Rigid bronchoscopy: a consultant survey

INTRODUCTION

Inhalation of foreign bodies represents a potentially fatal emergency in both adults and children. Chest x-ray, in isolation, is neither sensitive nor specific. Rigid bronchoscopy represents the gold standard to diagnose and retrieve paediatric foreign bodies. Cases are encountered infrequently, creating anxieties about their management. Little is known about the confidence in, and maintenance of, rigid bronchoscopy skills by ear, nose and throat teams.

METHODS

A 15-question survey was completed by 50 practising otolaryngology consultants in England.

RESULTS

Results show that almost 40% of otolaryngology consultants covering rigid bronchoscopy have not performed bronchoscopy in more than 5 years. Consultants raised concerns about the anaesthetic support and the speed of equipment assembly. Questions on clinical practice showed disparities in practice in the same scenario.

CONCLUSIONS

The authors advocate addressing many of the issues raised by the study with a greater availability of simulation courses and regular scheduled intradepartmental teaching days for all professionals involved. National guidelines on criteria for transfer to tertiary centres would improve the consistency of practice.

Achievement of Target Gain Larger than Unity in an Inertial Fusion Experiment

On December 5, 2022, an indirect drive fusion implosion on the National Ignition Facility (NIF) achieved a target gain G_{target} of 1.5. This is the first laboratory demonstration of exceeding "scientific breakeven" (or G_{target}>1) where 2.05 MJ of 351 nm laser light produced 3.1 MJ of total fusion yield, a result which significantly exceeds the Lawson criterion for fusion ignition as reported in a previous NIF implosion [H. Abu-Shawareb et al. (Indirect Drive ICF Collaboration), Phys. Rev. Lett. 129, 075001 (2022)PRLTAO0031-900710.1103/PhysRevLett.129.075001]. This achievement is the culmination of more than five decades of research and gives proof that laboratory fusion, based on fundamental physics principles, is possible. This Letter reports on the target, laser, design, and experimental advancements that led to this result.

Multiorgan MRI findings after hospitalisation with COVID-19 in the UK (C-MORE): a prospective, multicentre, observational cohort study

INTRODUCTION

The multiorgan impact of moderate to severe coronavirus infections in the post-acute phase is still poorly understood. We aimed to evaluate the excess burden of multiorgan abnormalities after hospitalisation with COVID-19, evaluate their determinants, and explore associations with patient-related outcome measures.

METHODS

In a prospective, UK-wide, multicentre MRI follow-up study (C-MORE), adults (aged ≥18 years) discharged from hospital following COVID-19 who were included in Tier 2 of the Post-hospitalisation COVID-19 study (PHOSP-COVID) and contemporary controls with no evidence of previous COVID-19 (SARS-CoV-2 nucleocapsid antibody negative) underwent multiorgan MRI (lungs, heart, brain, liver, and kidneys) with quantitative and qualitative assessment of images and clinical adjudication when relevant. Individuals with end-stage renal failure or contraindications to MRI were excluded. Participants also underwent detailed recording of symptoms, and physiological and biochemical tests. The primary outcome was the excess burden of multiorgan abnormalities (two or more organs) relative to controls, with further adjustments for potential confounders. The C-MORE study is ongoing and is registered with ClinicalTrials.gov, NCT04510025.

FINDINGS

Of 2710 participants in Tier 2 of PHOSP-COVID, 531 were recruited across 13 UK-wide C-MORE sites. After exclusions, 259 C-MORE patients (mean age 57 years [SD 12]; 158 [61%] male and 101 [39%] female) who were discharged from hospital with PCR-confirmed or clinically diagnosed COVID-19 between March 1, 2020, and Nov 1, 2021, and 52 non-COVID-19 controls from the community (mean age 49 years [SD 14]; 30 [58%] male and 22 [42%] female) were included in the analysis. Patients were assessed at a median of 5·0 months (IQR 4·2-6·3) after hospital discharge. Compared with non-COVID-19 controls, patients were older, living with more obesity, and had more comorbidities. Multiorgan abnormalities on MRI were more frequent in patients than in controls (157 [61%] of 259 vs 14 [27%] of 52; p<0·0001) and independently associated with COVID-19 status (odds ratio [OR] 2·9 [95% CI 1·5-5·8]; padjusted=0·0023) after adjusting for relevant confounders. Compared with controls, patients were more likely to have MRI evidence of lung abnormalities (p=0·0001; parenchymal abnormalities), brain abnormalities (p<0·0001; more white matter hyperintensities and regional brain volume reduction), and kidney abnormalities (p=0·014; lower medullary T1 and loss of corticomedullary differentiation), whereas cardiac and liver MRI abnormalities were similar between patients and controls. Patients with multiorgan abnormalities were older (difference in mean age 7 years [95% CI 4-10]; mean age of 59·8 years [SD 11·7] with multiorgan abnormalities vs mean age of 52·8 years [11·9] without multiorgan abnormalities; p<0·0001), more likely to have three or more comorbidities (OR 2·47 [1·32-4·82]; padjusted=0·0059), and more likely to have a more severe acute infection (acute CRP >5mg/L, OR 3·55 [1·23-11·88]; padjusted=0·025) than those without multiorgan abnormalities. Presence of lung MRI abnormalities was associated with a two-fold higher risk of chest tightness, and multiorgan MRI abnormalities were associated with severe and very severe persistent physical and mental health impairment (PHOSP-COVID symptom clusters) after hospitalisation.

INTERPRETATION

After hospitalisation for COVID-19, people are at risk of multiorgan abnormalities in the medium term. Our findings emphasise the need for proactive multidisciplinary care pathways, with the potential for imaging to guide surveillance frequency and therapeutic stratification.

FUNDING

UK Research and Innovation and National Institute for Health Research.

