Vitiligo blood transcriptomics provides new insights into disease mechanisms and identifies potential novel therapeutic targets

Exploring the Potential Molecular Mechanism of Sijunzi Decoction in the Treatment of Non-Segmental Vitiligo Based on Network Pharmacology and Molecular Docking

Background

Non-segmental vitiligo is a common decolorized skin disease. The purpose of this study was to reveal the active components of Sijunzi decoction (SJZD) and the target genes for the treatment of non-segmental vitiligo.

Methods

Based on TCMSP and GEO databases, effective components and targets of SJZD in the treatment of non-segmental vitiligo were revealed by network pharmacology. GO and KEGG were used to analyze the biological functions of SJZD targets. The Cytoscape-cytoHubba plugin was used to identify hub target genes. SsGSEA method was used to analyze the infiltration level of immune cells in non-segmental vitiligo. Molecular docking was performed to predict the interaction between active compounds and hub target genes. Finally, real-time PCR detection was also performed.

Results

It was found that 104 active compounds may be effective ingredients in the treatment of non-segmental vitiligo. These 104 compounds acted on 42 differentially expressed target genes. KEGG analysis showed that target genes were significantly enriched in immune-related pathways such as MAPK and TNF signaling pathways. A total of 6 hub target genes (AKT1, CASP3, PPARG, SIRT1, TNF and TP53) were identified using the Cytoscape-cytoHubba plugin. Molecular docking showed that active compounds quercetin, kaempferol, formononetin and naringenin had good binding to hub target genes. We also found that Type 2 T helper cells, CD56bright natural killer cell and CD56dim natural killer cell infiltration levels were abnormal in non-segmental vitiligo and correlated with AKT1.

Conclusion

The results of this study indicate that quercetin, kaempferol, formononetin and naringenin in SJZD may play an important role in the treatment of non-segmental vitiligo by acting on AKT1, CASP3, PPARG, SIRT1, TNF and TP53 to regulate immune cell infiltration and multiple signaling pathways.

RNA sequencing reveals dynamic expression of lncRNAs and mRNAs in caprine endometrial epithelial cells induced by Neospora caninum infection

Background

The effective transmission mode of Neospora caninum, with infection leading to reproductive failure in ruminants, is vertical transmission. The uterus is an important reproductive organ that forms the maternal–fetal interface. Neospora caninum can successfully invade and proliferate in the uterus, but the molecular mechanisms underlying epithelial-pathogen interactions remain unclear. Accumulating evidence suggests that host long noncoding RNAs (lncRNAs) play important roles in cellular molecular regulatory networks, with reports that these RNA molecules are closely related to the pathogenesis of apicomplexan parasites. However, the expression profiles of host lncRNAs during N. caninum infection has not been reported.

Methods

RNA sequencing (RNA-seq) analysis was used to investigate the expression profiles of messenger RNAs (mRNAs) and lncRNAs in caprine endometrial epithelial cells (EECs) infected with N. caninum for 24 h (TZ_24h) and 48 h (TZ_48 h), and the potential functions of differentially expressed (DE) lncRNAs were predicted by using Gene Ontology (GO) enrichment and Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis of their mRNA targets.

Results

RNA-seq analysis identified 1280.15 M clean reads in 12 RNA samples, including six samples infected with N. caninum for 24 h (TZ1_24h-TZ3_24h) and 48 h (TZ1_48h-TZ3_48h), and six corresponding control samples (C1_24h-C3_24h and C1_48h-C3_48h). Within the categories TZ_24h-vs-C_24h, TZ_48h-vs-C_48h and TZ_48h-vs-TZ_24h, there were 934 (665 upregulated and 269 downregulated), 1238 (785 upregulated and 453 downregulated) and 489 (252 upregulated and 237 downregulated) DEmRNAs, respectively. GO enrichment and KEGG analysis revealed that these DEmRNAs were mainly involved in the regulation of host immune response (e.g. TNF signaling pathway, MAPK signaling pathway, transforming growth factor beta signaling pathway, AMPK signaling pathway, Toll-like receptor signaling pathway, NOD-like receptor signaling pathway), signaling molecules and interaction (e.g. cytokine-cytokine receptor interaction, cell adhesion molecules and ECM-receptor interaction). A total of 88 (59 upregulated and 29 downregulated), 129 (80 upregulated and 49 downregulated) and 32 (20 upregulated and 12 downregulated) DElncRNAs were found within the categories TZ_24h-vs-C_24h, TZ_48h-vs-C_48h and TZ_48h-vs-TZ_24h, respectively. Functional prediction indicated that these DElncRNAs would be involved in signal transduction (e.g. MAPK signaling pathway, PPAR signaling pathway, ErbB signaling pathway, calcium signaling pathway), neural transmission (e.g. GABAergic synapse, serotonergic synapse, cholinergic synapse), metabolism processes (e.g. glycosphingolipid biosynthesis-lacto and neolacto series, glycosaminoglycan biosynthesis-heparan sulfate/heparin) and signaling molecules and interaction (e.g. cytokine-cytokine receptor interaction, cell adhesion molecules and ECM-receptor interaction).

