Transcriptomic profiling of pemphigus lesion infiltrating mononuclear cells reveals a distinct local immune microenvironment and novel lncRNA regulators

Authentication and validation of key genes in the treatment of atopic dermatitis with Runfuzhiyang powder: combined RNA-seq, bioinformatics analysis, and experimental research

Background

Atopic dermatitis (AD) is inflammatory disease. So far, therapeutic mechanism of Runfuzhiyang powder on AD remains to be studied. This study aimed to mine key biomarkers to explore potential molecular mechanism for AD incidence and Runfuzhiyang powder treatment.

Methods

The control group, AD group, treat group (AD mice treated with Runfuzhiyang powder were utilized for studying. Differentially expressed AD-related genes were acquired by intersecting of key module genes related to control group, AD group and treatment group which were screened by WGCNA and AD-related differentially expressed genes (DEGs). KEGG and GO analyses were further carried out. Next, LASSO regression analysis was utilized to screen feature genes. The ROC curves were applied to validate the diagnostic ability of feature genes to obtain AD-related biomarkers. Then protein-protein interaction (PPI) network, immune infiltration analysis and single-gene gene set enrichment analysis (GSEA) were presented. Finally, TF-mRNA-lncRNA and drug-gene networks of biomarkers were constructed.

Results

4 AD-related biomarkers (Ddit4, Sbf2, Senp8 and Zfp777) were identified in AD groups compared with control group and treat group by LASSO regression analysis. The ROC curves revealed that four biomarkers had good distinguishing ability between AD group and control group, as well as AD group and treatment group. Next, GSEA revealed that pathways of E2F targets, KRAS signaling up and inflammatory response were associated with 4 biomarkers. Then, we found that Ddit4, Sbf2 and Zfp777 were significantly positively correlated with M0 Macrophage, and were significantly negatively relevant to Resting NK. Senp8 was the opposite. Finally, a TF-mRNA-lncRNA network including 200 nodes and 592 edges was generated, and 20 drugs targeting SENP8 were predicted.

Conclusion

4 AD-related and Runfuzhiyang powder treatment-related biomarkers (Ddit4, Sbf2, Senp8 and Zfp777) were identified, which could provide a new idea for targeted treatment and diagnosis of AD.

Beyond the skin: B cells in pemphigus vulgaris, tolerance and treatment

Pemphigus vulgaris (PV) is a rare autoimmune bullous disease characterized by blistering of the skin and mucosa owing to the presence of autoantibodies against the desmosome proteins desmoglein 3 and occasionally in conjunction with desmoglein 1. Fundamental research into the pathogenesis of PV has revolutionized its treatment and outcome with rituximab, a B-cell-depleting therapy. The critical contribution of B cells to the pathogenesis of pemphigus is well accepted. However, the exact pathomechanism, mechanisms of onset, disease course and relapse remain unclear. In this narrative review, we provide an overview of the fundamental research progress that has unfolded over the past few centuries to give rise to current and emerging therapies. Furthermore, we summarize the multifaceted roles of B cells in PV, including their development, maturation and antibody activity. Finally, we explored how these various aspects of B-cell function contribute to disease pathogenesis and pave the way for innovative therapeutic interventions.

Immune interplay from circulation to local lesion in pemphigus pathogenesis

Pemphigus, a potentially lethal autoimmune skin disease, is mediated by desmoglein-specific antibodies, manifesting cutaneous and mucosal blisters and erosions. The interaction between multiple immune counterparts contributes to the progress of pemphigus. Currently, the emergence of bioinformatic analysis enables investigators to gain a global picture of the pemphigus immune network, based on the exhaustive pedigree annotation of multiple subsets. T helper subsets dominate the landscape as mentioned previously, and innate immune cells have been involved as well. Of particular interests is which phenotype of T cells orchestrates the autoimmune process and chronic inflammation in a certain condition. In this review, the circulatory and peripheral immune cells and cytokine components constituting the immune microenvironment are separately discussed to provide a perspective on pemphigus pathogenesis, with particular reference to insights provided by the bioinformation technique.