Psychological impact of lung cancer screening using a novel antibody blood test followed by imaging: the ECLS randomized controlled trial

BACKGROUND

The Early CDT®-Lung antibody blood test plus serial computed tomography scans for test-positives (TPGs) reduces late-stage lung cancer presentation. This study assessed the psychological outcomes of this approach.

METHODS

Randomized controlled trial (n = 12 208) comparing psychological outcomes 1-12 months post-recruitment in a subsample (n = 1032) of TPG, test-negative (TNG) and control groups (CG).

RESULTS

Compared to TNG, TPG had lower positive affect (difference between means (DBM), 3 months (3m: -1.49 (-2.65, - 0.33)), greater impact of worries (DBM 1m: 0.26 (0.05, 0.47); 3m: 0.28 (0.07, 0.50)), screening distress (DBM 1m: 3.59 (2.28, 4.90); 3m: 2.29 (0.97, 3.61); 6m: 1.94 (0.61, 3.27)), worry about tests (odds ratio (OR) 1m: 5.79 (2.66, 12.63) and more frequent lung cancer worry (OR 1m: 2.52 (1.31, 4.83); 3m: 2.43 (1.26, 4.68); 6m: 2.87 (1.48, 5.60)). Compared to CG, TPG had greater worry about tests (OR 1m: 3.40 (1.69, 6.84)). TNG had lower negative affect (log-transformed DBM 3m: -0.08 (-0.13, -0.02)), higher positive affect (DBM 1m: 1.52 (0.43, 2.61); 3m: 1.43 (0.33, 2.53); 6m: 1.27 (0.17, 2.37)), less impact of worries (DBM 3m: -0.27 (-0.48, -0.07)) and less-frequent lung cancer worry (OR 3m: 0.49 (0.26, 0.92)).

CONCLUSIONS

Negative psychological effects in TPG and positive effects in TNG were short-lived and most differences were small.

Lawson Criterion for Ignition Exceeded in an Inertial Fusion Experiment

For more than half a century, researchers around the world have been engaged in attempts to achieve fusion ignition as a proof of principle of various fusion concepts. Following the Lawson criterion, an ignited plasma is one where the fusion heating power is high enough to overcome all the physical processes that cool the fusion plasma, creating a positive thermodynamic feedback loop with rapidly increasing temperature. In inertially confined fusion, ignition is a state where the fusion plasma can begin "burn propagation" into surrounding cold fuel, enabling the possibility of high energy gain. While "scientific breakeven" (i.e., unity target gain) has not yet been achieved (here target gain is 0.72, 1.37 MJ of fusion for 1.92 MJ of laser energy), this Letter reports the first controlled fusion experiment, using laser indirect drive, on the National Ignition Facility to produce capsule gain (here 5.8) and reach ignition by nine different formulations of the Lawson criterion.

Clinical characteristics with inflammation profiling of long COVID and association with 1-year recovery following hospitalisation in the UK: a prospective observational study

BACKGROUND

No effective pharmacological or non-pharmacological interventions exist for patients with long COVID. We aimed to describe recovery 1 year after hospital discharge for COVID-19, identify factors associated with patient-perceived recovery, and identify potential therapeutic targets by describing the underlying inflammatory profiles of the previously described recovery clusters at 5 months after hospital discharge.

METHODS

The Post-hospitalisation COVID-19 study (PHOSP-COVID) is a prospective, longitudinal cohort study recruiting adults (aged ≥18 years) discharged from hospital with COVID-19 across the UK. Recovery was assessed using patient-reported outcome measures, physical performance, and organ function at 5 months and 1 year after hospital discharge, and stratified by both patient-perceived recovery and recovery cluster. Hierarchical logistic regression modelling was performed for patient-perceived recovery at 1 year. Cluster analysis was done using the clustering large applications k-medoids approach using clinical outcomes at 5 months. Inflammatory protein profiling was analysed from plasma at the 5-month visit. This study is registered on the ISRCTN Registry, ISRCTN10980107, and recruitment is ongoing.

FINDINGS

2320 participants discharged from hospital between March 7, 2020, and April 18, 2021, were assessed at 5 months after discharge and 807 (32·7%) participants completed both the 5-month and 1-year visits. 279 (35·6%) of these 807 patients were women and 505 (64·4%) were men, with a mean age of 58·7 (SD 12·5) years, and 224 (27·8%) had received invasive mechanical ventilation (WHO class 7-9). The proportion of patients reporting full recovery was unchanged between 5 months (501 [25·5%] of 1965) and 1 year (232 [28·9%] of 804). Factors associated with being less likely to report full recovery at 1 year were female sex (odds ratio 0·68 [95% CI 0·46-0·99]), obesity (0·50 [0·34-0·74]) and invasive mechanical ventilation (0·42 [0·23-0·76]). Cluster analysis (n=1636) corroborated the previously reported four clusters: very severe, severe, moderate with cognitive impairment, and mild, relating to the severity of physical health, mental health, and cognitive impairment at 5 months. We found increased inflammatory mediators of tissue damage and repair in both the very severe and the moderate with cognitive impairment clusters compared with the mild cluster, including IL-6 concentration, which was increased in both comparisons (n=626 participants). We found a substantial deficit in median EQ-5D-5L utility index from before COVID-19 (retrospective assessment; 0·88 [IQR 0·74-1·00]), at 5 months (0·74 [0·64-0·88]) to 1 year (0·75 [0·62-0·88]), with minimal improvements across all outcome measures at 1 year after discharge in the whole cohort and within each of the four clusters.

INTERPRETATION

The sequelae of a hospital admission with COVID-19 were substantial 1 year after discharge across a range of health domains, with the minority in our cohort feeling fully recovered. Patient-perceived health-related quality of life was reduced at 1 year compared with before hospital admission. Systematic inflammation and obesity are potential treatable traits that warrant further investigation in clinical trials.

FUNDING

UK Research and Innovation and National Institute for Health Research.

