Genomic catastrophes frequently arise in esophageal adenocarcinoma and drive tumorigenesis

Oesophageal adenocarcinoma (EAC) incidence is rapidly increasing in Western countries. A better understanding of EAC underpins efforts to improve early detection and treatment outcomes. While large EAC exome sequencing efforts to date have found recurrent loss-offunction mutations, oncogenic driving events have been underrepresented. Here we use a combination of whole-genome sequencing (WGS) and single-nucleotide polymorphism-array profiling to show that genomic catastrophes are frequent in EAC, with almost a third (32%, n¼40/123) undergoing chromothriptic events. WGS of 22 EAC cases show that catastrophes may lead to oncogene amplification through chromothripsis-derived double-minute chromosome formation (MYC and MDM2) or breakage-fusion-bridge (KRAS, MDM2 and RFC3). Telomere shortening is more prominent in EACs bearing localized complex rearrangements. Mutational signature analysis also confirms that extreme genomic instability in EAC can be driven by somatic BRCA2 mutations. These findings suggest that genomic catastrophes have a significant role in the malignant transformation of EAC

Genome-Wide Copy Number Analysis in Esophageal Adenocarcinoma Using High-Density Single-Nucleotide Polymorphism Arrays

We applied whole-genome single-nucleotide polymorphism arrays to define a comprehensive genetic profile of 23 esophageal adenocarcinoma (EAC) primary tumor biopsies based on loss of heterozygosity (LOH) and DNA copy number changes. Alterations were common, averaging 97 (range, 23-208) per tumor. LOH and gains averaged 33 (range, 3-83) and 31 (range, 11-73) per tumor, respectively. Copy neutral LOH events averaged 27 (range, 7-57) per EAC. We noted 126 homozygous deletions (HD) across the EAC panel (range, 0-11 in individual tumors). Frequent HDs within FHIT (17 of 23), WWOX (8 of 23), and DMD (6 of 23) suggest a role for common fragile sites or genomic instability in EAC etiology. HDs were also noted for known tumor suppressor genes (TSG), including CDKN2A, CDKN2B, SMAD4, and GALR1, and identified PDE4D and MGC48628 as potentially novel TSGs. All tumors showed LOH for most of chromosome 17p, suggesting that TSGs other than TP53 may be targeted. Frequent gains were noted around MYC (13 of 23), BCL9 (12 of 23), CTAGE1 (14 of 23), and ZNF217 (12 of 23). Thus, we have confirmed previous reports indicating frequent changes to FHIT, CDKN2A, TP53, and MYC in EAC and identified additional genes of interest. Meta-analysis of previous genome-wide EAC studies together with the data presented here highlighted consistent regions of gain on 8q, 18q, and 20q and multiple LOH regions on 4q, 5q, 17p, and 18q, suggesting that more than one gene may be targeted on each of these chromosome arms. The focal gains and deletions documented here are a step toward identifying the key genes involved in EAC development

'Choosing shoes': a preliminary study into the challenges facing clinicians in assessing footwear for rheumatoid patients

Background: Footwear has been accepted as a therapeutic intervention for the foot affected by rheumatoid arthritis (RA). Evidence relating to the objective assessment of footwear in patients with RA is limited. The aims of this study were to identify current footwear styles, footwear characteristics, and factors that influence footwear choice experienced by patients with RA. Methods: Eighty patients with RA were recruited from rheumatology clinics during the summer months. Clinical characteristics, global function, and foot impairment and disability measures were recorded. Current footwear, footwear characteristics and the factors associated with choice of footwear were identified. Suitability of footwear was recorded using pre-determined criteria for assessing footwear type, based on a previous study of foot pain. Results: The patients had longstanding RA with moderate-to severe disability and impairment. The foot and ankle assessment demonstrated a low-arch profile with both forefoot and rearfoot structural deformities. Over 50% of shoes worn by patients were opentype footwear. More than 70% of patients’ footwear was defined as being poor. Poor footwear characteristics such as heel rigidity and sole hardness were observed. Patients reported comfort (17%) and fit (14%) as important factors in choosing their own footwear. Only five percent (5%) of patients wore therapeutic footwear. Conclusions: The majority of patients with RA wear footwear that has been previously described as poor. Future work needs to aim to define and justify the specific features of footwear that may be of benefit to foot health for people with RA

Of shepherds, sheep and sheepdogs?: governing the adherent self through complementary and competing ‘pastorates’

Foucault’s concept of ‘pastoral power’ describes an important technique for constituting obedient subjects. Derived from his analysis of the Christian pastorate, he saw pastoral power as a prelude to contemporary technologies of governing ‘beyond the State’, where ‘experts’ shepherd self-governing subjects. However, the specific practices of modern pastorate have been little developed. This papers examines the relational practices of pastoral power associated with the government of medicine use within the English healthcare system. The study shows how multiple pastors align their complimentary and variegated practices to conduct behaviours, but also how pastors compete for legitimacy, and face resistance through the mobilisation of alternate discourses and the strategic exploitation of pastoral competition. The paper offers a dynamic view of the modern pastorate within the contemporary assemblages of power

