Claire T Deakin

Impact of next-generation sequencing error on analysis of barcoded plasmid libraries of known complexity and sequence

Barcoded vectors are promising tools for investigating clonal diversity and dynamics in hematopoietic gene therapy. Analysis of clones marked with barcoded vectors requires accurate identification of potentially large numbers of individually rare barcodes, when the exact number, sequence identity and abundance are unknown. This is an inherently challenging application, and the feasibility of using contemporary next-generation sequencing technologies is unresolved. To explore this potential application empirically, without prior assumptions, we sequenced barcode libraries of known complexity. Libraries containing 1, 10 and 100 Sanger-sequenced barcodes were sequenced using an Illumina platform, with a 100-barcode library also sequenced using a SOLiD platform. Libraries containing 1 and 10 barcodes were distinguished from false barcodes generated by sequencing error by a several log-fold difference in abundance. In 100-barcode libraries, however, expected and false barcodes overlapped and could not be resolved by bioinformatic filtering and clustering strategies. In independent sequencing runs multiple false-positive barcodes appeared to be represented at higher abundance than known barcodes, despite their confirmed absence from the original library. Such errors, which potentially impact barcoding studies in an application-dependent manner, are consistent with the existence of both stochastic and systematic error, the mechanism of which is yet to be fully resolved.

Accepting Risk in Clinical Research: Is the Gene Therapy Field Becoming Too Risk-averse?

Risk is an inescapable aspect of clinical research and is increasingly pertinent to the gene therapy field as the imperative for clinical trial activity grows. In recent years, the widely reported occurrence of serious adverse events (SAEs) in gene therapy studies, including trials for ornithine transcarbamylase (OTC) deficiency, X-linked severe combined immunodeficiency (SCID-X1), and rheumatoid arthritis, has heightened fear in public perceptions of gene therapy. Although it is essential to be cognizant of the risks involved in gene therapy research, there is a danger that gene therapy may become too risk-averse. If the field is to make progress, it is necessary to understand how risk is defined in gene therapy research, how understandings of risk differ, how risk is assessed, how decisions about risk are made, and how gene therapy risks are communicated to subjects and research participants during the informed consent process. In addition to minimizing the risks of clinical research through extensive preclinical safety studies, attention should be given to how decisions about risk and risk acceptability are made by researchers and subjects, and to the methods used to communicate risks to patients. Critical attention to risk will help ensure that the safety of subjects is protected, while also enabling research to develop better treatments for patients.

Muscle biopsy in combination with myositis-specific autoantibodies aids prediction of outcomes in juvenile dermatomyositis.

Juvenile dermatomyositis (DM) is a rare and severe autoimmune condition characterized by rash and proximal muscle weakness. While some patients respond to standard treatment, others do not. This study was carried out to investigate whether histopathologic findings and myositis‐specific autoantibodies (MSAs) have prognostic significance in juvenile DM.

Comparison of the Utility and Validity of Three Scoring Tools to Measure Skin Involvement in Patients With Juvenile Dermatomyositis

To compare the abbreviated Cutaneous Assessment Tool (CAT), Disease Activity Score (DAS), and Myositis Intention to Treat Activity Index (MITAX) and correlate them with the physicians 10‐cm skin visual analog scale (VAS) in order to define which tool best assesses skin disease in patients with juvenile dermatomyositis.

Efficacy and Safety of Cyclophosphamide Treatment in Severe Juvenile Dermatomyositis Shown by Marginal Structural Modeling

In patients with severe or refractory juvenile dermatomyositis (DM), second‐line treatments may be required. Cyclophosphamide (CYC) is used to treat some connective tissue diseases, but evidence of its efficacy in juvenile DM is limited. This study was undertaken to describe clinical improvement in juvenile DM patients treated with CYC and model the efficacy of CYC treatment compared to no CYC treatment.

