A subset of methylated CpG sites differentiate psoriatic from normal skin.

Psoriasis is a chronic inflammatory immune-mediated disorder affecting the skin and other organs including joints. Over 1,300 transcripts are altered in psoriatic involved skin compared with normal skin. However, to our knowledge, global epigenetic profiling of psoriatic skin is previously unreported. Here, we describe a genome-wide study of altered CpG methylation in psoriatic skin. We determined the methylation levels at 27,578 CpG sites in skin samples from individuals with psoriasis (12 involved, 8 uninvolved) and 10 unaffected individuals. CpG methylation of involved skin differed from normal skin at 1,108 sites. Twelve mapped to the epidermal differentiation complex, upstream or within genes that are highly upregulated in psoriasis. Hierarchical clustering of 50 of the top differentially methylated (DM) sites separated psoriatic from normal skin samples with uninvolved skin exhibiting intermediate methylation. CpG sites where methylation was correlated with gene expression are reported. Sites with inverse correlations between methylation and nearby gene expression include those of KYNU, OAS2, S100A12, and SERPINB3, whose strong transcriptional upregulation is an important discriminator of psoriasis. Pyrosequencing of bisulfite-treated DNA from skin biopsies at three DM loci confirmed earlier findings and revealed reversion of methylation levels toward the non-psoriatic state after 1 month of anti-TNF-α therapy

The Development of a Patient-Reported Outcome Measure for Assessment of Genital Psoriasis Symptoms: The Genital Psoriasis Symptoms Scale (GPSS)

INTRODUCTION: Patient-reported outcome measures (PROs) specific for genital psoriasis (GenPs) have not been described. METHODS: In this cross-sectional, qualitative study in patients with moderate-to-severe GenPs, we sought to develop a PRO useful for GenPs symptom assessment. A literature review was performed to identify relevant psoriasis or GenPs symptoms and existing PROs that may be useful in the evaluation of symptom severity in GenPs patients. The literature review findings were discussed with clinicians, and then patients with GenPs. RESULTS: Relevant psoriasis or GenPs symptoms from the literature review included itch, pain, scaling, redness/erythema, and stinging/burning. The validity of these symptoms for GenPs and potentially relevant PROs was corroborated by clinical experts. After gap analysis, a draft symptom scale consisting of Numeric Rating Scale (NRS) items was constructed. We then conducted interviews with GenPs patients (n = 20) to support content validity and use of the draft symptom NRS items in routine practice and in clinical trials. Participants identified and confirmed relevant symptoms and evaluated the utility of the draft PRO. A new PRO was developed: the Genital Psoriasis Symptoms Scale (GPSS). Cognitive debriefing and cultural adaptation/translation interviews with a second group of patients confirmed cultural appropriateness of the GPSS. CONCLUSION: The GPSS may be useful for assessing symptoms before, during, and after treatment in routine clinical practice and in clinical trials involving patients with GenPs. FUNDING: Eli Lilly & Company. Plain language summary available for this article

The Development of the Genital Psoriasis Sexual Frequency Questionnaire (GenPs-SFQ) to Assess the Impact of Genital Psoriasis on Sexual Health

INTRODUCTION: Patient-reported outcome measures (PROs) exist for psoriasis but not genital psoriasis (GenPs). METHODS: This cross-sectional, qualitative study in patients with moderate-to-severe GenPs was conducted to support development of a PRO for measuring the impact of GenPs on sexual activity and to establish content validity. The impacts of GenPs were identified in a literature review. Findings from the literature review were discussed with clinicians, and then patients with GenPs were interviewed. RESULTS: From the literature review, 52 articles, 44 abstracts, and 41 clinical trials met predefined search criteria. Of these, 11 concepts emerged as having theoretical support for use as measurable impacts of psoriasis symptoms on patients; these concepts included sexual functioning and general health-related quality of life (HRQoL). These concepts were confirmed and expanded upon by two clinicians who routinely care for patients with GenPs. Interviews were then conducted with GenPs patients (n = 20) to discuss the impact of GenPs on their HRQoL. Eighty percent of patients reported that GenPs impacted sexual frequency. The two-item GenPs Sexual Frequency Questionnaire (GenPs-SFQ) was developed to assess limitations on sexual activity frequency because of GenPs. Cognitive debriefing with an additional 50 patients with GenPs confirmed the utility and understandability of the GenPs-SFQ. CONCLUSION: The GenPs-SFQ may have utility in clinical trials involving GenPs patients and in routine clinical practice. FUNDING: Eli Lilly and Company. Plain language summary available for this article

COVID-19 symptoms at hospital admission vary with age and sex: results from the ISARIC prospective multinational observational study

