Polygenic prediction of atopic dermatitis improves with atopic training and filaggrin factors

Understanding Atopic Dermatitis in Asian and European Population Cohorts Using Complementary Omics Techniques

Atopic dermatitis is highly heterogeneous with respect to pathogenesis, clinical manifestations, and treatment response. There is evidence that ancestry and skin type each contribute to this heterogeneity, indicating the need to improve understanding of disease mechanisms in diverse populations. Methods to integrate multiomics studies have been well-described, but this review focuses on the importance and the strategies needed to integrate data across different ancestral groups, focusing, because of data availability, on Asian and European populations. Skin scientists and clinicians will each benefit from an understanding of how the multiple complimentary layers of omics data may inform future clinical management, from insight into disease pathogenesis and treatment targets.

Polygenic transcriptome risk scores enhance predictive accuracy in atopic dermatitis

BACKGROUND

Incorporation of gene expression when estimating polygenic risk scores (PRS) in atopic dermatitis (AD) may provide additional insights in disease pathogenesis and enhance predictive accuracy. In this study, we developed polygenic transcriptome risk scores (PTRSs) derived from AD-enriched tissues and evaluated their performance against traditional PRS models and a baseline risk model incorporating eosinophil and lymphocyte counts in the prediction of AD.

METHODS

We conducted transcriptome-wide association studies (TWAS) using the PrediXcan framework to construct tissue-specific PTRSs. Risk score performance was assessed in 256,888 Europeans (10,816 cases) and validated in an independent cohort of 64,152 Europeans (2669 cases) from the UK Biobank.

RESULTS

We observed a modest correlation between PRS and PTRS, exerting independent effects on AD risk. While PRS demonstrated superior predictive performance compared to single-tissue PTRSs, combining both models significantly enhanced prediction accuracy, yielding a c-statistic of 0.646 (95% confidence intervals: 0.634-0.656). Notably, tissue-specific PTRSs revealed stronger associations with baseline risk factors, where Eppstein-Bar virus (EBV)-transformed lymphocytes and unexposed skin PTRSs tissues reported positive associations with lymphocyte counts.

CONCLUSIONS

Our findings highlight the value of integrating transcriptome-based risk models to incorporating additional omics layer to refine risk prediction and enhance our understanding of genetic architecture of complex traits.

The Current and Future of Biomarkers of Immune Related Adverse Events

With their groundbreaking clinical responses, immune checkpoint inhibitors (ICIs) have ushered in a new chapter in cancer therapeutics. However, they are often associated with life-threatening or organ-threatening autoimmune/autoinflammatory phenomena, collectively termed immune-related adverse events (irAEs). In this review, we will first describe the mechanisms of action of ICIs as well as irAEs. Next, we will review biomarkers for predicting the development of irAEs or stratifying risks.

Polygenic Score: A Tool for Evaluating the Genetic Background of Sporadic Hidradenitis Suppurativa

Sporadic hidradenitis suppurativa (spHS) is a multifactorial disease in which genetic predisposition is intertwined with environmental factors. Owing to the still-to-date limited knowledge of spHS genetics, we calculated polygenic scores (PGSs) to study the genetic underpinnings that contribute to spHS within European demographic. A total of 256 patients with spHS and 1686 healthy controls were analyzed across 6 European clinical centers. PGSs were calculated using a clumping and thresholding technique on 70% of the total sample, with the remaining 30% used for testing. The PANTHER tool was used to identify overrepresented genes. We generated a PGS characterized by 923 SNPs with a statistically significant association with spHS (P = 2 × 10-2). The statistically significant age-, sex-, and ancestry-adjusted association of our developed PGSs in spHS allows us to attribute a genetic contribution to the susceptibility of spHS (pseudo-R2 = 0.0053). Variants enriched for developing PGSs show a statistically significant preference for mapping to genes that encode primarily for cell adhesion proteins. Although this study developed a polygenic model associated with spHS, the low number of patients enrolled is a limitation. However, we believe that with larger experimental datasets, our model has the potential to serve as a valuable tool for predicting spHS states in future studies.