825 DEVELOPMENT OF THE ANTICHOLINERGIC MEDICATION INDEX (ACMI)

Introduction

Medications with Anticholinergic (AC) properties, are prescribed to treat a range of conditions. Older people are increasingly likely to be prescribed multiple AC medications, but are also more likely to experience unwanted adverse effects, such as falls and delirium. The risks of adverse outcomes increase with the number and potency of AC medications prescribed. The aim of this study was to use a prognostic modelling approach to develop an AC Medication Index (ACMI) that identifies patients at high risk of AC medication side effects.

Methods

The prognostic model was developed using data on patients aged 65–95 years, registered with a general practice contributing data to ‘Connected Bradford’ in 2019. A Time-dependent Cox model was fitted, with hospital admission for delirium or falls as the composite outcome and AC medications, age, sex and important clinical factors (e.g. dementia, arthritis, urinary incontinence) as predictors. Concordance and Negalkerke’s R2 derived from five-fold cross-validation were used to assess model performance.

Results

There were 151,604 patients included in the study, of whom 47,035 (31.0%) were prescribed ≥1 AC medication during 2019. Codeine, Prednisolone, Furosemide and Amitriptyline were most commonly prescribed with 7.4%, 4.0%, 3.8% and 3.1% of patients prescribed these medications at least once in 2019, respectively. During 2019, 6,078 (4.0%) patients experienced a hospital admission with delirium or a fall, with the rate being increased in those prescribed ≥1 AC medication during 2019 (4.8% vs 3.7%; p &lt; 0.001). The prognostic model yielded a discrimination statistic of 0.86 with an R2 of 0.1.

Conclusion

The model used to develop the ACMI shows good discrimination. External validation will soon be performed using data from the SAIL databank and the ACMI will be further developed as a tool for use in primary care.

Conventional landmark palpation vs. preprocedural ultrasound for neuraxial analgesia and anaesthesia in obstetrics - a systematic review and meta-analysis with trial sequential analyses

The aim of this systematic review and meta-analysis was to examine the efficacy, time taken and the safety of neuraxial blockade performed for obstetric patients with the assistance of preprocedural ultrasound, in comparison with the landmark palpation method. The bibliographic databases Central, CINAHL, EMBASE, Global Health, MEDLINE, Scopus and Web of Science were searched from inception to 13 February 2020 for randomised controlled trials that included pregnant women having neuraxial procedures with preprocedural ultrasound as the intervention and conventional landmark palpation as the comparator. For continuous and dichotomous outcomes, respectively, we calculated the mean difference using the inverse-variance method and the risk ratio with the Mantel-Haenszel method. In all, 22 trials with 2462 patients were included. Confirmed by trial sequential analysis, preprocedural ultrasound increased the first-pass success rate by a risk ratio (95%CI) of 1.46 (1.16-1.82), p = 0.001 in 13 trials with 1253 patients. No evidence of a difference was found in the total time taken between preprocedural ultrasound and landmark palpation, with a mean difference (95%CI) of 50.1 (-13.7 to 113.94) s, p = 0.12 in eight trials with 709 patients. The quality of evidence was graded as low and very low, respectively, for these co-primary outcomes. Sub-group analysis underlined the increased benefit of preprocedural ultrasound for those in whom the neuraxial procedure was predicted to be difficult. Complications, including postpartum back pain and headache, were decreased with preprocedural ultrasound. The adoption of preprocedural ultrasound for neuraxial procedures in obstetrics is recommended and, in the opinion of the authors, should be considered as a standard of care, in view of its potential to increase efficacy and reduce complications without significant prolongation of the total time required.

Core outcome set for uncomplicated acute appendicitis in children and young people

Background

Research studies to inform clinical practice and policy in children and young people with appendicitis are hampered by inconsistent selection and reporting of outcomes. The aim of this study was to develop a core outcome set for reporting all studies of uncomplicated acute appendicitis in children and young people.

Methods

Systematic literature reviews, qualitative interviews with parents and patients treated for uncomplicated acute appendicitis, and a Study‐Specific Advisory Group informed a long list of outcomes. Outcomes were then prioritized by stakeholders based in the UK (patients, parents, and paediatric and general surgeons) in an online three‐round Delphi consensus process, followed by face‐to‐face consensus meetings.

Results

A long list of 40 items was scored by 147 key stakeholders in the first Delphi round, of whom 90 completed the two subsequent Delphi rounds. The final core outcome set comprises 14 outcomes: intra‐abdominal abscess, reoperation (including interventional radiology procedure), readmission to hospital, bowel obstruction, wound infection, antibiotic failure, wound complication, negative appendicectomy, recurrent appendicitis, death, patient stress/psychological distress, length of hospital stay, time away from full activity and child's quality of life.

Conclusion

A core outcome set comprising 14 outcomes across five key domains has been developed for reporting studies in children and young people with uncomplicated acute appendicitis. Further work is required to determine how and when to measure these outcomes.

Recurrent hyperactive ESR1 fusion proteins in endocrine therapy-resistant breast cancer

Background

Estrogen receptor-positive (ER-positive) metastatic breast cancer is often intractable due to endocrine therapy resistance. Although ESR1 promoter switching events have been associated with endocrine-therapy resistance, recurrent ESR1 fusion proteins have yet to be identified in advanced breast cancer.

Patients and methods

To identify genomic structural rearrangements (REs) including gene fusions in acquired resistance, we undertook a multimodal sequencing effort in three breast cancer patient cohorts: (i) mate-pair and/or RNAseq in 6 patient-matched primary-metastatic tumors and 51 metastases, (ii) high coverage (>500×) comprehensive genomic profiling of 287-395 cancer-related genes across 9542 solid tumors (5216 from metastatic disease), and (iii) ultra-high coverage (>5000×) genomic profiling of 62 cancer-related genes in 254 ctDNA samples. In addition to traditional gene fusion detection methods (i.e. discordant reads, split reads), ESR1 REs were detected from targeted sequencing data by applying a novel algorithm (copyshift) that identifies major copy number shifts at rearrangement hotspots.