Conclusions

This is the first investigation of global gene expression profiles of lncRNAs during N. caninum infection. The results provide valuable information for further studies of the roles of lncRNAs during N. caninum infection.

Graphical Abstract

Supplementary Information

The online version contains supplementary material available at 10.1186/s13071-022-05405-5.

Investigating melanogenesis-related microRNAs as disease biomarkers in vitiligo

Vitiligo is considered a disabling disease that affects physical, social, psychological, and occupational aspects of an individual's quality of life. The search for non-invasive and reliable biomarkers for vitiligo's early diagnosis, prognosis, and treatment prediction is under intensive investigation. There is currently an emerging interest in employing miRNAs as biomarkers to predict vitiligo diagnosis and prognosis, inspired by the well-preserved nature of miRNAs in serum or plasma. In the current study, we assessed a panel of 20 melanogenesis pathway-related microRNAs (miRNAs) using quantitative real-time PCR technique in 85 non-segmental vitiligo (NSV) patients compared to 85 normal controls followed by function and pathway enrichment analysis for the miRNAs with significant results. Twelve out of the 20 circulating miRNAs showed significantly higher expression levels in vitiligo patients relative to controls where miR-423 show the highest expression level followed by miR-182, miR-106a, miR-23b, miR-9, miR-124, miR-130a, miR-203a, miR-181, miR-152, and miR-320a. While six miRNAs (miR-224, miR-148a, miR-137, and miR-7, miR-148b, miR-145, miR-374b, and miR-196b) didn’t show significant expression level. The analysis of the receiver operating curve indicated that miR-423, miR-106a, and miR-182 were outstanding biomarkers with the highest areas under the curve in vitiligo. This study is the first Egyptian study to investigate a panel of miRNAs expression profile in the plasma of patients with NSV. Our results suggest that specific circulating miRNAs signature might be implicated in vitiligo pathogenesis and could potentially be used as biomarkers in vitiligo.

The Promising Role of Chemokines in Vitiligo: From Oxidative Stress to the Autoimmune Response

Vitiligo is a common chronic autoimmune skin disorder featured with depigmented patches and underlying destruction of melanocytes in the lesional skin. Multiple factors and mechanisms have been proposed for the etiopathogenesis of vitiligo, among which oxidative stress has been widely accepted as a key factor in initiating melanocyte loss. The altered redox status caused by oxidative stress, including the overproduction of reactive oxygen species (ROS) and the decreased activity of the antioxidant system in the skin, surrenders the resistance of melanocytes to exogenous or endogenous stimuli and eventually impairs the normal defense mechanism, leading to the absence of melanocytes. Considering the important role of innate and adaptive immunity in vitiligo, there is mounting evidence revealing an association between oxidative stress and autoimmunity. Since the significant changes of chemokines have been documented in vitiligo in many recent studies, it has been suggested that ROS-mediated chemotactic signals are not only the biomarkers of disease progression and prognosis but also are involved in the pathogenesis of vitiligo by facilitating the innate and adaptive immune cells, especially melanocyte-specific T cells, trafficking to the lesional areas of vitiligo. In this review, we discuss the interaction between oxidative stress and autoimmune response orchestrated by chemokines, including CXCL16-CXCR6 axis, CXCL9/CXCL10-CXCR3 axis, and other altered chemokines in vitiligo, and we also try to provide insight into potential therapeutic options through targeting these pathways.

Variations in TAP1 and PSMB9 Genes Involved in Antigen Processing and Presentation Increase the Risk of Vitiligo in the Saudi Community

Background

The antigen processing 1 (TAP1) and proteasome 20S subunit beta 9 (PSMB9) genes are associated with strong susceptibility to many autoimmune diseases. Here, we explored whether TAP1/PSMB9 genetic variants, individually or combined, affected susceptibility to the complex, autoimmune-based skin disorder vitiligo.