Identifying Atopic Dermatitis Risk Loci in 1,094,060 Individuals with Subanalysis of Disease Severity and Onset

Atopic dermatitis (AD) is a common inflammatory skin disease highly attributable to genetic factors. In this study, we report results from a genome-wide meta-analysis of AD in 37,541 cases and 1,056,519 controls with data from the FinnGen project, the Estonian Biobank, the UK Biobank, the EAGLE Consortium, and the BioBank Japan. We detected 77 independent AD-associated loci, of which 10 were, to our knowledge, previously unreported. The associated loci showed enrichment in various immune regulatory processes. We further performed subgroup analyses of mild and severe AD and of early- and late-onset AD, with data from the FinnGen project. Fifty-five of the 79 tested variants in the associated loci showed larger effect estimates for severe than for mild AD as determined through administered treatment. The age of onset, as determined by the first hospital visit with AD diagnosis, was lower in patients with particular AD-risk alleles. Our findings add to the knowledge of the genetic background of AD and may underlie the development of new therapeutic strategies.

The clinical, mechanistic, and social impacts of air pollution on atopic dermatitis

Atopic dermatitis (AD) is a complex disease characterized by dry, pruritic skin and significant atopic and psychological sequelae. Although AD has always been viewed as multifactorial, early research was dominated by overlapping genetic determinist views of either innate barrier defects leading to inflammation or innate inflammation eroding skin barrier function. Since 1970, however, the incidence of AD in the United States has increased at a pace that far exceeds genetic drift, thus suggesting a modern, environmental etiology. Another implicated factor is Staphylococcus aureus; however, a highly contagious microorganism is unlikely to be the primary etiology of a noncommunicable disease. Recently, the roles of the skin and gut microbiomes have received greater attention as potentially targetable drivers of AD. Here too, however, dysbiosis on a population scale would require induction by an environmental factor. In this review, we describe the evidence supporting the environmental hypothesis of AD etiology and detail the molecular mechanisms of each of the AD-relevant toxins. We also outline how a pollution-focused paradigm demands earnest engagement with environmental injustice if the field is to meaningfully address racial and geographic disparities. Identifying specific toxins and their mechanisms can also inform in-home and national mitigation strategies.

Genetic landscape of atopic dermatitis

PURPOSE OF REVIEW

This review summarizes recent advances in identifying genetic risk factors for atopic dermatitis and how these genetic associations are being used to explore the causal relationships between atopic dermatitis and potential risk factors and downstream outcomes.

RECENT FINDINGS

A recent large-scale GWAS meta-analysis has identified 91 genetic loci associated with atopic dermatitis. Rare variant studies have also identified new gain-of-function or loss-of-function variants implicated in atopic dermatitis, particularly for FLG and STAT6/JAK1 . Finally, there has been a surge in utilizing genetic association data to investigate the causal relationships between atopic dermatitis and other traits. Mendelian randomization studies have found that various metabolites and gut microbiota are causal for atopic dermatitis and have causally implicate atopic dermatitis in the development of alopecia areata, diabetes, vascular dementia and some cancers.

SUMMARY

The past year has seen a huge increase in the genes implicated for atopic dermatitis and in the use of genetics to explore causal relationships. The latter requires caution in implementation and interpretation, but is a promising area of research. In the coming years, increasing the ethnic diversity of atopic dermatitis genetic studies would be very welcome and the translation of current genetic findings into new drugs will be an exciting area of development.

Integrating multi-omics approaches in deciphering atopic dermatitis pathogenesis and future therapeutic directions

Atopic dermatitis (AD), a complex and heterogeneous chronic inflammatory skin disorder, manifests in a spectrum of clinical subtypes. The application of genomics has elucidated the role of genetic variations in predisposing individuals to AD. Transcriptomics, analyzing gene expression alterations, sheds light on the molecular underpinnings of AD. Proteomics explores the involvement of proteins in AD pathophysiology, while epigenomics examines the impact of environmental factors on gene expression. Lipidomics, which investigates lipid profiles, enhances our understanding of skin barrier functionalities and their perturbations in AD. This review synthesizes insights from these omics approaches, highlighting their collective importance in unraveling the intricate pathogenesis of AD. The review culminates by projecting future trajectories in AD research, particularly the promise of multi-omics in forging personalized medicine and novel therapeutic interventions. Such an integrated multi-omics strategy is poised to transform AD comprehension and management, steering towards more precise and efficacious treatment modalities.