Single-cell sequencing reveals distinct immune cell features in cutaneous lesions of pemphigus vulgaris and bullous pemphigoid

Bullous pemphigoid (BP) and pemphigus vulgaris (PV) are two common subtypes of autoimmune bullous disease (AIBD). The key role of circulating autoreactive immune cells contributing to skin damage of AIBD has been widely recognized. Nevertheless, the immune characteristics in cutaneous lesions remain unclear. Here, we performed single-cell RNA sequencing (scRNA-seq) and single-cell VDJ sequencing (scRNA-seq) to generate transcriptional profiles for cells and T/B cell clonetype in skin lesions of BP and PV. We found that the proportions of NK&T, macrophages/ dendritic cells, B cells, and mast cells increased in BP and PV lesions. Then, BP and PV cells constituted over 75% of all myeloid cell subtypes, CD4+ T cell subtypes and CD8+ T cell subtypes. Strikingly, CD8+ Trm was identified to be expanded in PV, and located in the intermediate state of the pseudotime trajectory from CD8+ Tm to CD8+ Tem. Interestingly, CD8+ Tem and CD4+ Treg highly expressed exhaustion-related genes, especially in BP lesions. Moreover, the enhanced cell communication between stromal cells and immune cells like B cells and macrophages/ dendritic cells was also identified in BP and PV lesions. Finally, clone expansion was observed in T cells of BP and PV compared with HC, while CD8+ Trm represented the highest ratio of hyperexpanded TCR clones among all T cell subtypes. Our study generally depicts a large and comprehensive single-cell landscape of cutaneous lesions and highlights immune cell features in BP and PV. This offers potential research targets for further investigation.

Linc01588 deletion inhibits the malignant biological characteristics of hydroquinone-induced leukemic cells via miR-9-5p/SIRT1

Leukemia caused by environmental chemical pollutants has attracted great attention, the malignant leukemic transformation model of TK6 cells induced by hydroquinone (HQ) has been previously found in our team. However, the type of leukemia corresponding to this malignant transformed cell line model needs further study and interpretation. Furthermore, the molecular mechanism of malignant proliferation of leukemic cells induced by HQ remains unclear. This study is the first to reveal the expression of aberrant genes in leukemic cells of HQ-induced malignant transformation, which may correspond to chronic lymphocytic leukemia (CLL). The expression of Linc01588, a long non-coding RNA (lncRNA), was significantly up-regulated in CLL patients and leukemic cell line model which previously described. After gain-of-function assays and loss-of-function assays, feeble cell viability, severe apoptotic phenotype and the increased secretion of TNF-α were easily observed in malignant leukemic TK6 cells with Linc01588 deletion after HQ intervention. The tumors derived from malignant TK6 cells with Linc01588 deletion inoculated subcutaneously in nude mice were smaller than controls. In CLL and its cell line model, the expression of Linc01588 and miR-9-5p, miR-9-5p and SIRT1 were negative correlation respectively in CLL and cell line model, while the expression of Linc01588 and SIRT1 were positive correlation. The dual-luciferase reporter assay showed that Linc01588 & miR-9-5p, miR-9-5p & SIRT1 could bind directly, respectively. Furthermore, knockdown of miR-9-5p successfully rescued the severe apoptotic phenotype and the increased secretion of TNF-α caused by the Linc01588 deletion, the deletion of Linc01588 in human CLL cell line MEC-2 could also inhibit malignant biological characteristics, and the phenotype caused by the deletion of Linc01588 could also be rescued after overexpression of SIRT1. Moreover, the regulation of SIRT1 expression in HQ19 cells by Linc01588 and miR-9-5 P may be related to the Akt/NF-κB pathway. In brief, Linc01588 deletion inhibits the malignant biological characteristics of HQ-induced leukemic cells via miR-9-5p/SIRT1, and it is a novel and hopeful clue for the clinical targeted therapy of CLL.

Sexual quality of life in patients with pemphigus: A case-control study

BACKGROUND

Pemphigus, an autoimmune blistering disease that affects the skin and mucous membranes, significantly impairs the quality of life (QoL) of affected individuals. While there are a variety of QoL measurement tools available for assessing this disease, there is a lack of studies that specifically evaluate the sexual QoL of patients with pemphigus.

OBJECTIVES

This case-control study aims to investigate the impact of the disease on sexual activity as well as its overall effect on QoL.