Results

We identify 88 ESR1 REs across 83 unique patients with direct confirmation of 9 ESR1 fusion proteins (including 2 via immunoblot). ESR1 REs are highly enriched in ER-positive, metastatic disease and co-occur with known ESR1 missense alterations, suggestive of polyclonal resistance. Importantly, all fusions result from a breakpoint in or near ESR1 intron 6 and therefore lack an intact ligand binding domain (LBD). In vitro characterization of three fusions reveals ligand-independence and hyperactivity dependent upon the 3' partner gene. Our lower-bound estimate of ESR1 fusions is at least 1% of metastatic solid breast cancers, the prevalence in ctDNA is at least 10× enriched. We postulate this enrichment may represent secondary resistance to more aggressive endocrine therapies applied to patients with ESR1 LBD missense alterations.

Conclusions

Collectively, these data indicate that N-terminal ESR1 fusions involving exons 6-7 are a recurrent driver of endocrine therapy resistance and are impervious to ER-targeted therapies.

The cost of diabetic foot ulcers and amputations to the National Health Service in England

AIM

To estimate the healthcare costs of diabetic foot disease in England.

METHODS

Patient-level data sets at a national and local level, and evidence from clinical studies, were used to estimate the annual cost of health care for foot ulceration and amputation in people with diabetes in England in 2014-2015.

RESULTS

The cost of health care for ulceration and amputation in diabetes in 2014-2015 is estimated at between £837 million and £962 million; 0.8% to 0.9% of the National Health Service (NHS) budget for England. More than 90% of expenditure was related to ulceration, and 60% was for care in community, outpatient and primary settings. For inpatients, multiple regression analysis suggested that ulceration was associated with a length of stay 8.04 days longer (95% confidence interval 7.65 to 8.42) than that for diabetes admissions without ulceration.

CONCLUSIONS

Diabetic foot care accounts for a substantial proportion of healthcare expenditure in England, more than the combined cost of breast, prostate and lung cancers. Much of this expenditure arises through prolonged and severe ulceration. If the NHS were to reduce the prevalence of diabetic foot ulcers in England by one-third, the gross annual saving would be more than £250 million. Diabetic foot ulceration is a large and growing problem globally, and it is likely that there is potential to improve outcomes and reduce expenditure in many countries.

Treatment preference and recruitment to pediatric RCTs: A systematic review

BACKGROUND

Recruitment to pediatric randomised controlled trials (RCTs) can be a challenge, with ethical issues surrounding assent and consent. Pediatric RCTs frequently recruit from a smaller pool of patients making adequate recruitment difficult. One factor which influences recruitment and retention in pediatric trials is patient and parent preferences for treatment.

PURPOSE

To systematically review pediatric RCTs reporting treatment preference.

METHODS

Database searches included: MEDLINE, CINAHL, EMBASE, and COCHRANE.Qualitative or quantitative papers were eligible if they reported: pediatric population, (0-17 years) recruited to an RCT and reported treatment preference for all or some of the participants/parents in any clinical area. Data extraction included: Number of eligible participants consenting to randomisation arms, number of eligible patients not randomised because of treatment preference, and any further information reported on preferences (e.g., if parent preference was different from child).

RESULTS

Fifty-two studies were included. The number of eligible families declining participation in an RCT because of preference for treatment varied widely (between 2 and 70%) in feasibility, conventional and preference trial designs. Some families consented to trial involvement despite having preferences for a specific treatment. Data relating to 'participant flow and recruitment' was not always reported consistently, therefore numbers who were lost to follow-up or withdrew due to preference could not be extracted.

CONCLUSIONS

Families often have treatment preferences which may affect trial recruitment. Whilst children appear to hold treatment preferences, this is rarely reported. Further investigation is needed to understand the reasons for preference and the impact preference has on RCT recruitment, retention and outcome.

Antiretroviral nonadherence and condomless sex in the HIV Outpatient Study, USA, 2007-2014

Effective antiretroviral therapy (ART) reduces plasma HIV RNA viral load (VL) to undetectable levels and its effectiveness depends on consistent adherence. Consistent adherence and use of safe sex practices may substantially decrease the risk of HIV transmission. We sought to explore the potential association between self-reported nonadherence to ART and engaging in unsafe sexual practices capable of transmitting HIV. Using clinical and audio computer-assisted self-interview data from the prospective HIV Outpatient Study from 2007 to 2014, we assessed the frequency of self-reported ART nonadherence during the three days prior to the survey among HIV-infected persons in care and factors associated with self-reported ART nonadherence. Of 1729 patients included in this analysis (median age = 48 years, 74.3% men who have sex with men), 17% were nonadherent, 15% had a detectable VL, and 42% reported condomless anal or vaginal sex in the past six months. In multivariable analysis, self-reported nonadherence was independently associated with younger age (adjusted odds ratio [aOR] 0.8 per additional ten years, [95% CI] 0.7-1.0), non-Hispanic black race/ethnicity (aOR 1.9; 95% CI 1.4-2.6 versus white), public health insurance (aOR 1.6, 95% CI 1.2-2.3 compared with private), survey date in 2011-2014 versus 2007-2010 (aOR 0.7, 95% CI 0.5-0.9), CD4 cell count ≥ 500 versus < 200 cells/mm³ (aOR 0.3, 95% CI 0.2-0.5), greater number of ART regimen doses (aOR 1.6, 95% CI 1.3-2.2), and binge drinking (aOR 1.4, 95% CI, 1.1-1.9). In this analysis, self-reported nonadherence was not associated with engaging in condomless sex.