Pharmacists in general practice: a qualitative interview case study of stakeholders’ experiences in a West London GP Federation

Background Increased patient demand for healthcare services coupled with a shortage of general practitioners necessitates changes in professional roles and service delivery. In 2016, NHS England began a three year pilot study of pharmacists in general practice, however, this is not an entirely new initiative. There is limited, current, evidence-based, UK research to inform the pilot so studies of pre-existing services must suffice until findings from a formal national evaluation are available. Methods The aim of this exploratory, descriptive interview study was to explore the experiences of stakeholders in eight general practices in the Ealing GP Federation, West London, where pharmacy services have been provided for several years. Forty-seven participants, including pharmacy team members (pre-registration and clinical pharmacists, independent prescribers and pharmacy technicians), general practitioners, patients, practice managers, practice nurses and receptionists took part in semi-structured, audio-recorded qualitative interviews which were transcribed verbatim, coded and analysed thematically to extract the issues raised by participants and the practicalities of providing pharmacy services in general practice. Results Findings are reported under the themes of Complementarity (incorporating roles, skills, education and workloads); Integration (incorporating relationships, trust and communication) and Practicalities (incorporating location and space, access, and costs). Participants reported the need for time to develop and understand the various roles, develop communication processes and build inter-professional trust. Once these were established, however, experiences were positive and included decreased workloads, increased patient safety, improved job satisfaction, improved patient relationships, and enhanced cost savings. Areas for improvement included patients’ awareness of services; pharmacists’ training; and regular, onsite access for practice staff to the pharmacy team. Conclusions Recommendations are made for the development of clear role definitions, identification of training needs, dedication of time for team building, production of educational materials for practice staff members and patients, and provision of on-site, full-time pharmacy services. Future work should focus on evaluation of various models of employing pharmacy teams in general practice; integration of pharmacists and pharmacy technicians into multidisciplinary general practice teams; relationships between local community pharmacy and general practice personnel and patients’ service and information needs. A formal national evaluation of the pilot scheme is overdue

FRA2A is a CGG repeat expansion associated with silencing of AFF3

Folate-sensitive fragile sites (FSFS) are a rare cytogenetically visible subset of dynamic mutations. Of the eight molecularly characterized FSFS, four are associated with intellectual disability (ID). Cytogenetic expression results from CGG tri-nucleotide-repeat expansion mutation associated with local CpG hypermethylation and transcriptional silencing. The best studied is the FRAXA site in the FMR1 gene, where large expansions cause fragile X syndrome, the most common inherited ID syndrome. Here we studied three families with FRA2A expression at 2q11 associated with a wide spectrum of neurodevelopmental phenotypes. We identified a polymorphic CGG repeat in a conserved, brain-active alternative promoter of the AFF3 gene, an autosomal homolog of the X-linked AFF2/FMR2 gene: Expansion of the AFF2 CGG repeat causes FRAXE ID. We found that FRA2A-expressing individuals have mosaic expansions of the AFF3 CGG repeat in the range of several hundred repeat units. Moreover, bisulfite sequencing and pyrosequencing both suggest AFF3 promoter hypermethylation. cSNP-analysis demonstrates monoallelic expression of the AFF3 gene in FRA2A carriers thus predicting that FRA2A expression results in functional haploinsufficiency for AFF3 at least in a subset of tissues. By whole-mount in situ hybridization the mouse AFF3 ortholog shows strong regional expression in the developing brain, somites and limb buds in 9.5-12.5dpc mouse embryos. Our data suggest that there may be an association between FRA2A and a delay in the acquisition of motor and language skills in the families studied here. However, additional cases are required to firmly establish a causal relationship

Fairness Principles In Allocating Water: Integrating Views Of Different Agents

The allocation, or re-allocation, of water to achieve environmental sustainability in farming communities canbe a source of considerable conflict. “What’s fair” when sharing water between different agents and theenvironment becomes paramount in people’s decision making. Issues such as self interest; efficient uses ofwater; business investments; viable communities and prior rights to water all play a part in the ways peopleview the fairness of the allocation decision. The different agents will form their fairness rules in differentways. For example, the small family farmer will not want to be disadvantaged by the greater economiccapacity of the corporate farmer. Those who have not used their allocations in the past may not consider itfair if they stand to lose their allocations, in the interests of achieving environmental sustainability, to thosewho have previously used their allocations and been a part of the over-allocation problem. What role caneconomic instruments play in achieving fair water allocation? When does the environment have greaterrights over individual and societal needs? This paper draws on a number of case studies in rural Australia tosee if allocation rules can be framed for the different community groups in deciding what’s fair in waterallocation. More importantly, we explore whether investigation of these rules can contribute to gainingcommunity consensus and suggest that Agent Based Modelling may be a useful tool for assisting in this

UK psychiatrists' experience of withdrawal of antipsychotics prescribed for challenging behaviours in adults with intellectual disabilities and/or autism.

