Cytokine responses in nonlesional psoriatic skin as clinical predictor to anti-TNF agents

GWAS meta-analysis of psoriasis identifies new susceptibility alleles impacting disease mechanisms and therapeutic targets

Psoriasis is a common, debilitating immune-mediated skin disease. Genetic studies have identified biological mechanisms of psoriasis risk, including those targeted by effective therapies. However, the genetic liability to psoriasis is not fully explained by variation at robustly identified risk loci. To refine the genetic map of psoriasis susceptibility we meta-analysed 18 GWAS comprising 36,466 cases and 458,078 controls and identified 109 distinct psoriasis susceptibility loci, including 46 that have not been previously reported. These include susceptibility variants at loci in which the therapeutic targets IL17RA and AHR are encoded, and deleterious coding variants supporting potential new drug targets (including in STAP2, CPVL and POU2F3). We conducted a transcriptome-wide association study to identify regulatory effects of psoriasis susceptibility variants and cross-referenced these against single cell expression profiles in psoriasis-affected skin, highlighting roles for the transcriptional regulation of haematopoietic cell development and epigenetic modulation of interferon signalling in psoriasis pathobiology.

Co-Expression Network and Machine Learning Analysis of Transcriptomics Data Identifies Distinct Gene Signatures and Pathways in Lesional and Non-Lesional Atopic Dermatitis

BACKGROUND

Atopic dermatitis (AD) is a common inflammatory skin condition with complex origins. Current treatments often yield suboptimal results due to an incomplete understanding of its underlying mechanisms. This study aimed to identify pathway and gene signatures that distinguish between lesional AD, non-lesional AD, and healthy skin.

METHOD

We conducted differential gene expression and co-expression network analyses to identify differentially co-expressed genes (DCEGs) in lesional AD vs. healthy skin, lesional vs. non-lesional AD, and non-lesional AD vs. healthy skin. Modules associated with lesional and non-lesional AD were identified based on the correlation coefficients between module eigengenes and clinical phenotypes (|R| ≥ 0.5, p-value < 0.05). Subsequently, we employed Ingenuity Pathway Analysis (IPA) on the identified DCEGs, followed by machine learning (ML) analysis within the pathway expression framework. The ML analysis of pathway expressions, selected by IPA and derived from gene expression data, identified relevant pathway signatures, which were validated using an independent dataset and correlated with AD severity measures (EASI and SCORAD).

RESULTS

We identified 975, 441, and 40 DCEGs in lesional vs. healthy skin, lesional vs. non-lesional, and non-lesional vs. healthy skin, respectively. IPA and ML analyses revealed 25 relevant pathway signatures, including wound healing, glucocorticoid receptor signaling, and S100 gene family signaling pathways. Validation confirmed the significance of 10 pathway signatures, which were correlated with the AD severity measures. DCEGs such as MMP12 and S100A8 demonstrated high diagnostic efficacy (AUC > 0.70) in both the discovery and validation datasets.

CONCLUSIONS

Differential gene expression, co-expression networks and ML analyses of pathway expression have unveiled relevant pathways and gene signatures that distinguish between lesional, non-lesional, and healthy skin, providing valuable insights into AD pathogenesis.

The Immunology of Psoriasis-Current Concepts in Pathogenesis

Psoriasis is one of the most common inflammatory skin diseases with a chronic, relapsing-remitting course. The last decades of intense research uncovered a pathological network of interactions between immune cells and other types of cells in the pathogenesis of psoriasis. Emerging evidence indicates that dendritic cells, TH17 cells, and keratinocytes constitute a pathogenic triad in psoriasis. Dendritic cells produce TNF-α and IL-23 to promote T cell differentiation toward TH17 cells that produce key psoriatic cytokines IL-17, IFN-γ, and IL-22. Their activity results in skin inflammation and activation and hyperproliferation of keratinocytes. In addition, other cells and signaling pathways are implicated in the pathogenesis of psoriasis, including TH9 cells, TH22 cells, CD8+ cytotoxic cells, neutrophils, γδ T cells, and cytokines and chemokines secreted by them. New insights from high-throughput analysis of lesional skin identified novel signaling pathways and cell populations involved in the pathogenesis. These studies not only expanded our knowledge about the mechanisms of immune response and the pathogenesis of psoriasis but also resulted in a revolution in the clinical management of patients with psoriasis. Thus, understanding the mechanisms of immune response in psoriatic inflammation is crucial for further studies, the development of novel therapeutic strategies, and the clinical management of psoriasis patients. The aim of the review was to comprehensively present the dysregulation of immune response in psoriasis with an emphasis on recent findings. Here, we described the role of immune cells, including T cells, B cells, dendritic cells, neutrophils, monocytes, mast cells, and innate lymphoid cells (ILCs), as well as non-immune cells, including keratinocytes, fibroblasts, endothelial cells, and platelets in the initiation, development, and progression of psoriasis.