Methods

Samples of genomic DNA from buccal cells of 172 patients with vitiligo and 129 healthy controls were analyzed using TaqMan™ genotyping assays for the TAP1 rs1135216 (A>G) and PSMB9 rs17587 (A>G) single nucleotide polymorphisms (SNPs). SNPStats software (https://www.snpstats.net) was utilized to choose the best interactive inheritance mode for selected SNPs.

Results

The genotype frequencies for the TAP1 rs1135216 and PSMB9 rs17587 SNPs were in Hardy-Weinberg equilibrium for cases (P= 0.11 and P= 0.10, respectively) but not for controls (P< 0.05). The TAP1 rs1135216 (D637G) and PSMB9 rs17587 (R60H) SNPs increased the risk of vitiligo four-fold and two-fold, respectively (odds ratio [OR]= 4.6; 95% confidence interval [CI], 3.2-6.5; P< 0.0001 and OR= 2.2; 95% CI, 1.5-3.1; P< 0.0001). The recessive model (G/G-D/G versus D/D) and the codominant model (R/R versus R/H) were the best models of inheritance for the rs113526 and rs17587 SNPs, respectively (OR= 16.4; 95% CI, 2.0-138; P= 0.0006 and OR= 1.7; 95% CI, 0.3-1.8; P= 0.013). Vulgaris, focal vulgaris, and acryl/acrofacial were the most common vitiligo subtypes in our sample (51%, 21%, and 19%, respectively). Heterozygous rs113526 (637D/G) and rs17587 (60R/H) were the most common genotypes in most vitiligo subtypes. The heterozygous 637D/G genotype and the 637G variant allele were significantly more common in patients with active disease than in patients with stable disease (P= 0.000052 and P= 0.0063, respectively).

Conclusion

Our findings suggest a crucial role for TAP1 rs1135216 and PSMB9 rs17587 in the risk and progression of vitiligo in the Saudi community. Genomic analyses are needed to identify more candidate genes and more genetic variants associated with vitiligo.

The Immunogenetics of Vitiligo: An Approach Toward Revealing the Secret of Depigmentation

Vitiligo is a hypomelanotic skin disease and considered to be of autoimmune origin due to breaching of immunological self-tolerance, resulting in inappropriate immune responses against melanocytes. The development of vitiligo includes a strong heritable component. Different strategies ranging from linkage studies to genome-wide association studies are used to explore the genetic factors responsible for the disease. Several vitiligo loci containing the respective genes have been identified which contribute to vitiligo and genetic variants for some of the genes are still unknown. These genes include mainly the proteins that play a role in immune regulation and a few other genes important for apoptosis and regulation of melanocyte functions. Despite the available data on genetic variants and risk alleles which influence the biological processes, only few immunological pathways have been found responsible for all ranges of severity and clinical manifestations of vitiligo. However, studies have concluded that vitiligo is of autoimmune origin and manifests due to complex interactions in immune components and their inappropriate response toward melanocytes. The genes involved in the immune regulation and processing the melanocytes antigen and its presentation can serve as effective immune-therapeutics that can target specific immunological pathways involved in vitiligo. This chapter highlights those immune-regulatory genes involved in vitiligo susceptibility and loci identified to date and their implications in vitiligo pathogenesis.

Novel immunological and genetic factors associated with vitiligo: A review

Vitiligo is a skin disorder characterized by depigmentation of the skin due to a lack of melanin. This condition affects men and woman of all ages and its incidence is not restricted by ethnicity or region. Vitiligo is a multifactorial disease, in which melanocytes, which serve important functions in skin pigmentation and immune processes, are impaired. There is sufficient evidence that immunological and genetic factors are primarily responsible for the destruction and dysfunction of melanocytes. Therefore, genetic DNA sequence variants that participate in skin homeostasis, pigmentation and immune response regulation, as well as altered expression patterns, may contribute to the risk of developing vitiligo. The current review presented an overview of the mechanism of pigmentation and of currently known factors involved in depigmentation, as well as the classification, epidemiology, associated comorbidities, risk factors, immunopathogenesis and several genetic and molecular changes associated with vitiligo.