Modelling disease activity in juvenile dermatomyositis: A Bayesian approach

Juvenile dermatomyositis is the most common form of the juvenile idiopathic inflammatory myopathies characterised by muscle and skin inflammation, leading to symmetric proximal muscle weakness and cutaneous symptoms. It has a fluctuating course and varying prognosis. In a Bayesian framework, we develop a joint model for four longitudinal outcomes, which accounts for within individual variability as well as inter-individual variability. Correlations among the outcome variables are introduced through a subject-specific random effect. Moreover, we exploit an approach similar to a hurdle model to account for excess of a specific outcome in the response. Clinical markers and symptoms are used as covariates in a regression set-up. Data from an ongoing observational cohort study are available, providing information on 340 subjects, who contributed 2725 clinical visits. The model shows good performance and yields efficient estimations of model parameters, as well as accurate predictions of the disease activity parameters, corresponding well to observed clinical patterns over time. The posterior distribution of the by-subject random intercepts shows a substantial correlation between two of the outcome variables. A subset of clinical markers and symptoms are identified as associated with disease activity. These findings have the potential to influence clinical practice as they can be used to stratify patients according to their prognosis and guide treatment decisions, as well as contribute to on-going research about the most relevant outcome markers for patients affected by juvenile dermatomyositis.

Expression of Myxovirus-resistance Protein A: A Possible Marker of Muscle Disease Activity and Autoantibody Specificities in Juvenile Dermatomyositis

To evaluate the relationship between expression of myxovirus‐resistance protein A (MxA) protein on muscle biopsies by immunohistochemistry and disease activity in juvenile dermatomyositis (JDM) patients. Also, another aim was to investigate whether the expression of MxA is related with myositis‐specific autoantibodies (MSA) status in JDM patients.

CD19+CD24hiCD38hi B Cells Are Expanded in Juvenile Dermatomyositis and Exhibit a Pro-Inflammatory Phenotype After Activation Through Toll-Like Receptor 7 and Interferon-α

Juvenile dermatomyositis (JDM) is a rare form of childhood autoimmune myositis that presents with proximal muscle weakness and skin rash. B cells are strongly implicated in the pathogenesis of the disease, but the underlying mechanisms are unknown. Therefore, the main objective of our study was to investigate mechanisms driving B cell lymphocytosis and define pathological features of B cells in JDM patients. Patients were recruited through the UK JDM Cohort and Biomarker study. Peripheral blood B cell subpopulations were immunophenotyped by flow cytometry. The results identified that immature transitional B cells were significantly expanded in active JDM, actively dividing, and correlated positively with disease activity. Protein and RNAseq analysis revealed high interferon alpha (IFNα) and TLR7-pathway signatures pre-treatment. Stimulation of B cells through TLR7/8 promoted both IL-10 and IL-6 production in controls but failed to induce IL-10 in JDM patient cells. Interrogation of the CD40–CD40L pathway (known to induce B cell IL-10 and IL-6) revealed similar expression of IL-10 and IL-6 in B cells cultured with CD40L from both JDM patients and controls. In conclusion, JDM patients with active disease have a significantly expanded immature transitional B cell population which correlated with the type I IFN signature. Activation through TLR7 and IFNα may drive the expansion of immature transitional B cells in JDM and skew the cells toward a pro-inflammatory phenotype.

Clinical signs and symptoms in a joint model of four disease activity parameters in juvenile dermatomyositis: a prospective, longitudinal, multicenter cohort study

BackgroundIt is currently impossible to predict the prognosis of patients with juvenile dermatomyositis (JDM). The aim of this study was to find clinical features most strongly associated with outcome variables in JDM as a first step towards tailor-made treatment.MethodsIn a large, prospectively followed, multicenter cohort study of 340 patients with JDM, each contributing multiple visits, a Bayesian model of disease activity was developed, using the four continuous outcome variables creatine kinase (CK), childhood myositis assessment score (CMAS), manual muscle testing of 8 muscle groups (MMT8) and the physician’s global assessment of disease activity (PGA). Covariates were clinical signs and symptoms. Correlations among visits of the same patient were resolved by introducing subject-specific random effects.ResultsMyalgia and dysphonia were associated with worse disease activity according to all outcome variables. Periorbital rash, rash on the trunk, rash over large joints, nail fold changes and facial swelling were associated with higher PGA. Notably, periorbital rash was also associated with higher CK and lower CMAS and nail fold changes with lower CMAS. Contractures were associated with lower CMAS and MMT8 and higher PGA. Patients with higher CMAS exhibited a higher MMT8 as well. PGA had the highest probability among the four outcome variables of being abnormal even if the other three outcome variables were normal.ConclusionsThe signs and symptoms associated with disease activity could be used to stratify patients and adapt treatment plans to disease activity. The correlation between CMAS and MMT8 and the unique information captured by PGA implied that PGA should be maintained as an outcome variable, whereas CMAS and MMT8 might be simplified.