The Role of Histone Modifying Enzyme SUV420H2 in Pediatric Ependymoma.

Cancer is the leading cause of non-accidental death in children. Pediatric ependymomas (PE) are the third most common brain tumor in children. Despite advances leading to better survival outcomes in some cancers, these tumors remain incurable in up to 45% of patients, with recurrent local relapse being the major cause of mortality[18, 19]. Surgical resection is currently the most effective treatment, but over 50% of children whose tumors have been totally resected will still experience tumor recurrence despite aggressive adjuvant therapy [22]. Key molecular events in the pathogenesis of PE have yet to be defined, and understanding these events are proving to be increasingly necessary to developing clinically-relevant applications. In particular, errors in epigenetic regulatory machinery appear to play a substantial role in the pathogenesis of numerous cancers. As such, this research used gene expression profiling data on a large cohort (n=102) of PE samples to search for potential driving mechanisms underlying recurrence and poor prognosis in this cancer. Through this, we developed a model for the role of the histone modifying enzyme SUV4-20H2 in carcinogenesis. SUV4-20H2 confers modifications that lead to chromatin compaction and resultant silencing of genes in component/surrounding DNA. We hypothesized that this enzyme acts to directly regulate proto-oncogenes and that its loss in this cancer leads to their increased expression. We find evidence to support this model for SUV4-20H2 regulation of TERT, the catalytic subunit of telomerase. This holds significant translational value as TERT is strongly associated with recurrence and has been shown to increase tumorigenicity of tumor initiating cells, and a better understanding of it\u27s regulation could lead to development of new therapies. Additionally, these findings implicate a potential broader role of SUV4-20H2 in driving carcinogenesis and warrant further investigation

SUV420-mediated heterochromatin changes in pediatric brain cancers

Silencing mechanisms play a role in genomic stability by maintaining condensed, non-active regions of the genome. SUV420 enzymes contain a SET domain conferring methyltransferase activity toward histones. The Histone H4 lysine 20 trimethylation (H4K20me3) mark maintained by SUV420H2 is associated with heterochromatin formation and gene silencing, whereas the dimethylated mark (H4K20me2) is associated with DNA repair. In studies of epigenetic factors in large patient cohorts with ependymoma, it was found that SUV420H2 expression was lost or diminished in patients with reciprocal increases in prognostic markers such as hTERT. To better understand the normal function of Suv4-20H1/H2 enzyme in neural progenitors, and pathological changes in cancers, a variety of differentiation paradigms were used. The NT2D1 neurally restricted cell line, and BGO1V and H9 human embryonic stem cells (ESCs), and differentiated progeny, were used alongside tumors to better understand enzyme targets and functional outcomes (e.g.,lineage, differentiation, regional chromatin modifications). Lineage stages were verified with stage-specific markers by immunofluorescence and qPCR. Suv4-20 H1 and H2 were present in ESCs and neural progenitors and decreased thereafter. RNAi knockdown of SUV420 enzymes led to decreased H4K20 methylation in cancer cells. DNA methylation microarrays and ChIP-PCR suggest 1) that SUV420 is not regulated by DNA methylation in ependymomas; 2) that active chromatin marks such as H3K4 dimethylation are enriched near the transcriptional start site in the SUV420H2 gene, and 3) that hTERT is hyper-methylated at specific CpG islands and histones in a tumor sub-group-specific manner. This data supports the hypothesis that Suv4-20H2 is highly active in progenitor cells and functionally lost in some brain cancers. These studies begin to elucidate coincident mechanisms of gene silencing active in neural progenitors that may be altered in a subset of pediatric brain cancers

High-resolution genome-wide functional dissection of transcriptional regulatory regions and nucleotides in human

Genome-wide epigenomic maps have revealed millions of putative enhancers and promoters, but experimental validation of their function and high-resolution dissection of their driver nucleotides remain limited. Here, we present HiDRA (High-resolution Dissection of Regulatory Activity), a combined experimental and computational method for high-resolution genome-wide testing and dissection of putative regulatory regions. We test ~7 million accessible DNA fragments in a single experiment, by coupling accessible chromatin extraction with self-transcribing episomal reporters (ATAC-STARR-seq). By design, fragments are highly overlapping in densely-sampled accessible regions, enabling us to pinpoint driver regulatory nucleotides by exploiting differences in activity between partially-overlapping fragments using a machine learning model (SHARPR-RE). In GM12878 lymphoblastoid cells, we find ~65,000 regions showing enhancer function, and pinpoint ~13,000 high-resolution driver elements. These are enriched for regulatory motifs, evolutionarily-conserved nucleotides, and disease-associated genetic variants from genome-wide association studies. Overall, HiDRA provides a high-throughput, high-resolution approach for dissecting regulatory regions and driver nucleotides.National Institutes of Health (U.S.) (R01 HG008155)Broad NextGen AwardNational Institutes of Health (U.S.) (R01 GM113708)National Institutes of Health (U.S.) (U01 HG007610