The Role of the NKG2D in Vitiligo

Vitiligo is an acquired multifactorial disease that affects melanocytes and results in skin depigmentation. In this review, we examine the role of cells stress and self-reactive T cells responses. Given the canonical and non-canonical functions of NKG2D, such as authenticating stressed target and enhance TCR signaling, we examine how melanocyte stress leads to the expression of ligands that are recognized by the activating receptor NKG2D, and how its signaling results in the turning of T cells against self (melanocyte suicide by proxy). We also discuss how this initiation phase is followed by T cell perpetuation, as NKG2D signaling results in self-sustained long-lasting T cells, with improved cytolytic properties.

Comprehensive Analysis of Cell Population Dynamics and Related Core Genes During Vitiligo Development

Vitiligo is a common immune-related depigmentation condition, and its pathogenesis remains unclear. This study used a combination of bioinformatics methods and expression analysis techniques to explore the relationship between immune cell infiltration and gene expression in vitiligo. Previously reported gene expression microarray data from the skin (GSE53146 and GSE75819) and peripheral blood (GSE80009 and GSE90880) of vitiligo patients and healthy controls was used in the analysis. R software was used to filter the differentially expressed genes (DEGs) in each dataset, and the KOBAS 2.0 server was used to perform functional enrichment analysis. Compared with healthy controls, the upregulated genes in skin lesions and peripheral blood leukocytes of vitiligo patents were highly enriched in immune response pathways and inflammatory response signaling pathways. Immunedeconv software and the EPIC method were used to analyze the expression levels of marker genes to obtain the immune cell population in the samples. In the lesional skin of vitiligo patients, the proportions of macrophages, B cells and NK cells were increased compared with healthy controls. In the peripheral blood of vitiligo patients, CD8+ T cells and macrophages were significantly increased. A coexpression analysis of the cell populations and DEGs showed that differentially expressed immune and inflammation response genes had a strong positive correlation with macrophages. The TLR4 receptor pathway, interferon gamma-mediated signaling pathway and lipopolysaccharide-related pathway were positively correlated with CD4+ T cells. Regarding immune response-related genes, the overexpression of IFITM2, TNFSF10, GZMA, ADAMDEC1, NCF2, ADAR, SIGLEC16, and WIPF2 were related to macrophage abundance, while the overexpression of ICOS, GPR183, RGS1, ILF2 and CD28 were related to CD4+ T cell abundance. GZMA and CXCL10 expression were associated with CD8+ T cell abundance. Regarding inflammatory response-related genes, the overexpression of CEBPB, ADAM8, CXCR3, and TNIP3 promoted macrophage infiltration. Only ADORA1 expression was associated with CD4+ T cell infiltration. ADAM8 and CXCL10 expression were associated with CD8+ T cell abundance. The overexpression of CCL18, CXCL10, FOS, NLRC4, LY96, HCK, MYD88, and KLRG1, which are related to inflammation and immune responses, were associated with macrophage abundance. We also found that immune cells infiltration in vitiligo was associated with antigen presentation-related genes expression. The genes and pathways identified in this study may point to new directions for vitiligo treatment.

Variations in TAP1 and PSMB9 Genes Involved in Antigen Processing and Presentation Increase the Risk of Vitiligo in the Saudi Community

BACKGROUND

The antigen processing 1 (TAP1) and proteasome 20S subunit beta 9 (PSMB9) genes are associated with strong susceptibility to many autoimmune diseases. Here, we explored whether TAP1/PSMB9 genetic variants, individually or combined, affected susceptibility to the complex, autoimmune-based skin disorder vitiligo.

METHODS

Samples of genomic DNA from buccal cells of 172 patients with vitiligo and 129 healthy controls were analyzed using TaqMan™ genotyping assays for the TAP1 rs1135216 (A>G) and PSMB9 rs17587 (A>G) single nucleotide polymorphisms (SNPs). SNPStats software (https://www.snpstats.net) was utilized to choose the best interactive inheritance mode for selected SNPs.

RESULTS

The genotype frequencies for the TAP1 rs1135216 and PSMB9 rs17587 SNPs were in Hardy-Weinberg equilibrium for cases (P= 0.11 and P= 0.10, respectively) but not for controls (P< 0.05). The TAP1 rs1135216 (D637G) and PSMB9 rs17587 (R60H) SNPs increased the risk of vitiligo four-fold and two-fold, respectively (odds ratio [OR]= 4.6; 95% confidence interval [CI], 3.2-6.5; P< 0.0001 and OR= 2.2; 95% CI, 1.5-3.1; P< 0.0001). The recessive model (G/G-D/G versus D/D) and the codominant model (R/R versus R/H) were the best models of inheritance for the rs113526 and rs17587 SNPs, respectively (OR= 16.4; 95% CI, 2.0-138; P= 0.0006 and OR= 1.7; 95% CI, 0.3-1.8; P= 0.013). Vulgaris, focal vulgaris, and acryl/acrofacial were the most common vitiligo subtypes in our sample (51%, 21%, and 19%, respectively). Heterozygous rs113526 (637D/G) and rs17587 (60R/H) were the most common genotypes in most vitiligo subtypes. The heterozygous 637D/G genotype and the 637G variant allele were significantly more common in patients with active disease than in patients with stable disease (P= 0.000052 and P= 0.0063, respectively).

