A transcriptome-wide association study identifies novel susceptibility genes for psoriasis

Bibliometric analysis and description of research trends in the treatment of psoriasis with biologic agents in the past two decades (2004-2023)

BACKGROUND

Biologics are essential in treating psoriasis. In recent years, the pathogenesis exploration and development of new target drugs have provided a more complete evidence-based foundation for the biological treatment of psoriasis. This study aims to use bibliometrics to analyze the research status and development trends of biologics in psoriasis.

METHODS

The bibliometric analysis of publications related to biologics in psoriasis from 2004 to 2023 was conducted using the Web of Science Core Collection (WoSCC) database as the search data source. To perform the bibliometric analysis and create visual knowledge graphs, CiteSpace, the Bibliometrix R package, and VOSviewers were utilized.

RESULTS

The study included a total of 3800 articles. The United States had the highest number of publications. The leading authors and institutions were Steven R. Feldman and the University of Manchester, respectively, in the global partnership. The cluster plot divided all keywords into 11 categories. Currently, Secukinumab and Guselkumab are representative biological agents being studied due to their considerable efficacy and long-term safety.

CONCLUSIONS

Targeted therapy has emerged as a significant trend in the current treatment of psoriasis. Early and active use of biologics can effectively control disease progression, prevent or delay the occurrence of comorbidities, and may even alter the natural course of psoriasis. However, further investigation is required to fully understand the specific mechanisms of psoriasis and the use of biological agents.

Functional Genomics and Insights into the Pathogenesis and Treatment of Psoriasis

Psoriasis is a lifelong, systemic, immune mediated inflammatory skin condition, affecting 1-3% of the world's population, with an impact on quality of life similar to diseases like cancer or diabetes. Genetics are the single largest risk factor in psoriasis, with Genome-Wide Association (GWAS) studies showing that many psoriasis risk genes lie along the IL-23/Th17 axis. Potential psoriasis risk genes determined through GWAS can be annotated and characterised using functional genomics, allowing the identification of novel drug targets and the repurposing of existing drugs. This review is focused on the IL-23/Th17 axis, providing an insight into key cell types, cytokines, and intracellular signaling pathways involved. This includes examination of currently available biological treatments, time to relapse post drug withdrawal, and rates of primary/secondary drug failure, showing the need for greater understanding of the underlying genetic mechanisms of psoriasis and how they can impact treatment. This could allow for patient stratification towards the treatment most likely to reduce the burden of disease for the longest period possible.

TWAS revealed significant causal loci for milk production and its composition in Murrah buffaloes

Milk yield is the most complex trait in dairy animals, and mapping all causal variants even with smallest effect sizes has been difficult with the genome-wide association study (GWAS) sample sizes available in geographical regions with small livestock holdings such as Indian sub-continent. However, Transcriptome-wide association studies (TWAS) could serve as an alternate for fine mapping of expression quantitative trait loci (eQTLs). This is a maiden attempt to identify milk production and its composition related genes using TWAS in Murrah buffaloes (Bubalus bubalis). TWAS was conducted on a test (N = 136) set of Murrah buffaloes genotyped through ddRAD sequencing. Their gene expression level was predicted using reference (N = 8) animals having both genotype and mammary epithelial cell (MEC) transcriptome information. Gene expression prediction was performed using Elastic-Net and Dirichlet Process Regression (DPR) model with fivefold cross-validation and without any cross-validation. DPR model without cross-validation predicted 80.92% of the total genes in the test group of Murrah buffaloes which was highest compared to other methods. TWAS in test individuals based on predicted gene expression, identified a significant association of one unique gene for Fat%, and two for SNF% at Bonferroni corrected threshold. The false discovery rates (FDR) corrected P-values of the top ten SNPs identified through GWAS were comparatively higher than TWAS. Gene ontology of TWAS-identified genes was performed to understand the function of these genes, it was revealed that milk production and composition genes were mainly involved in Relaxin, AMPK, and JAK-STAT signaling pathway, along with CCRI, and several key metabolic processes. The present study indicates that TWAS offers a lower false discovery rate and higher significant hits than GWAS for milk production and its composition traits. Hence, it is concluded that TWAS can be effectively used to identify genes and cis-SNPs in a population, which can be used for fabricating a low-density genomic chip for predicting milk production in Murrah buffaloes.

