Transcriptional profiling of psoriasis: RNA-sequencing of a large case-control sample

Transcriptional profiling of psoriasis: RNA-sequencing of a large case-control samplePsoriasis is a common inflammatory skin disease with a complex genetic background. In this project we have performed RNA sequencing of psoriasis related skin samples to study basic mechanisms of how genetic factors affect psoriasis development.Gene expression data has increased our understanding of molecular contributors of psoriasis. However, few aberrantly expressed miRNAs in psoriasis have confirmed mRNA targets with biological functions in skin and a limited number of combined miRNA and mRNA sequencing studies have been performed. To increase our understanding of the psoriasis transcriptome and the miRNA-mRNA network, we sequenced small RNAs and ribosomal RNA-depleted total RNA of skin biopsies from patients with psoriasis vulgaris (n=75) and non-psoriatic controls (n=46). Comparing lesional psoriatic and control skin, we identified 270 differentially expressed (|log2FC|>0.5, FDR <0.05) miRNAs, of which 130 were upregulated and 140 were downregulated. The number of up- and downregulated (|log2FC|>0.5, FDR <0.05) mRNAs were 4,216 and 4,121, respectively. The differentially expressed mRNAs were analyzed by functional enrichment analysis using DAVID v6.8. For the upregulated genes, enriched functional annotation clusters included 'Immunity', 'Cell division' and 'Keratinization', and for the downregulated genes 'Glycoprotein/Cell membrane', 'Disulphide bond' and 'Cell adhesion'. Our results support a model for psoriasis as a result of perturbed interaction between keratinocytes and activated immune cells, leading to an increased proliferation rate of keratinocytes and epidermal thickening. We aim for further systematic analysis using pathway and network tools on miRNA and mRNA pairs with anti-correlated expression patterns. Increased knowledge of the transcriptome of psoriasis has the potential to provide new insight into the pathogenesis of psoriasis in addition to identification of biomarkers and therapeutic targets.

Transcriptional profiling of psoriasis: RNA-sequencing of a large case-control samplePsoriasis is a common inflammatory skin disease with a complex genetic background. In this project we have performed RNA sequencing of psoriasis related skin samples to study basic mechanisms of how genetic factors affect psoriasis development.A strong genetic basis for psoriasis is now well established and heritability is estimated at 60 to 90%, which is among the highest for complex genetic diseases. Genetic studies have so far made successful contributions to the understanding of psoriasis, including informing the development of highly effective treatments. However, less than 25% of psoriasis heritability has been accounted for, hence a substantial proportion of the genetic risk for psoriasis is yet to be identified. In this study we aim to identify new genetic factors with obvious functional consequences that contribute to the risk for psoriasis as these have the potential for new clinical insight in prevention and treatment of the disease. In particular, we will examine synergies between DNA, RNA, and proteins. For these purposes, we have collected blood samples and skin biopsies to study basic mechanisms of how genetic factors affect psoriasis development. This has been made possible through the funding from the Joint Research Committee between St. Olavs Hospital and the Faculty of Medicine, NTNU (“Two-year research projects”). In total, we have collected skin biopsies from 57 psoriatic cases and 57 non-psoriatic controls, making this biobank one of the largest of its kind worldwide. We are utilizing well-established research infrastructures at St. Olavs Hospital and NTNU, including the Clinical Research Facility and Biobank1 for collection and handling of the samles. The collection is further done in collaboration with Department of Dermatology, St. Olavs Hospital, private dermatologists in Helse Midt-Norge, general practitioners in Trondheim municipality, and “Psoriasis- og eksemforbundet”. In addition, our colleagues in Tromsø has collected skin biopsies from 18 psoriatic cases for the purpose of this study. NTNU Genomic Core Facilities (GCF) performed RNA extraction which showed high-quality RNA, and the skin samples have been RNA sequenced (mRNA and miRNA) by the GCF. We are currently performing analyses of these data in collaboration with the Bioinformatics Core Faciliy, and additional funding received from St. Olavs Hospital have opened for a pilot on single cell RNA (scRNA) sequencing of psoriatic skin. So far our mRNA results are in compliance with previous transcriptomic studies for psoriasis, and we are currently applying a novel approach for psoriasis on integrated miRNA and mRNA analyses. Our preliminary results have been presented on several national and international conferences. We aim for further systematically analysis using pathway and network tools, and combined mRNA, miRNA and scRNA analysis. We hope that such combined analysis will conform mRNA targets of the differentially expressed genes with possible biological functions in skin. We will combine data from our already RNA sequenced psoriasis-related skin biopsies with genotype data (DNA) from the same individuals from the psoriasis biobank. This deep molecular phenotyping will be complemented by integrated analysis with our already genotyped HUNT population, and eQTL analysis for further functional follow-up. The identification of genomic factors associated with psoriasis have the potential to provide new insight into biological mechanisms underlying the pathogenesis of psoriasis that can catalyse breakthroughs in psoriasis prevention, diagnosis and treatment.

Transcriptional profiling of psoriasis: RNA-sequencing of a large case-control samplePsoriasis is a common inflammatory skin disease with a complex genetic background. In this project we will perform RNA sequencing of psoriasis related skin samples to study basic mechanisms of how genetic factors affect psoriasis development.A strong genetic basis for psoriasis is now well established and heritability is estimated at 60-90%. Genetic studies have so far made successful contributions to the understanding of psoriasis, including informing the development of highly effective treatments. However, less than 25% of psoriasis heritability has been accounted for, hence a substantial proportion of the genetic risk for psoriasis is yet to be identified. To enable investigations of synergies between DNA, RNA and proteins for psoriasis, we have collected skin biopsies from 46 psoriasis cases and 35 non-psoriatic controls, and the recruitment is ongoing. The collection is done in collaboration with Department of Dermatology, St. Olavs Hospital, private dermatologists in Helse Midt-Norge, general practitioners in Trondheim municipality, and "Psoriasis og eksem forbundet". We are utilizing well-established research infrastructures at St. Olavs Hospital and NTNU, including the Clinical Research Facility and Biobank1. We aim to further increase the number of study participants in Jan-April 2018. We have made preliminary agreements with the NTNU Genomic Core Facility to perform RNA extraction, concentration and normalization of the skin biopsies. We have obtained preliminary RNA extraction data on four skin biopsies that show high-quality RNA, and similar RNA extraction procedures will be followed in the study. We plan to perform RNA sequencing of the skin samples at NTNU Genomics Core Facility spring 2018. Identification of novel genes that are associated with psoriasis can offer the potential to identify new drug targets for treatment and prevention.