MATERIALS AND METHODS

Fifty pemphigus patients, who were referred to the Dermatology Department at the University Hospital of Brescia in the period March 2019-September 2021, completed several QoL surveys, including the 36-item Short Form Health survey (SF-36), the 12-Item General Health Questionnaire (GHQ-12), the Autoimmune Bullous Disease Quality of Life (ABQOL) and either the International Index of Erectile Function (IIEF) or the Female Sexual Function Index (FSFI). The severity of the disease was assessed using the Pemphigus Disease Area Index (PDAI). Differences in QoL surveys between the case and control groups were analysed using either the t-test or the Wilcoxon-Mann-Whitney test. The correlation between QoL surveys in pemphigus patients and disease severity were analysed using Spearman's coefficient (r).

RESULTS

The results revealed a marked impairment in overall QoL among patients with pemphigus compared to the healthy control subjects. Significant differences were observed in various domains of QoL, including physical health, mental well-being, social functioning and, notably, sexual health. Furthermore, disease severity as evaluated by the PDAI showed correlations with specific aspects of health status, and disease-specific QoL demonstrated associations with nearly all domains of health status. No significant correlations were found between sexual activity, mucosal involvement or steroid therapy and PDAI scores or disease-specific QoL measures.

CONCLUSION

These findings emphasize the significant impact of pemphigus on patients' well-being, with particular attention to the impaired sexual activity.

Microarray Gene Expression Analysis of Lesional Skin in Canine Pemphigus Foliaceus

Canine pemphigus foliaceus (PF) is considered the most common autoimmune skin disease in dogs; the mechanism of PF disease development is currently poorly understood. Therefore, this study aimed to characterize the molecular mechanisms and altered biological pathways in the skin lesions of canine PF patients. Using an RNA microarray on formalin-fixed, paraffin-embedded samples, we analyzed the transcriptome of canine PF lesional skin (n = 7) compared to healthy skin (n = 5). Of the 800 genes analyzed, 420 differentially expressed genes (DEGs) (p < 0.05) were found. Of those, 338 genes were significantly upregulated, including pro-inflammatory and Th17-related genes. Cell type profiling found enhancement of several cell types, such as neutrophils, T-cells, and macrophages, in PF skin compared to healthy skin. Enrichment analyses of the upregulated DEGs resulted in 78 statistically significant process networks (FDR < 0.05), including the Janus kinase signal transducer and activator of transcription (JAK-STAT) and mitogen-activated protein kinase (MAPK) signaling. In conclusion, canine PF lesional immune signature resembles previously published changes in human pemphigus skin lesions. Further studies with canine PF lesional skin using next-generation sequencing (e.g., RNA sequencing, spatial transcriptomics, etc.) and the development of canine keratinocyte/skin explant PF models are needed to elucidate the pathogenesis of this debilitating disease.

Integrative single-cell analysis reveals distinct adaptive immune signatures in the cutaneous lesions of pemphigus

Pemphigus, an autoimmune bullous disease affecting the skin and mucosal membranes, is primarily driven by anti-desmoglein (Dsg) autoantibodies. However, the underlying immune mechanisms of this disease remain largely elusive. Here, we compile an unbiased atlas of immune cells in pemphigus cutaneous lesions at single-cell resolution. We reveal clonally expanded antibody-secreting cells (ASCs) that exhibit variable hypermutation and accumulation of IgG4 class-switching in their immunoglobulin genes. Importantly, pathogenic Dsg-specific ASCs are localized within pemphigus lesions and can evolve from both Dsg-autoreactive and non-binding precursors. We observe an altered distribution of CD4+ T cell subsets within pemphigus lesions, including an imbalance of Th17/Th2 cells. Significantly, we identify a distinct subpopulation of Th17 cells expressing CXCL13 and IL-21 within pemphigus lesions, implying its pivotal role in B cell recruitment and local production of autoantibodies. Furthermore, we characterize multiple clonally expanded CD8+ subpopulations, including effector GMZB+ and GMZK+ subsets with augmented cytotoxic activities, within pemphigus lesions. Chemokine-receptor mapping uncovers cell-type-specific signaling programs involved in the recruitment of T/B cells within pemphigus lesions. Our findings significantly contribute to advancing the understanding of the heterogeneous immune microenvironment and the pathogenesis of pemphigus cutaneous lesions, thereby providing valuable insights for potential therapeutic interventions in this disease.