CONCLUSION

Our findings suggest a crucial role for TAP1 rs1135216 and PSMB9 rs17587 in the risk and progression of vitiligo in the Saudi community. Genomic analyses are needed to identify more candidate genes and more genetic variants associated with vitiligo.

Case Series: Gene Expression Analysis in Canine Vogt-Koyanagi-Harada/Uveodermatologic Syndrome and Vitiligo Reveals Conserved Immunopathogenesis Pathways Between Dog and Human Autoimmune Pigmentary Disorders

Vogt-Koyanagi-Harada syndrome (VKH) and vitiligo are autoimmune diseases that target melanocytes. VKH affects several organs such as the skin, hair follicle, eyes, ears, and meninges, whereas vitiligo is often limited to the skin and mucosa. Many studies have identified immune genes, pathways and cells that drive the pathogeneses of VKH and vitiligo, including interleukins, chemokines, cytotoxic T-cells, and other leukocytes. Here, we present case studies of 2 canines with VKH and 1 with vitiligo, which occurred spontaneously in client-owned companion dogs. We performed comparative transcriptomics and immunohistochemistry studies on lesional skin biopsies from these cases in order to determine if the immunopathogenesis of autoimmune responses against melanocytes are conserved. In dogs, we found enrichment of T cell gene signatures, with upregulation of IFNG, TNF, PRF1, IL15, CTSW, CXCL10, and CCL5 in both VKH and vitiligo in dogs compared to healthy controls. Similar findings were reported in humans, suggesting that these genes play a role in the pathogenesis of spontaneous VKH and vitiligo. T cell-associated genes, including FOXP3 and TBX21, were enriched, while IGFBP5, FOXO1, and PECAM1 were decreased compared to healthy controls. Further, we identified TGFB3, SFRP2, and CXCL7 as additional potential drivers of autoimmune pigmentary disorders. Future studies exploring the immunopathogenesis of spontaneous autoimmunity will expand our understanding of these disorders, and will be useful in developing targeted therapies, repurposing drugs for veterinary and human medicine, and predicting disease prognosis and treatment response.

Premature cell senescence in human skin: Dual face in chronic acquired pigmentary disorders

Although senescence was originally described as an in vitro acquired cellular characteristic, it was recently recognized that senescence is physiologically and pathologically involved in aging and age-related diseases in vivo. The definition of cellular senescence has expanded to include the growth arrest caused by various cellular stresses, including DNA damage, inadequate mitochondria function, activated oncogene or tumor suppressor genes and oxidative stress. While senescence in normal aging involves various tissues over time and contributes to a decline in tissue function even with healthy aging, disease-induced premature senescence may be restricted to one or a few organs triggering a prolonged and more intense rate of accumulation of senescent cells than in normal aging. Organ-specific high senescence rate could lead to chronic diseases, especially in post-mitotic rich tissue. Recently, two opposite acquired pathological conditions related to skin pigmentation were described to be associated with premature senescence: vitiligo and melasma. In both cases, it was demonstrated that pathological dysfunctions are not restricted to melanocytes, the cell type responsible for melanin production and transport to surrounding keratinocytes. Similar to physiological melanogenesis, dermal and epidermal cells contribute directly and indirectly to deregulate skin pigmentation as a result of complex intercellular communication. Thus, despite senescence usually being reported as a uniform phenotype sharing the expression of characteristic markers, skin senescence involving mainly the dermal compartment and its paracrine function could be associated with the disappearance of melanocytes in vitiligo lesions and with the exacerbated activity of melanocytes in the hyperpigmentation spots of melasma. This suggests that the difference may arise in melanocyte intrinsic differences and/or in highly defined microenvironment peculiarities poorly explored at the current state of the art. A similar dualistic phenotype has been attributed to intratumoral stromal cells as cancer-associated fibroblasts presenting a senescent-like phenotype which influence the behavior of neoplastic cells in either a tumor-promoting or tumor-inhibiting manner. Here, we present a framework dissecting senescent-related molecular alterations shared by vitiligo and melasma patients and we also discuss disease-specific differences representing new challenges for treatment.