Background: The ISARIC prospective multinational observational study is the largest cohort of hospitalized patients with COVID-19. We present relationships of age, sex, and nationality to presenting symptoms. Methods: International, prospective observational study of 60 109 hospitalized symptomatic patients with laboratory-confirmed COVID-19 recruited from 43 countries between 30 January and 3 August 2020. Logistic regression was performed to evaluate relationships of age and sex to published COVID-19 case definitions and the most commonly reported symptoms. Results: ‘Typical’ symptoms of fever (69%), cough (68%) and shortness of breath (66%) were the most commonly reported. 92% of patients experienced at least one of these. Prevalence of typical symptoms was greatest in 30- to 60-year-olds (respectively 80, 79, 69%; at least one 95%). They were reported less frequently in children (≤ 18 years: 69, 48, 23; 85%), older adults (≥ 70 years: 61, 62, 65; 90%), and women (66, 66, 64; 90%; vs. men 71, 70, 67; 93%, each P < 0.001). The most common atypical presentations under 60 years of age were nausea and vomiting and abdominal pain, and over 60 years was confusion. Regression models showed significant differences in symptoms with sex, age and country. Interpretation: This international collaboration has allowed us to report reliable symptom data from the largest cohort of patients admitted to hospital with COVID-19. Adults over 60 and children admitted to hospital with COVID-19 are less likely to present with typical symptoms. Nausea and vomiting are common atypical presentations under 30 years. Confusion is a frequent atypical presentation of COVID-19 in adults over 60 years. Women are less likely to experience typical symptoms than men

Optimal bayesian experimental design for models with intractable likelihoods using indirect inference applied to biological process models

This paper addresses the problem of determining optimal designs for biological process models with intractable likelihoods, with the goal of parameter inference. The Bayesian approach is to choose a design that maximises the mean of a utility, and the utility is a function of the posterior distribution. Therefore, its estimation requires likelihood evaluations. However, many problems in experimental design involve models with intractable likelihoods, that is, likelihoods that are neither analytic nor can be computed in a reasonable amount of time. We propose a novel solution using indirect inference (II), a well established method in the literature, and the Markov chain Monte Carlo (MCMC) algorithm of Müller et al. (2004). Indirect inference employs an auxiliary model with a tractable likelihood in conjunction with the generative model, the assumed true model of interest, which has an intractable likelihood. Our approach is to estimate a map between the parameters of the generative and auxiliary models, using simulations from the generative model. An II posterior distribution is formed to expedite utility estimation. We also present a modification to the utility that allows the Müller algorithm to sample from a substantially sharpened utility surface, with little computational effort. Unlike competing methods, the II approach can handle complex design problems for models with intractable likelihoods on a continuous design space, with possible extension to many observations. The methodology is demonstrated using two stochastic models; a simple tractable death process used to validate the approach, and a motivating stochastic model for the population evolution of macroparasites

High-Throughput Sequencing Reveals the Incomplete, Short-Term Recovery of Infant Gut Microbiota following Parenteral Antibiotic Treatment with Ampicillin and Gentamicin

peer-reviewedThe infant gut microbiota undergoes dramatic changes during the first 2 years of life. The acquisition and development of this population can be influenced by numerous factors, and antibiotic treatment has been suggested as one of the most significant. Despite this, however, there have been relatively few studies which have investigated the short-term recovery of the infant gut microbiota following antibiotic treatment. The aim of this study was to use high-throughput sequencing (employing both 16S rRNA and rpoB-specific primers) and quantitative PCR to compare the gut microbiota of nine infants who underwent parenteral antibiotic treatment with ampicillin and gentamicin (within 48 h of birth), 4 and 8 weeks after the conclusion of treatment, relative to that of nine matched healthy controls. The investigation revealed that the gut microbiota of the antibiotic-treated infants had significantly higher proportions of Proteobacteria (P = 0.0049) and significantly lower proportions of Actinobacteria (P = 0.00001) (and the associated genus Bifidobacterium [P = 0.0132]) as well as the genus Lactobacillus (P = 0.0182) than the untreated controls 4 weeks after the cessation of treatment. By week 8, the Proteobacteria levels remained significantly higher in the treated infants (P = 0.0049), but the Actinobacteria, Bifidobacterium, and Lactobacillus levels had recovered and were similar to those in the control samples. Despite this recovery of total Bifidobacterium numbers, rpoB-targeted pyrosequencing revealed that the number of different Bifidobacterium species present in the antibiotic-treated infants was reduced. It is thus apparent that the combined use of ampicillin and gentamicin in early life can have significant effects on the evolution of the infant gut microbiota, the long-term health implications of which remain unknown.Irish Research Council for Science, Engineering and Technology EMBARK scholarship; Teagasc Walsh Fellowship; Science Foundation Ireland (Investigator award 11/PI/1137); Science Foundation of Ireland-funded Centre for Science, Engineering and Technology, the Alimentary Pharmabiotic Centre