Integrative Genomics Identifies the Molecular Basis of Resistance to Azacitidine Therapy in Myelodysplastic Syndromes

Myelodysplastic syndromes and chronic myelomonocytic leukemia are blood disorders characterized by ineffective hematopoiesis and progressive marrow failure that can transform into acute leukemia. The DNA methyltransferase inhibitor 5-azacytidine (AZA) is the most effective pharmacological option, but only ∼50% of patients respond. A response only manifests after many months of treatment and is transient. The reasons underlying AZA resistance are unknown, and few alternatives exist for non-responders. Here, we show that AZA responders have more hematopoietic progenitor cells (HPCs) in the cell cycle. Non-responder HPC quiescence is mediated by integrin α5 (ITGA5) signaling and their hematopoietic potential improved by combining AZA with an ITGA5 inhibitor. AZA response is associated with the induction of an inflammatory response in HPCs in vivo. By molecular bar coding and tracking individual clones, we found that, although AZA alters the sub-clonal contribution to different lineages, founder clones are not eliminated and continue to drive hematopoiesis even in complete responders.

Communication with young people in paediatric and adult endocrine consultations: an intervention development and feasibility study

BACKGROUND

Communication is complex in endocrine care, particularly during transition from paediatric to adult services. The aims of this study were to examine the feasibility of interventions to support young people to interact with clinicians.

METHODS

Development and evaluation of a complex intervention in 2 phases: Pre-intervention observational study; Intervention feasibility study. Purposive sample of recordings of 62 consultations with 58 young people aged 11-25 years with long-term endocrine conditions in two paediatric and two adult endocrine clinics. Proportion of time talked during consultations, number and direction of questions asked; Paediatric Consultation Assessment Tool (PCAT); OPTION shared decision making tool; Medical Information Satisfaction Scale (MISS- 21). Young people were invited to use one or more of: a prompt sheet to help them influence consultation agendas and raise questions; a summary sheet to record key information; and the www.explain.me.uk website.

RESULTS

Nearly two thirds of young people (63%) chose to use at least one communication intervention. Higher ratings for two PCAT items (95% CI 0.0 to 1.1 and 0.1 to 1.7) suggest interventions can support consultation skills. A higher proportion of accompanying persons (83%) than young people (64%) directed questions to clinicians. The proportion of young people asking questions was higher (84%) in the intervention phase than in the observation phase (71%).

CONCLUSIONS

Interventions were acceptable and feasible. The Intervention phase was associated with YP asking more questions, which implies that the availability of interventions could promote interactivity.

Abstract P1-05-23: Utilities and challenges of RNA-Seq based expression and variant calling in a clinical setting

Introduction

Variant calling based on DNA samples has been the gold standard of clinical testing since the advent of Sanger sequencing. The use of DNA variants has proved a great value to guide treatment in cancer patients. However, DNA based analysis will not inform about expression status of the gene harboring a particular variant. RNA has long been used to monitor expression. To this point RNA assays and analysis are confined to the research laboratory and rarely used clinically except in specifically defined gene signatures such as PAM50 and OncoType Dx. Beyond expression, RNA has the ability to confirm expression of DNA variants and identify fusion events. We hypothesize that the combination of DNA and RNA based data will allow the determination of variant specific expression status and improve clinical diagnostics. It has been previously shown that RNA sequencing (RNA-Seq) based variant calls are highly accurate and confirm DNA based variant calls. In this study we investigated the utility of RNA-Seq as a diagnostic assay integrated with DNA based sequencing data.

Materials and Methods

Targeted DNA sequencing of 321 genes was performed on 37 patient samples (FFPE), including 22 breast cancer samples by a commercial vendor. RNA-Seq on the same patient samples was performed using 100ng of total RNA. Libraries were run on the Illumina NextSeq 500 with a minimum of 75M paired 75bp reads. To evaluate RNA-seq expression reproducibility, replicates of 6 normal ovarian tissue samples (min. 50M reads) were run in sets of triplicates. STAR was used for alignment (hg19) and gene expression quantification (RefSeq). RNA-Seq based variant calling was performed using the SNPiR pipeline. Based on the results of the commercial assay, DNA based variants were examined for expression of the corresponding genes and ability to confirm variants in the RNA-Seq data.

Results

RNA expression data showed no corresponding gene expression for at least one single nucleotide variant (SNV) in 9/37 patients analyzed (24.3%). In 18/37 patients (48.6%) SNV corresponding expression was in the lowest quartile of expression values. Variant calls could be confirmed by RNA-Seq for 95/455 SNVs, with adequate coverage in 263 of the remaining 360 variant locations (median coverage: 34). Of these, a homozygous reference call was made in 166/263 SNVs. Concordance for RNA-Seq gene level expression data between replicates was &gt; 0.995.

Conclusions

These findings suggest that RNA-Seq based data can provide clinical value when using gene expression values in combination with DNA based variant calls. We found gene level expression to be highly reproducible and will further investigate the use of spike in controls to determine clinically usable expression ranges and lower limit of expression values. To our knowledge, it has not been shown that RNA-Seq based variant calls are reproducible which is the focus of our current research as this will be one requirement for usage in a regulated environment. While our use of RNA Seq is currently limited to gene expression level data, we have demonstrated a clinically relevant benefit to using RNA Seq data as an additive feature to the current standard of DNA variant calling.

Citation Format: Young B, Mark A, Meissner T, Amallraja A, Andrews A, Connolly C, Williams C, Leyland-Jones B. Utilities and challenges of RNA-Seq based expression and variant calling in a clinical setting [abstract]. In: Proceedings of the 2016 San Antonio Breast Cancer Symposium; 2016 Dec 6-10; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2017;77(4 Suppl):Abstract nr P1-05-23.