Staphylococcus warneri strain XSB102 exacerbates psoriasis and promotes keratinocyte proliferation in imiquimod-induced psoriasis-like dermatitis mice

Psoriasis is one of the common chronic inflammatory skin diseases worldwide. The skin microbiota plays a role in psoriasis through regulating skin homeostasis. However, the studies on the interactions between symbiotic microbial strains and psoriasis are limited. In this study, Staphylococcus strain XSB102 was isolated from the skin of human, which was identified as Staphylococcus warneri using VITEK2 Compact. To reveal the roles of Staphylococcus warneri on psoriasis, XSB102 were applied on the back of imiquimod-induced psoriasis-like dermatitis mice. The results indicated that it exacerbated the psoriasis and significantly increased the thickening of the epidermis. Furthermore, in vitro experiments confirmed that inactivated strain XSB102 could promote the proliferation of human epidermal keratinocytes (HaCaT) cell. However, real-time quantitative PCR and immunofluorescence results suggested that the expression of inflammatory factors such as IL-17a, IL-6, and so on were not significantly increased, while extracellular matrix related factors such as Col6a3 and TGIF2 were significantly increased after XSB102 administration. This study indicates that Staphylococcus warneri XSB102 can exacerbate psoriasis and promote keratinocyte proliferation independently of inflammatory factors, which paves the way for further exploration of the relationship between skin microbiota and psoriasis.

Disentangling the complexity of psoriasis in the post-genome-wide association era

In recent years, genome-wide association studies (GWAS) have been instrumental in unraveling the genetic architecture of complex diseases, including psoriasis. The application of large-scale GWA studies in psoriasis has illustrated several associated loci that participate in the cutaneous inflammation, however explaining a fraction of the disease heritability. With the advent of high-throughput sequencing technologies and functional genomics approaches, the post-GWAS era aims to unravel the functional mechanisms underlying the inter-individual variability in psoriasis patients. In this review, we present the key advances of psoriasis GWAS in under-represented populations, rare, non-coding and structural variants and epistatic phenomena that orchestrate the interplay between different cell types. We further review the gene-gene and gene-environment interactions contributing to the disease predisposition and development of comorbidities through Mendelian randomization studies and pleiotropic effects of psoriasis-associated loci. We finally examine the holistic approaches conducted in psoriasis through system genetics and state-of-the-art transcriptomic analyses, discussing their potential implication in the expanding field of precision medicine and characterization of comorbidities.

A Transcriptome-Wide Analysis of Psoriasis: Identifying the Potential Causal Genes and Drug Candidates

Psoriasis is a chronic inflammatory skin disease characterized by cutaneous eruptions and pruritus. Because the genetic backgrounds of psoriasis are only partially revealed, an integrative and rigorous study is necessary. We conducted a transcriptome-wide association study (TWAS) with the new Genotype-Tissue Expression version 8 reference panels, including some tissue and multi-tissue panels that were not used previously. We performed tissue-specific heritability analyses on genome-wide association study data to prioritize the tissue panels for TWAS analysis. TWAS and colocalization (COLOC) analyses were performed with eight tissues from the single-tissue panels and the multi-tissue panels of context-specific genetics (CONTENT) to increase tissue specificity and statistical power. From TWAS, we identified the significant associations of 101 genes in the single-tissue panels and 64 genes in the multi-tissue panels, of which 26 genes were replicated in the COLOC. Functional annotation and network analyses identified that the genes were associated with psoriasis and/or immune responses. We also suggested drug candidates that interact with jointly significant genes through a conditional and joint analysis. Together, our findings may contribute to revealing the underlying genetic mechanisms and provide new insights into treatments for psoriasis.

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.