The roles of lncRNAs in Th17-associated diseases, with special focus on JAK/STAT signaling pathway

One of the most crucial T cell subsets in a variety of autoimmune and chronic inflammatory illnesses is T helper (Th) 17 cells. Th17 cells appear to have an essential role in the clearance of extracellular pathogens during infections. However, Th17 cells are also involved in inflammation and have been implicated in the pathogenesis of several autoimmune diseases and human inflammatory conditions. Due to the involvement of Th17 cells in the onset of Th17-associated diseases, understanding molecular mechanisms of Th17 cell functions may open the door to developing tailored therapies to address these difficult disorders. However, the molecular mechanisms governing Th17 differentiation in various diseases are still not well understood. The JAK/STAT signaling pathway plays a critical role in immune responses and has been linked to various aspects of Th17 cell differentiation and function. In this article, we conducted a comprehensive review of various molecular mechanisms (JAK/STAT, microRNAs, etc.), that can affect the differentiation of Th17 cells in various Th17-associated diseases.

Characterization of the serum and skin inflammatory profile in canine pemphigus foliaceus using multiplex assay and quantitative real-time polymerase chain reaction (qRT-PCR)

Canine pemphigus foliaceus (PF) is a common autoimmune skin disease characterized by autoantibodies binding to epithelial adhesion molecules resulting inflammatory response. The immune network of cytokine and chemokine abnormalities that characterize the immune response in canine PF are poorly explored. This study evaluated serum and lesional skin cytokine and chemokine profiles of dogs diagnosed with PF compared to healthy control dogs. Serum samples obtained from 11 PF dogs and 16 healthy control dogs were analyzed using commercially available canine multiplex assay for 13 biomarkers (Canine Milliplex assay). Eight lesional skin samples from seven PF dogs and five healthy site-matched samples from five healthy dogs were evaluated for 20 immune markers using quantitative real-time PCR. Immunomodulating medications were suspended for at least four weeks in all dogs before obtaining serum and skin samples. PF patients showed significantly higher serum concentrations of tumor necrosis factor-α, interleukin (IL)- 6, IL-8, IL-18, CCL2, KC-like, and granulocyte-macrophages colony-stimulating factor when compared to healthy controls (Mann-Whitney U test; p < 0.05 for all). Lesional PF skin exhibited significant expression and upregulation of pro-inflammatory/T helper (Th1) 1 markers IL-1β, MX1, GZMB, OAS1, and IFN-γ as well as Th2 cytokines IL-13, IL-33, TSLP, IL-31 and Th17/22 markers IL-17A and IL-22 (Mann-Whitney U test; p < 0.05 for all). Taken together, the findings from this study describe the role of numerous cytokines and chemokines associated with immune response in the skin and serum of canine PF patients. Further larger-sample proteomics and RNA-sequencing transcriptomics studies are needed to understand the immune pathogenesis of canine PF skin lesions.

Targeting Th17 cells: a promising strategy to treat oral mucosal inflammatory diseases

With the improved quality of life, oral health is under increased pressure. Numerous common oral mucosal diseases, such as oral lichen planus(OLP) and gingivitis, are related to the destruction of the oral immune barrier. The cytokines secreted by T-helper 17 (Th17) cells are essential for maintaining oral immune homeostasis and play essential roles in immune surveillance. When antigens stimulate the epithelium, Th17 cells expand, differentiate, and generate inflammatory factors to recruit other lymphocytes, such as neutrophils, to clear the infection, which helps to maintain the integrity of the epithelial barrier. In contrast, excessive Th17/IL-17 axis reactions may cause autoimmune damage. Therefore, an in-depth understanding of the role of Th17 cells in oral mucosa may provide prospects for treating oral mucosal diseases. We reviewed the role of Th17 cells in various oral and skin mucosal systemic diseases with oral characteristics, and based on the findings of these reports, we emphasize that Th17 cellular response may be a critical factor in inflammatory diseases of the oral mucosa. In addition, we should pay attention to the role and relationship of "pathogenic Th17" and "non-pathogenic Th17" in oral mucosal diseases. We hope to provide a reference for Th17 cells as a potential therapeutic target for treating oral mucosal inflammatory disorders in the future.

