Markus C. Elze

Wellington: a novel method for the accurate identification of digital genomic footprints from DNase-seq data

The expression of eukaryotic genes is regulated by cis-regulatory elements such as promoters and enhancers, which bind sequence-specific DNA-binding proteins. One of the great challenges in the gene regulation field is to characterise these elements. This involves the identification of transcription factor (TF) binding sites within regulatory elements that are occupied in a defined regulatory context. Digestion with DNase and the subsequent analysis of regions protected from cleavage (DNase footprinting) has for many years been used to identify specific binding sites occupied by TFs at individual cis-elements with high resolution. This methodology has recently been adapted for high-throughput sequencing (DNase-seq). In this study, we describe an imbalance in the DNA strand-specific alignment information of DNase-seq data surrounding protein–DNA interactions that allows accurate prediction of occupied TF binding sites. Our study introduces a novel algorithm, Wellington, which considers the imbalance in this strand-specific information to efficiently identify DNA footprints. This algorithm significantly enhances specificity by reducing the proportion of false positives and requires significantly fewer predictions than previously reported methods to recapitulate an equal amount of ChIP-seq data. We also provide an open-source software package, pyDNase, which implements the Wellington algorithm to interface with DNase-seq data and expedite analyses.

Differences in globus pallidus neuronal firing rates and patterns relate to different disease biology in children with dystonia

Background The pathophysiology underlying different types of dystonia is not yet understood. We report microelectrode data from the globus pallidus interna (GPi) and globus pallidus externa (GPe) in children undergoing deep brain stimulation (DBS) for dystonia and investigate whether GPi and GPe firing rates differ between dystonia types. Methods Single pass microelectrode data were obtained to guide electrode position in 44 children (3.3–18.1 years, median 10.7) with the following dystonia types: 14 primary, 22 secondary Static and 8 progressive secondary to neuronal brain iron accumulation (NBIA). Preoperative stereotactic MRI determined coordinates for the GPi target. Digitised spike trains were analysed offline, blind to clinical data. Electrode placement was confirmed by a postoperative stereotactic CT scan. Findings We identified 263 GPi and 87 GPe cells. Both GPi and GPe firing frequencies differed significantly with dystonia aetiology. The median GPi firing frequency was higher in the primary group than in the secondary static group (13.5 Hz vs 9.6 Hz; p=0.002) and higher in the NBIA group than in either the primary (25 Hz vs 13.5 Hz; p=0.006) or the secondary static group (25 Hz vs 9.6 Hz; p=0.00004). The median GPe firing frequency was higher in the NBIA group than in the secondary static group (15.9 Hz vs 7 Hz; p=0.013). The NBIA group also showed a higher proportion of regularly firing GPi cells compared with the other groups (p<0.001). A higher proportion of regular GPi cells was also seen in patients with fixed/tonic dystonia compared with a phasic/dynamic dystonia phenotype (p<0.001). The GPi firing frequency showed a positive correlation with 1-year outcome from DBS measured by improvement in the Burke-Fahn-Marsden Dystonia Rating Scale (BFMDRS-m) score (p=0.030). This association was stronger for the non-progressive patients (p=0.006). Interpretation Pallidal firing rates and patterns differ significantly with dystonia aetiology and phenotype. Identification of specific firing patterns may help determine targets and patient-specific protocols for neuromodulation therapy. Funding National Institute of Health Research, Guys and St. Thomas’ Charity, Dystonia Society UK, Action Medical Research, German National Academic Foundation.

Progression to musculoskeletal deformity in childhood dystonia

AIM Dystonia is a movement disorder characterized by involuntary muscle contractions, resulting in abnormalities of posture and movement. Children with dystonia are at risk of developing fixed musculoskeletal deformities (FMDs). FMDs cause pain, limit function and participation and interfere with care. We aimed to explore factors relating to the development of FMD in a large cohort of children with dystonia. METHOD The case notes of all children referred to our Complex Motor Disorder service between July 2005 and December 2011 were reviewed. Data from 279 children (median age 9 years 10 months, Standard Deviation 4 years 2 months) with motor disorders including a prominent dystonic element were analyzed. Parametric accelerated failure time regression was used to identify the factors related to development of contractures. RESULTS FMDs were present at referral in more than half (n = 163, 58%) of cases. Three quarters (n = 120, 74%) of children with FMD had deformities around the hip, and 42% had spinal deformity (n = 68). Compared to pure primary dystonia, FMD onset was earlier with a diagnosis of secondary or heredodegenerative dystonia, and a mixed spastic-dystonic phenotype (all p < 0.001). FMD onset was also earlier with increasing Gross Motor Function Classification System (GMFCS) level (p < 0.001). The effect of aetiological classification was lost when controlling for GMFCS level and motor phenotype. INTERPRETATION Children with secondary or heredodegenerative dystonia are at greater risk of progression to FMD compared to primary dystonia, likely due to more severe dystonia within these groups. Children with additional spasticity are at particular risk, requiring close monitoring.