How to Prevent Atopic Dermatitis (Eczema) in 2024: Theory and Evidence

Atopic dermatitis (AD) or eczema is a chronic inflammatory skin disease characterized by dry, itchy, and inflamed skin. We review emerging concepts and clinical evidence addressing the pathogenesis and prevention of AD. We examine several interventions ranging from skin barrier enhancement strategies to probiotics, prebiotics, and synbiotics; and conversely, from antimicrobial exposure to vitamin D and omega fatty acid supplementation; breastfeeding and hydrolyzed formula; and house dust mite avoidance and immunotherapy. We appraise the available evidence base within the context of the Grades of Recommendation, Assessment, Development, and Evaluation approach. We also contextualize our findings in relation to concepts relating AD and individual-patient allergic life trajectories versus a linear concept of the atopic march and provide insights into future knowledge gaps and clinical trial design considerations that must be addressed in forthcoming research. Finally, we provide implementation considerations to detect population-level differences in AD risk. Major international efforts are required to provide definitive evidence regarding what works and what does not for preventing AD.

Genetic and Immunological Pathogenesis of Atopic Dermatitis

Type 2 immune-mediated diseases give a clear answer to the issue of nature (genetics) versus nurture (environment). Both genetics and environment play vital complementary roles in the development of atopic dermatitis (AD). As a key component of the atopic march, AD demonstrates the interactive nature of genetic and environmental contributions to atopy. From sequence variants in the epithelial barrier gene encoding FLG to the hygiene hypothesis, AD combines a broad array of contributions into a single syndrome. This review will focus on the genetic contribution to AD and where genetics facilitates the elicitation or enhancement of AD pathogenesis.

The Current and Future of Biomarkers of Immune Related Adverse Events

With their groundbreaking clinical responses, immune checkpoint inhibitors (ICIs) have ushered in a new chapter in cancer therapeutics. However, they are often associated with life-threatening or organ-threatening autoimmune/autoinflammatory phenomena, collectively termed immune-related adverse events (irAEs). In this review, we will first describe the mechanisms of action of ICIs as well as irAEs. Next, we will review biomarkers for predicting the development of irAEs or stratifying risks.

Atopic Polygenic Risk Score Is Associated with Paradoxical Eczema Developing in Patients with Psoriasis Treated with Biologics

Biologic therapies for psoriasis can cause paradoxical eczema. The role of genetic factors in its pathogenesis is unknown. To identify risk variants, we conducted a GWAS of 3,212 patients with psoriasis, of whom 88 developed paradoxical eczema. Two lead SNPs reached genome-wide significance (P ≤ 5 × 10-8) for association with paradoxical eczema: rs192705221 (near UNC5B, P = 9.52 × 10-10) and rs72925168 (within SLC1A2, P = 1.66 × 10-9). Genome-wide significant SNPs from published GWAS were used to generate polygenic risk scores (PRSs) for atopic eczema, general atopic disease, or a combination, which were tested for association with paradoxical eczema. Improvement over a clinical risk model was assessed by the area under the curve. All three atopy polygenic risk scores were associated with paradoxical eczema (P < 0.05); polygenic risk score for a combination of atopic eczema and general atopic disease had the strongest association (OR = 1.83, 95% CI = 1.17-2.84, P = 0.0078). Including atopic polygenic risk scores in the multivariable model, which included age, sex, atopic background, and psoriatic arthritis history, increased the area under the curve from 0.671 to 0.681-0.686. Atopic genetic burden is associated with paradoxical eczema occurring in biologic-treated patients with psoriasis, indicating shared underlying mechanisms. Incorporating genetic risk may improve treatment outcome prediction models for psoriasis.