Pan-cancer survey of lncRNA rewiring and functional alternation in tumor-infiltrating T cell by scLNC

Long non-coding RNAs (lncRNAs) have been reported to involve in diverse biological processes, including tumor immunity. Since lncRNAs are expressed with high cell-type specificity, investigation of lncRNAs at the single-cell level will unveil the cell-type-specific functions of lncRNAs. However, at the single-cell level, a systematic pan-cancer analysis of lncRNA functions in tumor immune microenvironments (TIMEs) remains lacking. Here, we performed pan-cancer single-cell profiling of lncRNA functions in TIMEs and developed a tool, scLNC, tailored for lncRNA functional characterization at the single-cell level. scLNC enabled the comparison of lncRNA function from the levels of lncRNA-mRNA pairs, lncRNA regulatory unit activity and unit function in a cell-type-specific manner. Applying scLNC, our analysis depicted the cross-tumor and tumor-specific lncRNA regulatory profiles in the T cell subtypes and revealed the new regulatory units that lncRNAs established in tumor-infiltrating T cells, particularly in the tumor-enriched T cells. We further characterized the activity and functional alternations of lncRNAs through their regulatory units. Overall, our findings suggested that lncRNAs played an important role in the regulation of cytokine production, cell activation and migration in tumor-enriched T cells and further in immunotherapy.

Towards multiomic analysis of oral mucosal pathologies

Oral mucosal pathologies comprise an array of diseases with worldwide prevalence and medical relevance. Affecting a confined space with crucial physiological and social functions, oral pathologies can be mutilating and drastically reduce quality of life. Despite their relevance, treatment for these diseases is often far from curative and remains vastly understudied. While multiple factors are involved in the pathogenesis of oral mucosal pathologies, the host's immune system plays a major role in the development, maintenance, and resolution of these diseases. Consequently, a precise understanding of immunological mechanisms implicated in oral mucosal pathologies is critical (1) to identify accurate, mechanistic biomarkers of clinical outcomes; (2) to develop targeted immunotherapeutic strategies; and (3) to individualize prevention and treatment approaches. Here, we review key elements of the immune system's role in oral mucosal pathologies that hold promise to overcome limitations in current diagnostic and therapeutic approaches. We emphasize recent and ongoing multiomic and single-cell approaches that enable an integrative view of these pathophysiological processes and thereby provide unifying and clinically relevant biological signatures.

Non-coding RNAs in immunoregulation and autoimmunity: Technological advances and critical limitations

Immune cell function is critically dependent on precise control over transcriptional output from the genome. In this respect, integration of environmental signals that regulate gene expression, specifically by transcription factors, enhancer DNA elements, genome topography and non-coding RNAs (ncRNAs), are key components. The first three have been extensively investigated. Even though non-coding RNAs represent the vast majority of cellular RNA species, this class of RNA remains historically understudied. This is partly because of a lag in technological and bioinformatic innovations specifically capable of identifying and accurately measuring their expression. Nevertheless, recent progress in this domain has enabled a profusion of publications identifying novel sub-types of ncRNAs and studies directly addressing the function of ncRNAs in human health and disease. Many ncRNAs, including circular and enhancer RNAs, have now been demonstrated to play key functions in the regulation of immune cells and to show associations with immune-mediated diseases. Some ncRNAs may function as biomarkers of disease, aiding in diagnostics and in estimating response to treatment, while others may play a direct role in the pathogenesis of disease. Importantly, some are relatively stable and are amenable to therapeutic targeting, for example through gene therapy. Here, we provide an overview of ncRNAs and review technological advances that enable their study and hold substantial promise for the future. We provide context-specific examples by examining the associations of ncRNAs with four prototypical human autoimmune diseases, specifically rheumatoid arthritis, psoriasis, inflammatory bowel disease and multiple sclerosis. We anticipate that the utility and mechanistic roles of these ncRNAs in autoimmunity will be further elucidated in the near future.