformatic analysis toolkit reveals biologically relevant pathways which assist in understanding basic pathophysiological mechanisms. Conventional classification systems of inflammatory skin diseases rely on descriptive assessments by pathologists. In contrast to this, molecular profiling may uncover previously unknown disease classifying features. Thereby, treatments and prognostics of patients may be improved. Furthermore, disease models in basic research in comparison to the human disease can be directly validated. The aim of this article is not only to provide the reader with information on the opportunities of these techniques, but to outline potential pitfalls and technical limitations as well. Major published findings are briefly discussed to provide a broad overview on the current findings in transcriptomics in inflammatory skin diseases.

Significant reduction in the expression of interleukins-17A, 22 and 23A, forkhead box p3 and interferon gamma delineates lichen planus pigmentosus from lichen planus

Recent studies have noticed significant role of interleukin (IL)-17, 22, 23, Foxp3, interferon-gamma (IFN-γ) and Wnt5a in oral and cutaneous lichen planus (LP). This study was undertaken to assess whether similar expression exists in lichen planus pigmentosus (LPP). We recruited 30 patients of treatment-naïve 'LPP' (in absence of cutaneous/mucosal LP elsewhere, group 1), 10 patients having active treatment-naïve cutaneous 'LP' (group 2), 10 patients having 'post-LP' hyperpigmentation (in absence of active LP and off treatment for at least past 3 months, group 3), and 10 controls. Quantitative real-time polymerase chain reaction (qRT-PCR, peripheral blood mononuclear cells [PBMCs] and skin) and immunohistochemistry (IHC, skin) was performed. mRNA expression (in PBMCs) of IL-17A, IL-22, IL-23A, IFN-γ and Foxp3 was significantly decreased in group 1 and 3 as compared to group 2 (p < 0.05). Wnt5a expression was maximal in controls; and while there was no difference between group 1 and 2; whereas expression in group 3 was significantly lesser than group 1 and 2 (p < 0.05). qRT-PCR (skin) and IHC (skin) revealed similar results; and mRNA expression and mean fluorescence intensity of IL-17A, IL-22, IL-23A/R was significantly increased in group 2 and 3 compared to group 1 (p < 0.05). Mean fluorescence intensity and mRNA expression of IFN-γ, Foxp3 and Wnt5a were significantly increased in group 2 compared to group 1 (p < 0.05); whereas the difference between group 1 and 3 was not significant. Mean fluorescence intensity and mRNA expression of IL-17A, 1L-22 and IFN-γ showed no difference between group 2 and 3; whereas that of IL-23A/R, foxp3 and wnt5a were significantly higher in group 2 than group 3 (p < 0.05). Overall, maximal expression of IL-17A, IL-22, IL-23A, IFN-γ and Foxp3 (mRNA PBMCs) was observed in LP. Minimal expression of IL-17A, IL-22, IL-23A/R, IFN-γ and Foxp3 (mRNA skin and IHC skin) was seen in LPP patients. In contrast to LP, LPP lacks the expression of IFN-γ, Foxp3 and the cytokines representing Th17 pathway, and thus seems to have a distinct pathogenesis.

Interference RNA in immune-mediated oral diseases - minireview

Immune-mediated oral disorders are characterised by their chronicity, and some are refractory to treatment. Interference RNA (iRNA) has been implicated in the underlying mechanism of such immune-mediate oral and refractory inflammatory oral diseases. iRNA-based understanding of the mechanism in these diseases may help to produce non-invasive diagnostic methodologies and treatment modalities of such drug non-responsive diseases. Oral lesions in these immune-mediated diseases can precede the occurrence of lesions in other regions of the body. The early diagnosis and treatment of these drug non-responsive diseases might benefit the patient by reducing chronicity and probably even resolving the disease. This aim of the present minireview is to give an overview of the possible implications of iRNA on the pathogenesis, diagnosis, and treatments of immune-mediated and inflammatory oral diseases. The manuscript can form the framework for research on iRNA in these immune-mediated oral disorders.

Differences in metabolic biomarkers in the blood and gene expression profiles of peripheral blood mononuclear cells among normal weight, mildly obese and moderately obese subjects

We compared metabolic biomarkers in the blood and peripheral blood mononuclear cell (PBMC) gene expression profiles among normal weight (BMI, 18·5–23 kg/m2), mildly obese (BMI, 25–27·5 kg/m2) and moderately obese Korean adult men (BMI, 27·5–30 kg/m2). High leptin, lipids (except LDL- and HDL-cholesterol) and apoB levels and low adiponectin and HDL-cholesterol levels were present in the plasma of both mildly and moderately obese subjects. Circulating levels of inflammatory cytokines and markers of insulin resistance, oxidative stress and liver damage were altered in moderately obese subjects but not in mildly obese subjects. PBMC transcriptome data showed enrichment of pathways involved in energy metabolism, insulin resistance, bone metabolism, cancer, inflammation and fibrosis in both mildly and moderately obese subjects. Signalling pathways involved in oxidative phosphorylation, TAG synthesis, carbohydrate metabolism and insulin production; mammalian target of rapamycin, forkhead box O, ras-proximate-1, RAS and transforming growth factor-β signalling; as well as extracellular matrix–receptor interaction were enriched only in moderately obese subjects, indicating that changes in PBMC gene expression profiles, according to metabolic disturbances, were associated with the development and/or aggravation of obesity. In particular, fourteen and fifteen genes differentially expressed only in mildly obese subjects and in both mildly and moderately obese subjects, respectively, could be used as early or stable biomarkers for diagnosing and treating obesity-associated metabolic disturbance. We characterised BMI-associated metabolic and molecular biomarkers in the blood and provided clues about potential blood-based targets for preventing or treating obesity-related complications.