Risk factors for situs defects and congenital heart disease in primary ciliary dyskinesia

Primary ciliary dyskinesia (PCD) is associated with abnormal organ positioning (situs) and congenital heart disease (CHD). This study investigated genotype–phenotype associations in PCD to facilitate risk predictions for cardiac and laterality defects. This retrospective cohort study of 389 UK patients with PCD found 51% had abnormal situs and 25% had CHD and/or laterality defects other than situs inversus totalis. Patients with biallelic mutations in a subset of nine PCD genes had normal situs. Patients with consanguineous parents had higher odds of situs abnormalities than patients with non-consanguineous parents. Patients with abnormal situs had higher odds of CHD and/or laterality defects

The effects of centralising electoral management board design

The public administration of elections frequently fails. Variation in the performance of electoral management boards around the world has been demonstrated, illustrated by delays in the count, inaccurate or incomplete voter registers, or severe queues at polling stations. Centralising the management of the electoral process has often been proposed as a solution. There has been little theorisation and no empirical investigations into the effects that centralising an already decentralised system would have, however. This article addresses this lacuna by conceptualising centralisation through the literature on bureaucratic control and discretion. It then empirically investigates the effects through a case study of centralisation in two UK referendums. Semi-structured interviews were used with those who devised the policy instrument and those who were subject to it. The introduction of central directions had some of the desired effects such as producing more consistent services and eliminating errors. It also had side effects, however, such as reducing economic efficiency in some areas and overlooking local knowledge. Furthermore, the reforms caused a decline of staff morale, job satisfaction and souring of relations among stakeholder organisations. The process of making organisational change therefore warrants closer attention by policy makers and future scholarship on electoral integrity

Clinical utility of NGS diagnosis and disease stratification in a multiethnic primary ciliary dyskinesia cohort

Background Primary ciliary dyskinesia (PCD), a genetically heterogeneous condition enriched in some consanguineous populations, results from recessive mutations affecting cilia biogenesis and motility. Currently, diagnosis requires multiple expert tests.Methods The diagnostic utility of multigene panel next-generation sequencing (NGS) was evaluated in 161 unrelated families from multiple population ancestries.Results Most (82%) families had affected individuals with biallelic or hemizygous (75%) or single (7%) pathogenic causal alleles in known PCD genes. Loss-of-function alleles dominate (73% frameshift, stop-gain, splice site), most (58%) being homozygous, even in non-consanguineous families. Although 57% (88) of the total 155 diagnostic disease variants were novel, recurrent mutations and mutated genes were detected. These differed markedly between white European (52% of families carry DNAH5 or DNAH11 mutations), Arab (42% of families carry CCDC39 or CCDC40 mutations) and South Asian (single LRRC6 or CCDC103 mutations carried in 36% of families) patients, revealing a striking genetic stratification according to population of origin in PCD. Genetics facilitated successful diagnosis of 81% of families with normal or inconclusive ultrastructure and 67% missing prior ultrastructure results.Conclusions This study shows the added value of high-throughput targeted NGS in expediting PCD diagnosis. Therefore, there is potential significant patient benefit in wider and/or earlier implementation of genetic screening

Gradient language dominance affects talker learning

Traditional conceptions of spoken language assume that speech recognition and talker identification are computed separately. Neuropsychological and neuroimaging studies imply some separation between the two faculties, but recent perceptual studies suggest better talker recognition in familiar languages than unfamiliar languages. A familiar-language benefit in talker recognition potentially implies strong ties between the two domains. However, little is known about the nature of this language familiarity effect. The current study investigated the relationship between speech and talker processing by assessing bilingual and monolingual listeners' ability to learn voices as a function of language familiarity and age of acquisition. Two effects emerged. First, bilinguals learned to recognize talkers in their first language (Korean) more rapidly than they learned to recognize talkers in their second language (English), while English-speaking participants showed the opposite pattern (learning English talkers faster than Korean talkers). Second, bilinguals' learning rate for talkers in their second language (English) correlated with age of English acquisition. Taken together, these results suggest that language background materially affects talker encoding, implying a tight relationship between speech and talker representations

HLA-DQA1*05 carriage associated with development of anti-drug antibodies to infliximab and adalimumab in patients with Crohn's Disease

Anti-tumor necrosis factor (anti-TNF) therapies are the most widely used biologic drugs for treating immune-mediated diseases, but repeated administration can induce the formation of anti-drug antibodies. The ability to identify patients at increased risk for development of anti-drug antibodies would facilitate selection of therapy and use of preventative strategies.This article is freely available via Open Access. Click on Publisher URL to access the full-text