Abstract P3-03-06: Characterization of HER2-positive breast cancer (BC) cells selected for tolerance to trastuzumab-induced antibody-dependent cell-mediated cytotoxicity (ADCC)

Cellular mechanisms of trastuzumab resistance include alteration(s) in cell signaling pathways (PTEN loss, activation of PI3K/Akt signaling), steric hindrance of antibody binding (by Muc-1/Muc-3), over-activation of alternate receptor kinases (HER3/c-Met/IGF-1R), and proteolysis of HER2 extracellular domain harboring target epitopes for antibody-based therapeutics. Prior studies of trastuzumab resistance have focused largely on cells selected ex vivo with the antibody in absence of human immune effector cells. We developed a selection model, wherein human HER2 positive BC cells (BT474, SKBR3) were subjected to acute ADCC (&gt;90% cell death), trastuzumab concentration 100ug/mL, effector-target ratio 100:1, using human peripheral blood mononuclear cells (PBMCs) as effectors. Surviving cells were allowed to recover to confluence over 8-10 weeks, for 10 total rounds of ADCC selection ex vivo. Mock-treated parent, IgG1 isotype control, trastuzumab, and PBMCs alone were used as controls. ADCC assays based on calcein fluorescent labeling of live target cells, revealed significant reduction (maximum 20%, p&lt;0.005) in cell lysis in immune-selected BT474 cell lines compared to parental controls (immune-selected SKBR3 cells exhibited a non-significant trend towards reduced ADCC). Transcriptome-wide next-generation RNA sequencing (Illumina NextSeq 500, 2 x 75 bp paired-end, median of 46 million paired-end reads/sample), coupled with pathway enrichment analysis (Reactome), followed by q-PCR validation, confirmed significant changes in expression in immune-selected cells (compared to parent control) for genes including: ALDH1, ANK1, TMPRSS3, HINT1, DNM2, TNNC1, COL4A4 in BT474; and ALDH1, ANK1, CAMP1, CPE, IDO1 in SKBR3 cells. Whole-genome sequencing (Illumina HiSeq X, 150 bp paired end, 30x coverage) elucidated 180 genes with single nucleotide variations (SNVs) in immune-selected cells compared to parent in BT474 cells, and 215 genes in SKBR3 cells. Thirty-four SNVs were shared in both cell lines. Further screening and validation confirm genes with SNVs demonstrating significant transcript up-regulation. These include: COL4A3, LEP, SOX-9 in BT474; and HLA-B, TNFRSF10B, HLA-B, PSMA6 in SKBR3. In further phenotypic analysis, ADCC-conditioned BT474 cells exhibit an elongated fibroblast-like morphology with multiple processes, in contrast to control. Immune-selected SKBR3 cells (and not BT474 cells) demonstrate significantly increased motility compared to control in transwell migration assays (p&lt;0.001), and demonstrated increased cell proliferation (MTT assay, 10-15%, 48h; p=0.0242) as compared to parent controls. Our data indicate immune-selection by effector cells contributes to ADCC tolerance in vitro, and is associated with distinct genotypic and phenotypic alterations. Future investigation will determine whether Fc-engineered MAbs (afucosylated), antibody drug conjugates (T-DM1), or potentiation of ADCC by co-stimulatory agonist CD137 antibodies will re-sensitize ADCC-tolerance. This investigation will help to elucidate potentially targetable pathways that emerge from immune-selection with trastuzumab.

Citation Format: Biswas T, Fritzemeier R, Mark A, Meißner T, Young B, Jones BL, Pegram M. Characterization of HER2-positive breast cancer (BC) cells selected for tolerance to trastuzumab-induced antibody-dependent cell-mediated cytotoxicity (ADCC) [abstract]. In: Proceedings of the 2016 San Antonio Breast Cancer Symposium; 2016 Dec 6-10; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2017;77(4 Suppl):Abstract nr P3-03-06.

Abstract P1-05-22: The value of RNA-Seq for the detection of clinically actionable targets in breast cancer - A small cohort analysis

Introduction

Next generation sequencing has facilitated the understanding of pathogenesis and molecular heterogeneity of breast cancer (BC) as well as accelerated the path towards precision medicine. DNA sequencing (DNA-Seq) based assays for the detection of mutations and alterations in solid and hematologic cancers are finding their way into clinical practice and are readily available as clinical products. RNA sequencing (RNA-Seq), so far being vastly applied in the research context, promises to expand the diagnostic, prognostic and therapeutic use of this technology in cancer. Beyond mutational status, RNA-Seq enables the detection of fusions, quantification of gene expression level, detection of differentially expressed genes, molecular based subtyping, and risk-stratification. In this study we analyzed RNA-Seq and copy number data from BC patients that had undergone DNA-Seq based diagnostics through commercial providers with the goal to detect additional actionable targets.

Materials and Methods

We included 18 BC patients (5/18 triple negative) that had previously undergone DNA-based targeted (321 genes) sequencing. RNA-Seq to a minimum of 75M reads (75pb) was performed using 100 ng of total RNA on the Illumina NextSeq 500 platform. STAR was used for alignment (hg19) and gene expression quantification (RefSeq). Fusions were detected using STAR-Fusion. DESeq2 was utilized to identify patient specific differentially expressed genes by analyzing samples individually against a set of 13 controls from healthy breast tissue generated in-house. Copy number variations (CNVs) were detected using the Nanostring CNV Cancer panel (89 genes) on the Nanostring nCounter platform. Differentially upregulated or amplified genes were queried against DGIdb and Gene Drug Knowledge database for suitable drug matches, limiting the queries to clinically actionable antineoplastic drugs.

Results

Analyzing the cohort of 18 BC patients, we detected on average 26 BC relevant genes (526 total, log2 FC &gt; 2) to be upregulated per patient. Querying the upregulated genes against DGIdb, we found a total of 18 genes that had drug matches and fulfilled the criteria of being actionable antineoplastic drugs, with 17/18 samples having a minimum of two gene targets (avg: 4). Most frequent upregulated genes were TOP2A (83%), AURKA (61%), AURKB (56%), RET (39%)and FGFR3 (28%). In the case of CNVs, 12/18 patients showed at least one gene target with clinically actionable drugs associated. This was observed across 12 gene targets that were amplified (avg: 3) and 4 gene targets that underwent deletions (avg: 1). Most frequent CNVs included MYC (14%) and CCND1 (12%). 4/7 patients having an AURKA overexpression also showed an AURKA amplification on the CNV assay. 10/18 patients had fusions events, with an average of three fusions per patient, including GAB2-WNT11, PAK1-TENM4 and FGFR2-CEP55 fusions.