Transcriptome Analysis and Emerging Driver Identification of CD8+ T Cells in Patients with Vitiligo

Activated CD8+ T cells play important roles in the pathogenesis of vitiligo. However, driving factors about the activation and migration of CD8+ T cells remain obscure. In this study, we aim to identify differentially expressed genes (DEGs) and uncover potential factors that drive the disease in melanocyte-specific CD8+ T cells in vitiligo. A total of 1147 DEGs were found through transcriptome sequencing in CD8+ T cells from lesional skin of vitiligo patients and normal controls. Based on KEGG pathway enrichment analysis and PPI, 16 upregulated and 23 downregulated genes were identified. Ultimately, 3 genes were figured out after RT-qPCR verification. The mRNA and protein expression levels of PIK3CB, HIF-1α, and F2RL1 were all elevated in CD8+ T cells from peripheral blood in vitiligo. HIF-1α and PIK3CB were significantly increased in lesional skin of vitiligo. Two CpG sites of the HIF-1α promoter were hypomethylated in vitiligo CD8+ T cells. In conclusion, HIF-1α, F2RL1, and PIK3CB may act as novel drivers for vitiligo, which are all closely associated with reactive oxygen species and possibly contribute to the activation and/or migration of melanocyte-specific CD8+ T cells in vitiligo. In addition, we uncovered a potential role for DNA hypomethylation of HIF-1α in CD8+ T cells of vitiligo.

A Parametric Targetability Evaluation Approach for Vitiligo Proteome Extracted through Integration of Gene Ontologies and Protein Interaction Topologies

Vitiligo is a well-known skin disorder with complex etiology. Vitiligo pathogenesis is multifaceted with many ramifications. A computational systemic path was designed to first propose candidate disease proteins by merging properties from protein interaction networks and gene ontology terms. All in all, 109 proteins were identified and suggested to be involved in the onset of disease or its progression. Later, a composite approach was employed to prioritize vitiligo disease proteins by comparing and benchmarking the properties against standard target identification criteria. This includes sequence-based, structural, functional, essentiality, protein-protein interaction, vulnerability, secretability, assayability, and druggability information. The existing information was seamlessly integrated into efficient pipelines to propose a novel protocol for assessment of targetability of disease proteins. Using the online data resources and the scripting, an illustrative list of 68 potential drug targets was generated for vitiligo. While this list is broadly consistent with the research community's current interest in certain specific proteins, and suggests novel target candidates that may merit further study, it can still be modified to correspond to a user-specific environment, either by adjusting the weights for chosen criteria (i.e., a quantitative approach) or by changing the considered criteria (i.e., a qualitative approach).

VitiVar: A locus specific database of vitiligo associated genes and variations

Vitiligo is the most common skin pigmentation disorder which affects around 1% of the population worldwide. The disease has complex pathogenesis and is of multifactorial etiology, that finally culminates in patchy depigmentation of skin. Genetic contribution to the disease is well studied, however the information about multiple associated genes and contributing variations are scattered across the literature. To address this complex disorder affecting the skin, we systematically cataloged the genes and variations by creating a Locus Specific Database for vitiligo called, “VitiVar”. This comprehensive resource houses manually curated 322 genes and 254 variations, from 202 articles indexed in PubMed. We applied an integrative approach to stratify genes and variations to facilitate dissection of vitiligo pathogenesis by layering it with expression status in specific constituent cell types of skin and in-house vitiligo expression data. Finally, we were able to demonstrate the utility of VitiVar by generating a vitiligo interactome using GeneMANIA and overlaying the vitiligo and cell type specific information. This interaction network yielded 20 new genes (apart from 322 VitiVar genes) of which we were able to prioritize IFI27 and IFI6 for further validation. This, thereby makes VitiVar a comprehensive integrative platform in unravelling disease biology by providing meaningful leads for functional interrogation. VitiVar is freely accessible to the research community for prioritizing and validating the candidate genes and variations (http://vitivar.igib.res.in/).

•

We developed a Vitiligo centric web resource cataloguing the associated genes and variations

•

Overlaid the information of cell type specificity and expression status in Vitiliginous skin

•

Utilizing the network approach, we prioritized IFI6 & IFI27 which could be functionally interrogated in disease pathology

Nuclear Factor Kappa-B Is Enriched in Eyelid Specimens of Rosacea: Implications for Pathogenesis and Therapy

PURPOSE

To assess the role of nuclear factor kappa-B (NFKB) in cutaneous specimens of rosacea and unaffected tissue.