Characterization of a monoclonal antibody against CREPT, a novel protein highly expressed in tumors

CREPT (cell-cycle related and expression-elevated protein in tumor), a novel gene also called RPRD1B and C20ORF77, was recently identified to promote tumorigenesis through up-regulation of the expression of genes related to cell cycle. The previous study demonstrated that CREPT is highly expressed in a variety of tumors and enhances the expression of Cyclin D1 by promoting the formation of a chromatin loop. To study the correlation of CREPT expression with clinical factors in different tumors, we generated a monoclonal antibody (3E10) using purified recombinant human GST-CREPT protein as an antigen. In this study, we characterized the specificity of the monoclonal antibody and cloned the gene encoding the antibody for preparation of industrial production. Our results showed that the monoclonal antibody 3E10 was sensitive and specific to recognize human endogenous CREPT protein. We have mapped the epitope of the antibody and cloned the variable region sequence of the gene encoding the antibody. We confirmed that the cloned gene produced an equivalent antibody as that produced by the original hybridoma. This study provided a basis for large-scale production of the CREPT antibody, which will be useful for the study of the role of CREPT in different tumors.

Regulators of G-protein-signaling proteins: negative modulators of G-protein-coupled receptor signaling

Regulators of G-protein-signaling (RGS) proteins are a category of intracellular proteins that have an inhibitory effect on the intracellular signaling produced by G-protein-coupled receptors (GPCRs). RGS along with RGS-like proteins switch on through direct contact G-alpha subunits providing a variety of intracellular functions through intracellular signaling. RGS proteins have a common RGS domain that binds to G alpha. RGS proteins accelerate GTPase and thus enhance guanosine triphosphate hydrolysis through the alpha subunit of heterotrimeric G proteins. As a result, they inactivate the G protein and quickly turn off GPCR signaling thus terminating the resulting downstream signals. Activity and subcellular localization of RGS proteins can be changed through covalent molecular changes to the enzyme, differential gene splicing, and processing of the protein. Other roles of RGS proteins have shown them to not be solely committed to being inhibitors but behave more as modulators and integrators of signaling. RGS proteins modulate the duration and kinetics of slow calcium oscillations and rapid phototransduction and ion signaling events. In other cases, RGS proteins integrate G proteins with signaling pathways linked to such diverse cellular responses as cell growth and differentiation, cell motility, and intracellular trafficking. Human and animal studies have revealed that RGS proteins play a vital role in physiology and can be ideal targets for diseases such as those related to addiction where receptor signaling seems continuously switched on.

Wnt5a is involved in the pathogenesis of cutaneous lichen planus

BACKGROUND

Cutaneous lichen planus (CLP) is a chronic inflammatory and immune-mediated disease. Wnt5a is one of the most extensively studied Wnt proteins, and has important functions in stimulating inflammation, cell proliferation, cell fate determination and cell differentiation. Wnt5a expression in CLP has not been comprehensively studied to date.

AIM

To determine the expression and distribution of Wnt5a in CLP.

METHODS

Skin samples were obtained from patients with CLP and healthy controls (HCs). The WNT5A gene was detected by real-time quantitative PCR, and Wnt5a protein by immunohistochemical analysis and western blotting.

RESULTS

WNT5A mRNA was upregulated in CLP samples compared with the HC skin samples (P < 0.001). Wnt5a protein was overexpressed in all layers of the epidermis and dermis in CLP lesions compared with HC skin (all P < 0.001). These results were confirmed by western blotting.

CONCLUSIONS

The data presented in this study suggest that Wnt5a pathway may play an important role in the pathogenesis of CLP.

Coherent somatic mutation in autoimmune disease

BACKGROUND

Many aspects of autoimmune disease are not well understood, including the specificities of autoimmune targets, and patterns of co-morbidity and cross-heritability across diseases. Prior work has provided evidence that somatic mutation caused by gene conversion and deletion at segmentally duplicated loci is relevant to several diseases. Simple tandem repeat (STR) sequence is highly mutable, both somatically and in the germ-line, and somatic STR mutations are observed under inflammation.

RESULTS

Protein-coding genes spanning STRs having markers of mutability, including germ-line variability, high total length, repeat count and/or repeat similarity, are evaluated in the context of autoimmunity. For the initiation of autoimmune disease, antigens whose autoantibodies are the first observed in a disease, termed primary autoantigens, are informative. Three primary autoantigens, thyroid peroxidase (TPO), phogrin (PTPRN2) and filaggrin (FLG), include STRs that are among the eleven longest STRs spanned by protein-coding genes. This association of primary autoantigens with long STR sequence is highly significant (p<3.0x10(-7)). Long STRs occur within twenty genes that are associated with sixteen common autoimmune diseases and atherosclerosis. The repeat within the TTC34 gene is an outlier in terms of length and a link with systemic lupus erythematosus is proposed.

CONCLUSIONS

The results support the hypothesis that many autoimmune diseases are triggered by immune responses to proteins whose DNA sequence mutates somatically in a coherent, consistent fashion. Other autoimmune diseases may be caused by coherent somatic mutations in immune cells. The coherent somatic mutation hypothesis has the potential to be a comprehensive explanation for the initiation of many autoimmune diseases.