A single-cell atlas of IL-23 inhibition in cutaneous psoriasis distinguishes clinical response

Psoriasis vulgaris and other chronic inflammatory diseases improve markedly with therapeutic blockade of interleukin-23 (IL-23) signaling, but the genetic mechanisms underlying clinical responses remain poorly understood. Using single-cell transcriptomics, we profiled immune cells isolated from lesional psoriatic skin before and during IL-23 blockade. In clinically responsive patients, a psoriatic transcriptional signature in skin-resident memory T cells was strongly attenuated. In contrast, poorly responsive patients were distinguished by persistent activation of IL-17-producing T (T17) cells, a mechanism distinct from alternative cytokine signaling or resistance isolated to epidermal keratinocytes. Even in IL-23 blockade-responsive patients, we detected a recurring set of recalcitrant, disease-specific transcriptional abnormalities. This irreversible immunological state may necessitate ongoing IL-23 inhibition. Spatial transcriptomic analyses also suggested that successful IL-23 blockade requires dampening of >90% of IL-17-induced response in lymphocyte-adjacent keratinocytes, an unexpectedly high threshold. Collectively, our data establish a patient-level paradigm for dissecting responses to immunomodulatory treatments.

Retrospective pharmacogenetic study of psoriasis highlights the role of KLK7 in tumour necrosis factor signalling

BACKGROUND

Multiple treatment options are available for the management of psoriasis, but clinical response varies among individual patients and no biomarkers are available to facilitate treatment selection for improved patient outcomes.

OBJECTIVES

To utilize retrospective data to conduct a pharmacogenetic study to explore the potential genetic pathways associated with drug response in the treatment of psoriasis.

METHODS

We conducted a retrospective pharmacogenetic study using self-evaluated treatment response from 1942 genotyped patients with psoriasis. We examined 6 502 658 genetic markers to model their associations with response to six treatment options using linear regression, adjusting for cohort variables and demographic features. We further utilized an integrative approach incorporating epigenomics, transcriptomics and a longitudinal clinical cohort to provide biological implications for the topmost signals associated with drug response.

RESULTS

Two novel markers were revealed to be associated with treatment response: rs1991820 (P = 1.30 × 10-6) for anti-tumour necrosis factor (TNF) biologics; and rs62264137 (P = 2.94 × 10-6) for methotrexate, which was also associated with cutaneous mRNA expression levels of two known psoriasis-related genes KLK7 (P = 1.0 × 10-12) and CD200 (P = 5.4 × 10-6). We demonstrated that KLK7 expression was increased in the psoriatic epidermis, as shown by immunohistochemistry, as well as single-cell RNA sequencing, and its responsiveness to anti-TNF treatment was highlighted. By inhibiting the expression of KLK7, we further illustrated that keratinocytes have decreased proinflammatory responses to TNF.

CONCLUSIONS

Our study implicates the genetic regulation of cytokine responses in predicting clinical drug response and supports the association between pharmacogenetic loci and anti-TNF response, as shown here for KLK7.