Conclusions

We show that RNA-Seq and copy number assays provide additional clinical value by detecting suitable drug targets beyond traditional DNA-based approaches. We are conducting further analysis on how these additionally derived drug targets could improve the current treatment schedule of those patients.

Citation Format: Meissner T, Amallraja A, Mark A, Andrews A, Connolly C, Young B, De P, Williams C, Leyland-Jones B. The value of RNA-Seq for the detection of clinically actionable targets in breast cancer - A small cohort analysis [abstract]. In: Proceedings of the 2016 San Antonio Breast Cancer Symposium; 2016 Dec 6-10; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2017;77(4 Suppl):Abstract nr P1-05-22.

Questioning assent: how are children's views included as families make decisions about clinical trials?

BACKGROUND

Assent is used to take children's wishes into account when they are invited into clinical trials, but the concept has attracted considerable criticism. We investigated children's accounts of decision-making with the aim of informing practice in supporting children when invited to join a clinical trial.

METHODS

We audio-recorded qualitative, semi-structured interviews with 22 children aged 8-16 years about being invited to take part in a clinical trial. Most children were interviewed with their parents. Analysis of the transcribed interviews examined the content of participants' accounts thematically, whilst also drawing on principles of discourse analysis, which examines how individuals use talk to achieve certain effects or social practices.

RESULTS

It was not possible to separate children's knowledge of the clinical trial, or their decision-making processes from that of their parents, with parents taking a substantial mediating role in producing their children's decisions. Decision-making gradually unfolded across time and events and was interwoven within the family context, rather than happening in one moment or in the clinical setting. Whilst children valued their parents' role, a case study of child-parent disagreement indicated how children can struggle to be heard.

CONCLUSIONS

Decisions happen within a process of family dynamics, in contrast to ideas of assent that isolate it from this context. Parents have a substantial role in children's decisions, and thus how families come to provide consent. Reflecting this we argue that assent practices need to focus on supporting parents to support their children in learning and deliberating about trials. However, this needs to be accompanied by practitioners being alert to the possibility of divergence in child and parent views and enabling children's perspectives to be heard.

The use of qualitative methods to inform Delphi surveys in core outcome set development

Background

Core outcome sets (COS) help to minimise bias in trials and facilitate evidence synthesis. Delphi surveys are increasingly being used as part of a wider process to reach consensus about what outcomes should be included in a COS. Qualitative research can be used to inform the development of Delphi surveys. This is an advance in the field of COS development and one which is potentially valuable; however, little guidance exists for COS developers on how best to use qualitative methods and what the challenges are. This paper aims to provide early guidance on the potential role and contribution of qualitative research in this area. We hope the ideas we present will be challenged, critiqued and built upon by others exploring the role of qualitative research in COS development.

This paper draws upon the experiences of using qualitative methods in the pre-Delphi stage of the development of three different COS. Using these studies as examples, we identify some of the ways that qualitative research might contribute to COS development, the challenges in using such methods and areas where future research is required.

Results

Qualitative research can help to identify what outcomes are important to stakeholders; facilitate understanding of why some outcomes may be more important than others, determine the scope of outcomes; identify appropriate language for use in the Delphi survey and inform comparisons between stakeholder data and other sources, such as systematic reviews. Developers need to consider a number of methodological points when using qualitative research: specifically, which stakeholders to involve, how to sample participants, which data collection methods are most appropriate, how to consider outcomes with stakeholders and how to analyse these data. A number of areas for future research are identified.

Conclusions

Qualitative research has the potential to increase the research community’s confidence in COS, although this will be dependent upon using rigorous and appropriate methodology. We have begun to identify some issues for COS developers to consider in using qualitative methods to inform the development of Delphi surveys in this article.

Abstract P3-07-36: Immune related gene expression signatures predict benefit of letrozole over tamoxifen in BIG 1-98

Background: The prognostic significance of increased levels of CD8+ tumor infiltrating lymphocytes(TILs) in ER- breast cancer has been described. We sought to identify possible immune-related biomarkers for predicting benefit from letrozol(LET) or tamoxifen(TAM) for recurrence in ER+ breast cancer.

Patient and Methods: We used Illumina DASL Assay to measure gene expression in FFPE primary breast cancers from a subset of postmenopausal patients enrolled in the BIG 1-98 randomized phase 3 trial comparing 5 years LET (n=344) vs TAM (n=381) as adjuvant endocrine therapy. Gene sets (n=1910) that represent cell states and perturbations within the immune system from the Human Immunology Project Consortium were used in an exploratory analysis to identify possible predictive signatures.

Results: We identified five distinct gene signatures from previously reported laboratory experiments associated with immune cell differentiation that are highly predictive of benefit (reduced breast cancer recurrence risk) of LET over TAM, each with gene signature p-values&lt;1E-5 and signature-by-treatment interaction p&lt;1E-6. The signatures predict a similar pattern that patients at low-risk score benefit from LET and patients with high-risk score appear to have an advantage with TAM after 5 years. The gene signatures originate as a result of being differentially expressed in the following previously reported experiments. [RAP2A EEF2K TRAF3IP2 GPR37L1 DDX54] down regulated comparing TLR3 and TLR9 agonists in dendritic cells. [RPA1 DUSP4 NUDT18 ZFYVE28] up regulated in comparison of T follicular helper versus Th17 cells. [MAPK15 CCR4 SORCS2 RAMP1 SH3PXD2A] up regulated in regulatory T cell versus CD4+ T cells. [NDUFA6 GIMAP1 CPNE3 ST3GAL6 CCDC88A] down regulated in comparison of untreated CD8+ dendritic cells versus treated with IFNG. [GPN1 COX17 CUL2 CDSA] down regulated in naïve vs stimulated CD8 T cells after 48 hours. We further investigated the signatures using Hungarian Academy of Sciences (HAS) cohort (Gyorffy B 2010), which is a collection of smaller published affymetrix cohorts combined into a larger ER+, TAM treated cohort (n=700). One signature was not tested because two genes were not present in the affymetrix cohort. Three of the remaining four signatures gave informative prognostic results in the HAS cohort, and the signature associated with differentiation of CD8+ dendritic cells was highly prognostic with HR=0.36 (0.26-0.49) p=1E-11.