BACKGROUND: A high proportion of adults with intellectual disabilities are prescribed off-licence antipsychotics in the absence of a psychiatric illness. The National Health Service in England launched an initiative in 2016, 'Stopping over-medication of people with a learning disability [intellectual disability], autism or both' (STOMP), to address this major public health concern. AIMS: To gain understanding from UK psychiatrists working with adults with intellectual disabilities on the successes and challenges of withdrawing antipsychotics for challenging behaviours. METHOD: An online questionnaire was sent to all UK psychiatrists working in the field of intellectual disability (estimated 225). RESULTS: Half of the 88 respondents stated that they started withdrawing antipsychotics over 5 years ago and 52.3% stated that they are less likely to initiate an antipsychotic since the launch of STOMP. However, since then, 46.6% are prescribing other classes of psychotropic medication instead of antipsychotics for challenging behaviours, most frequently the antidepressants. Complete antipsychotic discontinuation in over 50% of patients treated with antipsychotics was achieved by only 4.5% of respondents (n = 4); 11.4% reported deterioration in challenging behaviours in over 50% of patients on withdrawal and the same proportion (11.4%) reported no deterioration. Only 32% of respondents made the diagnosis of psychiatric illness in all their patients themselves. Family and paid carers' concern, lack of multi-agency and multidisciplinary input and unavailability of non-medical psychosocial intervention are key reported factors hampering the withdrawal attempt. CONCLUSIONS: There is an urgent need to develop national guidelines to provide a framework for systematic psychotropic drug reviews and withdrawal where possible

The seasonal detection of strawberry viruses in Victoria, Australia

AbstractPCR tests were adopted from international, peer-reviewed literature and developed for the detection of Strawberry mottle sadwavirus (SMoV), Strawberry crinkle cytorhabdovirus (SCV), Strawberry mild yellow edge potexvirus (SMYEV), Strawberry vein banding caulimovirus (SVBV), Beet pseudos yellows crinivirus (BPYV), and Strawberry pallidosis associated crinivirus (SPaV) in Victoria, Australia. The PCR tests were applied to 23 positive control plants infected with one or more viruses and these plants have been tested monthly from May 2005 to April 2007. Our results have indicated that the viruses were most reliably detected by PCR during May-October. In November, December and January of each year a decline in the number of positive PCR results for BPYV, SVBV and SPaV was observed. Twelve positive control plants maintained at the AQIS post entry quarantine screenhouse at Knoxfield, Victoria, and also infected with one or more viruses, were tested monthly from August 2006 to April 2007. A similar decline in the ability to detect SMoV, SVBV and SPaV in the AQIS positive control plants was observed in 2006/07 and November was the least reliable month for detection of strawberry viruses in these plants. These results indicate that spring and autumn may be the optimal times for PCR detection of strawberry viruses in south east Australia.Keywords: Strawberry mottle sadwavirus; Strawberry crinkle cytorhabdovirus; Strawberry mild yellow edge potexvirus; Strawberry vein banding caulimovirus; Beet pseudos yellows crinivirus; Strawberry pallidosis associated crinivirus; detection; polymerase chain reaction; PCR; certificatio

The degree of segmental aneuploidy measured by total copy number abnormalities predicts survival and recurrence in superficial gastroesophageal adenocarcinoma

Background: Prognostic biomarkers are needed for superficial gastroesophageal adenocarcinoma (EAC) to predict clinical outcomes and select therapy. Although recurrent mutations have been characterized in EAC, little is known about their clinical and prognostic significance. Aneuploidy is predictive of clinical outcome in many malignancies but has not been evaluated in superficial EAC. Methods: We quantified copy number changes in 41 superficial EAC using Affymetrix SNP 6.0 arrays. We identified recurrent chromosomal gains and losses and calculated the total copy number abnormality (CNA) count for each tumor as a measure of aneuploidy. We correlated CNA count with overall survival and time to first recurrence in univariate and multivariate analyses. Results: Recurrent segmental gains and losses involved multiple genes, including: HER2, EGFR, MET, CDK6, KRAS (recurrent gains); and FHIT, WWOX, CDKN2A/B, SMAD4, RUNX1 (recurrent losses). There was a 40-fold variation in CNA count across all cases. Tumors with the lowest and highest quartile CNA count had significantly better overall survival (p = 0.032) and time to first recurrence (p = 0.010) compared to those with intermediate CNA counts. These associations persisted when controlling for other prognostic variables. Significance: SNP arrays facilitate the assessment of recurrent chromosomal gain and loss and allow high resolution, quantitative assessment of segmental aneuploidy (total CNA count). The non-monotonic association of segmental aneuploidy with survival has been described in other tumors. The degree of aneuploidy is a promising prognostic biomarker in a potentially curable form of EAC. © 2014 Davison et al