Intrinsic Effects of Exposome in Atopic Dermatitis: Genomics, Epigenomics and Regulatory Layers

Atopic dermatitis (AD) or atopic eczema is an increasingly manifested inflammatory skin disorder of complex etiology which is modulated by both extrinsic and intrinsic factors. The exposome includes a person's lifetime exposures and their effects. We recently reviewed the extrinsic exposome's environmental risk factors that contribute to AD. The periods of pregnancy, infancy, and teenage years are recognized as crucial stages in the formation of AD, where the exposome leads to enduring impacts on the immune system. However, research is now focusing on the interactions between intrinsic pathways that are modulated by the extrinsic exposome, including genetic variation, epigenetic modifications, and signals, such as diet, stress, and microbiome interactions. As a result, immune dysregulation, barrier dysfunction, hormonal fluctuations, and skin microbiome dysbiosis are important factors contributing to AD development, and their in-depth understanding is crucial not only for AD treatment but also for similar inflammatory disorders.

Novel insights into atopic dermatitis

Recent research into the pathophysiology and treatment of atopic dermatitis (AD) has shown notable progress. An increasing number of aspects of the immune system are being implicated in AD, including the epithelial barrier, TH2 cytokines, and mast cells. Major advances in therapeutics were made in biologic cytokine and receptor antagonists and among Janus kinase inhibitors. We focus on these areas and address new insights into AD epidemiology, biomarkers, endotypes, prevention, and comorbidities. Going forward, we expect future mechanistic insights and therapeutic advances to broaden physicians' ability to diagnose and manage AD patients, and perhaps to find a cure for this chronic condition.

Association of air pollution and genetic risks with incidence of elderly-onset atopic dermatitis: A prospective cohort study

BACKGROUND

Elderly-onset atopic dermatitis (AD) is a remarkable subtype and has been put on the agenda owing to its difficulty to control. Understanding the influence of genetic and environmental exposures is crucial to preventing elderly-onset AD.

OBJECTIVES

To explore the association between genes and air pollution on incident elderly-onset AD.

MATERIAL AND METHODS

This study was based on UK Biobank that recruited over 500,000 participants. The genetic risks were categorized into low, intermediate, and high groups according to tertiles of polygenic risk scores. Mixed exposure to various air pollutants was assessed using the weighted quantile sum (WQS) and also categorized based on tertiles. Within each genetic risk group, whether air pollutant mixture was associated with incident elderly-onset AD was estimated.

RESULTS

337,910 participants were included in the final analysis, and the mean age was 57.1. The median years for follow-up were 12.0, and the incident cases of AD were 2545. The medium and high air pollution mixture was significantly associated with incident AD compared with the low pollution group, with HRs of 1.182 (P = 0.003) and 1.359 (P < 0.001), respectively. In contrast, HR for medium and high genetic susceptibility was only 1.065 (P = 0.249) and 1.153 (P = 0.008). The population-attributable fraction of air pollution and genetic risk was 15.5 % (P < 0.001) and 6.4 % (P = 0.004). Additionally, compared with low genetic risk and low air pollution, high genetic risk and high air pollution was significantly associated with the incidence of elderly-onset AD with a HR of up to 1.523 (P < 0.001). There were no interactive effects between each group of genetic risks and air pollution. When grouped by sex, females could observe a stronger effect by genetic and air pollutant mixture exposure.

CONCLUSION

Air pollution and genetics both independently enhance the risk of newly developed AD, and the effect of air pollutants is stronger than the investigated genes.

Incorporating genetics in identifying peanut allergy risk and tailoring allergen immunotherapy: A perspective on the genetic findings from the LEAP trial

Examining the genetics of peanut allergy (PA) in the context of clinical trial interventions and outcomes provides an opportunity to not only understand gene-environment interactions for PA risk but to also understand the benefit of allergen immunotherapy. A consistent theme in the genetics of food allergy is that in keeping with the dual allergen exposure hypothesis, barrier- and immune-related genes are most commonly implicated in food allergy and tolerance. With a focus on PA, we review how genetic risk factors across 3 genes (FLG, MALT1, and HLA-DQA1) have helped delineate distinct allergic characteristics and outcomes in the context of environmental interventions in the Learning Early about Peanut Allergy (LEAP) study and other clinical trials. We specifically consider and present a framework for genetic risk prediction for the development of PA and discuss how genetics, age, and oral consumption intertwine to predict PA outcome. Although there is some promise in this proposed framework, a better understanding of the mechanistic pathways by which PA develops and persists is needed to develop targeted therapeutics for established disease. Only by understanding the mechanisms by which PA develops, persists, and resolves can we identify adjuvants to oral immunotherapy to make older children and adults immunologically similar to their younger, more malleable counterparts and thus more likely to achieve long-term tolerance.