METHODS

Immunohistochemical staining was performed for the activated, phosphorylated variant of NFKB (pNFKB) in eyelid specimens of rosacea (n = 12) and normal, healthy tissue (n = 12). The numbers of positively staining cells/40× microscopic field were counted across 5 consecutive fields. Additionally, quantitative Western blotting was carried out for pNFKB and NFKB in specimens of rosacea (n = 15) and normal controls (n = 14). Statistical comparisons were performed via a dedicated software package.

RESULTS

The mean number of cells/40× microscopic field that stained positively for pNFKB was 18.4 (standard deviation = 15.3) for control patients and 39.3 (standard deviation = 16.9) for rosacea patients, and the difference between the 2 groups was statistically significant (P = .0024). On Western blotting, the mean ratios of pNFKB:NFKB for control and rosacea patients measured 0.58 (standard deviation = 0.81) and 3.11 (standard deviation = 3.53), respectively. The 2 groups were statistically significantly different (P = .0002).

CONCLUSIONS

The activated form of NFKB is enriched in rosacea, indicating a role for this pathway in the pathogenesis of this disease. Interference with NFKB signaling may represent a novel therapy for rosacea as clinical agents become available. NOTE: Publication of this article is sponsored by the American Ophthalmological Society.

In silico Analyses of Skin and Peripheral Blood Transcriptional Data in Cutaneous Lupus Reveals CCR2-A Novel Potential Therapeutic Target

Cutaneous lesions feature prominently in lupus erythematosus (LE). Yet lupus and its cutaneous manifestations exhibit extraordinary clinical heterogeneity, making it imperative to stratify patients with varying organ involvement based on molecular criteria that may be of clinical value. We conducted several in silico bioinformatics-based analyses integrating chronic cutaneous lupus erythematosus (CCLE)-skin and blood expression profiles to provide novel insights into disease mechanisms and potential future therapy. In addition to substantiating well-known prominent apoptosis and interferon related response in both tissue environments, the overrepresentation of GO categories in the datasets, in the context of existing literature, led us to model a “disease road-map” demonstrating a coordinated orchestration of the autoimmune response in CCLE reflected in three phases: (1) initiation, (2) amplification, and (3) target damage in skin. Within this framework, we undertook in silico interactome analyses to identify significantly “over-connected” genes that are potential key functional players in the metabolic reprogramming associated with skin pathology in CCLE. Furthermore, overlapping and distinct transcriptional “hot spots” within CCLE skin and blood expression profiles mapping to specified chromosomal locations offer selected targets for identifying disease-risk genes. Lastly, we used a novel in silico approach to prioritize the receptor protein CCR2, whose expression level in CCLE tissues was validated by qPCR analysis, and suggest it as a drug target for use in future potential CCLE therapy.

Bioinformatics methodologies for coeliac disease and its comorbidities

Coeliac disease (CD) is a complex, multifactorial pathology caused by different factors, such as nutrition, immunological response and genetic factors. Many autoimmune diseases are comorbidities for CD, and a comprehensive and integrated analysis with bioinformatics approaches can help in evaluating the interconnections among all the selected pathologies. We first performed a detailed survey of gene expression data available in public repositories on CD and less commonly considered comorbidities. Then we developed an innovative pipeline that integrates gene expression, cell-type data and online resources (e.g. a list of comorbidities from the literature), using bioinformatics methods such as gene set enrichment analysis and semantic similarity. Our pipeline is written in R language, available at the following link: http://bioinformatica.isa.cnr.it/COELIAC_DISEASE/SCRIPTS/. We found a list of common differential expressed genes, gene ontology terms and pathways among CD and comorbidities and the closeness among the selected pathologies by means of disease ontology terms. Physicians and other researchers, such as molecular biologists, systems biologists and pharmacologists can use it to analyze pathology in detail, from differential expressed genes to ontologies, performing a comparison with the pathology comorbidities or with other diseases.

Transcriptomic immune profiling of ovarian cancers in paraneoplastic cerebellar degeneration associated with anti-Yo antibodies

BACKGROUND

Paraneoplastic neurological syndromes are rare conditions where an autoimmune reaction against the nervous system appears in patients suffering from a tumour, but not linked to the spreading of the tumour. A break in the immune tolerance is thought to be the trigger.