Phase II, Open-Label, Randomized, Multicenter Trial (HERBY) of Bevacizumab in Pediatric Patients With Newly Diagnosed High-Grade Glioma

Purpose Bevacizumab (BEV) is approved in more than 60 countries for use in adults with recurrent glioblastoma. We evaluated the addition of BEV to radiotherapy plus temozolomide (RT+TMZ) in pediatric patients with newly diagnosed high-grade glioma (HGG). Methods The randomized, parallel group, multicenter, open-label HERBY trial ( ClinicalTrials.gov identifier: NCT01390948) enrolled patients age ≥ 3 years to ≤ 18 years with localized, centrally neuropathology-confirmed, nonbrainstem HGG. Eligible patients were randomly assigned to receive RT + TMZ (RT: 1.8 Gy, 5 days per week, and TMZ: 75 mg/m2 per day for 6 weeks; 4-week treatment break; then up to 12 × 28-day cycles of TMZ [cycle 1: 150 mg/m2 per day, days 1 to 5; cycles 2 to 12: 200 mg/m2 per day, days 1 to 5]) with or without BEV (10 mg/kg every 2 weeks). The primary end point was event-free survival (EFS) as assessed by a central radiology review committee that was blinded to treatment. We report findings of EFS at 12 months after the enrollment of the last patient. Results One hundred twenty-one patients were enrolled (RT+TMZ [n = 59]; BEV plus RT+TMZ [n = 62]). Central radiology review committee-assessed median EFS did not differ significantly between treatment groups (RT+TMZ, 11.8 months; 95% CI, 7.9 to 16.4 months; BEV plus RT+TMZ, 8.2 months; 95% CI, 7.8 to 12.7 months; hazard ratio, 1.44; P = .13 [stratified log-rank test]). In the overall survival analysis, the addition of BEV did not reduce the risk of death (hazard ratio, 1.23; 95% CI, 0.72 to 2.09). More patients in the BEV plus RT+TMZ group versus the RT+TMZ group experienced one or more serious adverse events (n = 35 [58%] v n = 27 [48%]), and more patients who received BEV discontinued study treatment as a result of adverse events (n = 13 [22%] v n = 3 [5%]). Conclusion Adding BEV to RT+TMZ did not improve EFS in pediatric patients with newly diagnosed HGG. Our findings were not comparable to those of previous adult trials, which highlights the importance of performing pediatric-specific studies.

The variation of radiologists' performance over the course of a reading session

The radiologist’s task of reviewing many cases successively is highly repetitive and requires a high level of concentration. Fatigue effects have, for example, been shown in studies comparing performance at different times of day. However, little is known about changes in performance during an individual reading session. During a session reading an enriched case set, performance may be affected by both fatigue (i.e. decreasing performance) and training (i.e. increasing performance) effects. In this paper, we reanalyze 3 datasets from 4 studies for changes in radiologist performance during a reading session. Studies feature 8-20 radiologists reading and assessing 27-60 cases in single, uninterrupted sessions. As the studies were not designed for this analysis, study setups range from bone fractures to mammograms and randomization varies between studies. Thus, they are analyzed separately using mixed-effects models. There is some indication that, as time goes on, specificity increases (shown with p<0.05 for 2 out of 3 datasets, no significant difference for the other) while sensitivity may also increase (p<0.05 for 1 out of 3 datasets). The difficulty of ‘normal’ (healthy / non-malignant) and ‘abnormal’ (unhealthy / malignant) cases differs (p<0.05 for 3 out of 3 datasets) and the reader’s experience may also be relevant (p<0.05 for 1 out of 3 datasets). These results suggest that careful planning of breaks and session length may help optimize reader performance. Note that the overall results are still inconclusive and a targeted study to investigate fatigue and training effects within a reading session is recommended.

Somatosensory Evoked Potentials and Central Motor Conduction Times in Children with Dystonia and their correlation with outcomes from Deep Brain Stimulation of the Globus pallidus internus

Highlights • A high proportion (47%) of children with dystonia have evidence of abnormal sensory pathway function.• Central motor conduction times (CMCTs) and somatosensory evoked potentials (SEPs) show a significant relationship with deep brain stimulation (DBS) outcome, independent of aetiology or cranial MRI.• CMCTs and SEPs can guide patient selection and help counsel families about potential benefit of DBS.