Recent progress in the genetic and epigenetic underpinnings of atopy

In the past 2 years, there continue to be advances in our understanding of the genetic and epigenetic underpinnings of atopy pertaining to disease risk and disease severity. The joint role of genetics and the environment has been emphasized in multiple studies. Combining genetics with family history, biomarkers, and comorbidities is further refining our ability to predict the development of individual atopic diseases as well as the advancement of the atopic march. Polygenic risk scores will be an important next step for the field moving toward clinical translation of the genetic findings thus far. A systems biology approach, as illustrated by studies of the microbiome and epigenome, will be necessary to fully understand disease development and to develop increasingly targeted therapeutics.

Genetic/Environmental Contributions and Immune Dysregulation in Children with Atopic Dermatitis

Atopic dermatitis (AD) is one of the most common skin conditions in humans. AD affects up to 20% of children worldwide and results in morbidity for both patients and their caregivers. The basis of AD is an interplay between genetics and the environment characterized by immune dysregulation. A myriad of mutations that compromise the skin barrier and/or immune function have been linked to AD. Of these, filaggrin gene (FLG) mutations are the most evidenced. Many other mutations have been implicated in isolated studies that are often unreplicated, creating an archive of genes with potential but unconfirmed relevance to AD. Harnessing big data, polygenic risk scores (PRSs) and genome-wide association studies (GWAS) may provide a more practical strategy for identifying the genetic signatures of AD. Epigenetics may also play a role. Staphylococcus aureus is the most evidenced microbial contributor to AD. Cutaneous dysbiosis may result in over-colonization by pathogenic strains and aberrant skin immunity and inflammation. Aeroallergens, air pollution, and climate are other key environmental contributors to AD. The right climate and/or commensals may improve AD for some patients.

Factors associated with severity of atopic dermatitis - a Finnish cross-sectional study

BACKGROUND

Severity-associated factors in atopic dermatitis (AD) have focussed on early onset, concomitant atopic diseases, markers of Th2-shifted inflammation and filaggrin mutations.

OBJECTIVES

To investigate factors associated with severe AD in Finnish patients.

METHODS

We conducted a single-centre, cross-sectional observational study with 502 AD patients aged 4.79 to 79.90 years (mean 32.08 years). Disease severity was assessed with the Rajka-Langeland severity score and EASI and associated clinical signs were evaluated. Data regarding onset, relatives, atopic and other comorbidities was gathered retrospectively. We investigated total serum IgE-levels, a panel of filaggrin null mutations and functional variants of genes associated with skin barrier defects.

RESULTS

Factors more frequent in severe AD included early onset (P = 0.004, 95%CI 0.000-0.024), male sex (P = 0.002, 95%CI 0.000-0.11), history of smoking (P = 0.012, 95%CI 0.000-0.024), concomitant asthma (P = 0.001, 95%CI 0.000-0.011), palmar hyperlinearity (P = 0.013, 95%CI 0.014-0.059), hand dermatitis (P = 0.020, 95%CI 0.000-0.029) and history of contact allergy (P = 0.042, 95%CI 0.037-0.096). Body mass indices (P < 0.000, 95%CI 0.000-0.011) and total serum IgE-levels (P < 0.000, 95%CI 0.000-0.011) were higher in severe AD. No differences were observed for allergic rhinitis, allergic conjunctivitis, food allergy, peanut allergy, prick positivity, keratosis pilaris, history of herpes simplex infections, filaggrin null mutations and other gene variants.

CONCLUSIONS

Severity determinants in Finnish patients seem to be early-onset, male sex, smoking, overweight, concomitant asthma, palmar hyperlinearity, hand dermatitis and high IgE-levels. A sub-typing of patients in relation to confirmed severity determinants may be useful for course prediction, prognosis and targeted AD management.