METHODS

The transcriptomic profile of 12 ovarian tumours (OT) from patients suffering from paraneoplastic cerebellar degeneration (PCD) linked to anti-Yo antibodies (anti-Yo PCD OT) was compared with 733 ovarian tumours (OT control) from different public databases using linear model analysis.

RESULTS

A prominent significant transcriptomic over-representation of CD8+ and Treg cells was found in anti-Yo PCD OT, as compared to the OT control. However, the overall degree of immune cell infiltration was similar, according to the ESTIMATE immune score. We also found an under-representation of M2 macrophages in anti-Yo PCD OT. Furthermore, the differentially expressed genes were enriched for AIRE-related genes, a well-known transcription factor associated with a broad range of autoimmune diseases. Finally, we found that the differentially expressed genes were correlated to the transcriptomic profiling of the cerebellar structures.

CONCLUSIONS

Our data pinpointed the enrichment of acquired immune response, particularly high density of CD8+ lymphocytes, and high-level expression of CDR-related antigens in anti-Yo PCD OT.

The convergence theory for vitiligo: A reappraisal

Vitiligo is characterized by progressive loss of skin pigmentation. The search for aetiologic factors has led to the biochemical, the neurologic and the autoimmune theory. The convergence theory was then proposed several years ago to incorporate existing theories of vitiligo development into a single overview of vitiligo aetiology. The viewpoint that vitiligo is not caused only by predisposing mutations, or only by melanocytes responding to chemical/radiation exposure, or only by hyperreactive T cells, but rather results from a combination of aetiologic factors that impact melanocyte viability, has certainly stood the test of time. New findings have since informed the description of progressive depigmentation. Understanding the relative importance of such aetiologic factors combined with a careful selection of the most targetable pathways will continue to drive the next phase in vitiligo research: the development of effective therapeutics. In that arena, it is likewise important to acknowledge that pathways affected in some patients may not be altered in others. Taken together, the convergence theory continues to provide a comprehensive viewpoint of vitiligo aetiology. The theory serves to intertwine aetiologic pathways and will help to define pathways amenable to disease intervention in individual patients.

A case-control study on association of proteasome subunit beta 8 (PSMB8) and transporter associated with antigen processing 1 (TAP1) polymorphisms and their transcript levels in vitiligo from Gujarat

BACKGROUND

Autoimmunity has been implicated in the destruction of melanocytes from vitiligo skin. Major histocompatibility complex (MHC) class-II linked genes proteasome subunit beta 8 (PSMB8) and transporter associated with antigen processing 1 (TAP1), involved in antigen processing and presentation have been reported to be associated with several autoimmune diseases including vitiligo.

OBJECTIVES

To explore PSMB8 rs2071464 and TAP1 rs1135216 single nucleotide polymorphisms and to estimate the expression of PSMB8 and TAP1 in patients with vitiligo and unaffected controls from Gujarat.

METHODS

PSMB8 rs2071464 polymorphism was genotyped using polymerase chain reaction- restriction fragment length polymorphism (PCR-RFLP) and TAP1 rs1135216 polymorphism was genotyped by amplification refractory mutation system-polymerase chain reaction (ARMS-PCR) in 378 patients with vitiligo and 509 controls. Transcript levels of PSMB8 and TAP1 were measured in the PBMCs of 91 patients and 96 controls by using qPCR. Protein levels of PSMB8 were also determined by Western blot analysis.

RESULTS

The frequency of 'TT' genotype of PSMB8 polymorphism was significantly lowered in patients with generalized and active vitiligo (p = 0.019 and p = 0.005) as compared to controls suggesting its association with the activity of the disease. However, TAP1 polymorphism was not associated with vitiligo susceptibility. A significant decrease in expression of PSMB8 at both transcript level (p = 0.002) as well as protein level (p = 0.0460) was observed in vitiligo patients as compared to controls. No significant difference was observed between patients and controls for TAP1 transcripts (p = 0.553). Interestingly, individuals with the susceptible CC genotype of PSMB8 polymorphism showed significantly reduced PSMB8 transcript level as compared to that of CT and TT genotypes (p = 0.009 and p = 0.003 respectively).

CONCLUSIONS

PSMB8 rs2071464 was associated with generalized and active vitiligo from Gujarat whereas TAP1 rs1135216 showed no association. The down-regulation of PSMB8 in patients with risk genotype 'CC' advocates the vital role of PSMB8 in the autoimmune basis of vitiligo.