GWAS meta-analysis of psoriasis identifies new susceptibility alleles impacting disease mechanisms and therapeutic targets

Psoriasis is a common, debilitating immune-mediated skin disease. Genetic studies have identified biological mechanisms of psoriasis risk, including those targeted by effective therapies. However, the genetic liability to psoriasis is not fully explained by variation at robustly identified risk loci. To move towards a saturation map of psoriasis susceptibility we meta-analysed 18 GWAS comprising 36,466 cases and 458,078 controls and identified 109 distinct psoriasis susceptibility loci, including 45 that have not been previously reported. These include susceptibility variants at loci in which the therapeutic targets IL17RA and AHR are encoded, and deleterious coding variants supporting potential new drug targets (including in STAP2, CPVL and POU2F3). We conducted a transcriptome-wide association study to identify regulatory effects of psoriasis susceptibility variants and cross-referenced these against single cell expression profiles in psoriasis-affected skin, highlighting roles for the transcriptional regulation of haematopoietic cell development and epigenetic modulation of interferon signalling in psoriasis pathobiology.

Spatial transcriptomics stratifies psoriatic disease severity by emergent cellular ecosystems

Whereas the cellular and molecular features of human inflammatory skin diseases are well characterized, their tissue context and systemic impact remain poorly understood. We thus profiled human psoriasis (PsO) as a prototypic immune-mediated condition with a high predilection for extracutaneous involvement. Spatial transcriptomics (ST) analyses of 25 healthy, active lesion, and clinically uninvolved skin biopsies and integration with public single-cell transcriptomics data revealed marked differences in immune microniches between healthy and inflamed skin. Tissue-scale cartography further identified core disease features across all active lesions, including the emergence of an inflamed suprabasal epidermal state and the presence of B lymphocytes in lesional skin. Both lesional and distal nonlesional samples were stratified by skin disease severity and not by the presence of systemic disease. This segregation was driven by macrophage-, fibroblast-, and lymphatic-enriched spatial regions with gene signatures associated with metabolic dysfunction. Together, these findings suggest that mild and severe forms of PsO have distinct molecular features and that severe PsO may profoundly alter the cellular and metabolic composition of distal unaffected skin sites. In addition, our study provides a valuable resource for the research community to study spatial gene organization of healthy and inflamed human skin.

Pharmaco-Omics in Psoriasis: Paving the Way towards Personalized Medicine

The emergence of high-throughput approaches has had a profound impact on personalized medicine, evolving the identification of inheritable variation to trajectory analyses of transient states and paving the way for the unveiling of response biomarkers. The utilization of the multi-layered pharmaco-omics data, including genomics, transcriptomics, proteomics, and relevant biological information, has facilitated the identification of key molecular biomarkers that can predict the response to therapy, thereby optimizing treatment regiments and providing the framework for a tailored treatment plan. Despite the availability of multiple therapeutic options for chronic diseases, the highly heterogeneous clinical response hinders the alleviation of disease signals and exacerbates the annual burden and cost of hospitalization and drug regimens. This review aimed to examine the current state of the pharmaco-omic approaches performed in psoriasis, a common inflammatory disease of the skin. We sought to identify central studies that investigate the inter-individual variability and explore the underlying molecular mechanisms of drug response progression via biological profiling in psoriatic patients administered with the extended therapeutic armamentarium of psoriasis, incorporating conventional therapies, small molecules, as well as biological drugs that inhibit central pathogenic cytokines involved in the disease pathogenesis.

Review of biologics in allergy and immunology

Biologics or molecularly targeted drugs are often highly effective for the treatment of allergic diseases and other immunologic disorders, and they are relatively safe for short-term use as compared with conventional approaches such as the systemic use of corticosteroids. A number of studies published in 2021 consistently demonstrated their effectiveness and also revealed unanticipated findings. Among them, clinical trials for asthma and chronic obstructive pulmonary disease using biologics targeting thymic stromal lymphopoietin, IL-33, and IL-33 receptor demonstrated that these type 2 alarmin cytokines are also involved in non-type 2, noneosinophilic inflammation. Randomized controlled trials reporting the efficacies of 2 small-molecule oral drugs targeting Janus kinase-1 had a substantial impact on the management of atopic dermatitis. These drugs demonstrated superiority over dupilumab, which has previously demonstrated efficacy and is in wide use in clinical practice. As a concern, biologics are generally costly, and it should be noted that racial/ethnic minority populations may be less likely to receive biologics in the real world. Here, we have reviewed recent clinical trials and related topics dealing with the effects of biologics on allergic and immunologic diseases; in addition, we discuss how our understanding of the pathophysiology of these disorders has progressed.

Transcriptional Basis of Psoriasis from Large Scale Gene Expression Studies: The Importance of Moving towards a Precision Medicine Approach

Transcriptome profiling techniques, such as microarrays and RNA sequencing (RNA-seq), are valuable tools for deciphering the regulatory network underlying psoriasis and have revealed large number of differentially expressed genes in lesional and non-lesional skin. Such approaches provide a more precise measurement of transcript levels and their isoforms than any other methods. Large cohort transcriptomic analyses have greatly improved our understanding of the physiological and molecular mechanisms underlying disease pathogenesis and progression. Here, we mostly review the findings of some important large scale psoriatic transcriptomic studies, and the benefits of such studies in elucidating potential therapeutic targets and biomarkers for psoriasis treatment. We also emphasised the importance of looking into the alternatively spliced RNA isoforms/transcripts in psoriasis, rather than focussing only on the gene-level annotation. The neutrophil and blood transcriptome signature in psoriasis is also briefly reviewed, as it provides the immune status information of patients and is a less invasive platform. The application of precision medicine in current management of psoriasis, by combining transcriptomic data, improves the clinical response outcome in individual patients. Drugs tailored to individual patient's genetic profile will greatly improve patient outcome and cost savings for the healthcare system.

Machine learning reveals distinct gene signature profiles in lesional and nonlesional regions of inflammatory skin diseases

Analysis of gene expression from cutaneous lupus erythematosus, psoriasis, atopic dermatitis, and systemic sclerosis using gene set variation analysis (GSVA) revealed that lesional samples from each condition had unique features, but all four diseases displayed common enrichment in multiple inflammatory signatures. These findings were confirmed by both classification and regression tree analysis and machine learning (ML) models. Nonlesional samples from each disease also differed from normal samples and each other by ML. Notably, the features used in classification of nonlesional disease were more distinct than their lesional counterparts, and GSVA confirmed unique features of nonlesional disease. These data show that lesional and nonlesional skin samples from inflammatory skin diseases have unique profiles of gene expression abnormalities, especially in nonlesional skin, and suggest a model in which disease-specific abnormalities in "prelesional" skin may permit environmental stimuli to trigger inflammatory responses leading to both the unique and shared manifestations of each disease.

Skin-Expressing lncRNAs in Inflammatory Responses

Long non-coding RNAs (lncRNAs) have attracted attention for their potential roles in modulating keratinocyte differentiation and inflammatory response; however, for many identified skin-expressing lncRNAs, there is no comprehensive characterization regarding their biological roles. In addition, the reported expression profiles for lncRNAs can be ambiguous due to their low-expressing nature. The objective of this review is to utilize large scale genomic data to characterize the prominent skin-expressing lncRNAs, aiming to provide additional insights for their potential roles in the pathology of inflammatory skin of psoriasis and atopic dermatitis by integrating in vitro and in vivo data. We highlighted the different skin-expressing lncRNAs, including H19, which is significantly down-regulated in lesional skin of AD/psoriasis and upon cytokine stimulation in keratinocytes; it is also negatively correlated with CYP1A1 (r = -0.75, p = 8 × 10^-73), a gene involved in drug metabolism and skin barrier homeostasis, in keratinocytes. In addition, SPRR2C, a potential regulator that modulates IL-22 stimulation, was upregulated in both atopic dermatitis and psoriasis lesional skin and was also downstream of the IL-17A and IL-17 + TNF signaling in keratinocytes. Using scRNAseq, we further revealed the cell type specificity of lncRNAs, including basal-expressing nature of H19 in the epidermis. Interestingly, instead of having cell type specific expression profile, we found few lncRNAs that are express across different cell types in skin, including MALAT1, NEAT1, and GAS5. While lncRNAs in general have lower expression, our results combining in vitro and in vivo experimental data demonstrate how some of these lncRNAs can play mediator roles in the cytokine-stimulated pathway.