Conclusion: The role of selective estrogen receptor modulators on immune response has been well described, where TAM has been shown to prevent differentiation and activation of dendritic cells (Naibandian 2005). Similarly, it has been shown that MET inhibitors negatively regulate neutrophils suggesting that anti-MET drugs in cancer could impact immune response (Finisquerra 2015). These findings suggest that if TAM is a negative regulator of immune response why in the ATAC clinical trial, the combination therapy of anastrozole plus TAM were not significantly different from TAM alone were anastrozole was superior. With the increasing importance of understanding the role of immune response on outcome and the use of combination therapies the assessment of TILs in the neoadjuvant setting will be critical for guiding therapy.

Citation Format: Willis S, Gray KP, Regan MM, Rae JM, Kammler R, Young B, Ditzel HJ, Lyng MB, Colleoni M, Viale G, Leyland-Jones B. Immune related gene expression signatures predict benefit of letrozole over tamoxifen in BIG 1-98. [abstract]. In: Proceedings of the Thirty-Eighth Annual CTRC-AACR San Antonio Breast Cancer Symposium: 2015 Dec 8-12; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2016;76(4 Suppl):Abstract nr P3-07-36.

Genetic and phenotypic influences on copulatory plug survival in mice

Across a diversity of animals, male seminal fluid coagulates upon ejaculation to form a hardened structure known as a copulatory plug. Previous studies suggest that copulatory plugs evolved as a mechanism for males to impede remating by females, but detailed investigations into the time course over which plugs survive in the female's reproductive tract are lacking. Here, we cross males from eight inbred strains to females from two inbred strains of house mice (Mus musculus domesticus). Plug survival was significantly affected by male genotype. Against intuition, plug survival time was negatively correlated with plug size: long-lasting plugs were small and relatively more susceptible to proteolysis. Plug size was associated with divergence in major protein composition of seminal vesicle fluid, suggesting that changes in gene expression may play an important role in plug dynamics. In contrast, we found no correlation to genetic variation in the protein-coding regions of five genes thought to be important in copulatory plug formation (Tgm4, Svs1, Svs2, Svs4 and Svs5). Our study demonstrates a complex relationship between copulatory plug characteristics and survival. We discuss several models to explain unexpected variation in plug phenotypes.

Surgical manifestations of gastrointestinal cytomegalovirus infection in children: Clinical audit and literature review

INTRODUCTION

Gastrointestinal sequelae of cytomegalovirus are rare, usually associated with significant immune compromise, and carry a high morbidity and mortality. Gastrointestinal disease frequently requires surgical intervention for diagnosis and management.

AIM

The aim of the study is to evaluate the incidence, presentation and management of gastrointestinal cytomegalovirus disease in a pediatric population.

METHOD

Between January 2003 and June 2011, a retrospective folder review was conducted of all symptomatic children with proven CMV disease, presenting to the surgical service. Eligible patients were identified using the surgical, histopathology and serology databases.

RESULTS

Thirty-eight patients (1.8/1000 surgical admissions) were identified with a median presenting age of 5months (range 3days-12years). Esophagitis (n=18) and small bowel disease (n=16) predominated, but CMV was seen throughout the gastrointestinal tract. Risk factors included HIV infection (n=21, 55%) and recent gastrointestinal surgery or infection (n=10, 26%). Characteristic multiple jejunoileal perforations were seen in six patients. Compared to upper GIT disease, intestinal involvement was associated with younger age and doubled mortality. In HIV-infected children, median CD4 (%) was lower in intestinal compared to upper gastrointestinal disease. Morbidities included anastomotic breakdowns (5), anastomotic strictures (3), relook laparotomies (10), resistant esophageal strictures (5) and prolonged parenteral nutrition (5). Anti-CMV drugs were given in 63%. Overall mortality was 32% (12/38) and was associated with lower GIT disease.

CONCLUSION

Invasive CMV gastrointestinal disease in our children was predominantly HIV-associated, or followed a major lower gastrointestinal inflammatory insult in infants younger than 6months. Successful therapy requires a high index of suspicion of active CMV disease to allow early implementation of CMV viral load control and aggressive treatment of the underlying immune impairment. Multiple surgical interventions are often required for both tissue diagnosis and management of acute and chronic complications. CMV-viral-load-tailored anti-CMV therapy is supported by recent literature.

Risk and protective factors for falls on one level in young children: multicentre case-control study

BACKGROUND

Childhood falls are an important global public health problem, but there is lack of evidence about their prevention. Falls on one level result in considerable morbidity and they are costly to health services.

OBJECTIVE

To estimate ORs for falls on one level in children aged 0-4 years for a range of safety behaviours, safety equipment use and home hazards.

DESIGN, SETTING AND PARTICIPANTS

Multicentre case-control study at hospitals, minor injury units and general practices in and around four UK study centres. Participants included 582 children less than 5 years of age with a medically attended fall injury occurring at home and 2460 controls matched on age, sex, calendar time and study centre.

MAIN OUTCOME MEASURE

Fall on one level.

RESULTS

Cases' most common injuries were bangs on the head (52%), cuts or grazes not needing stitches (29%) or cuts or grazes needing stitches (17%). Comparing cases to community controls in the adjusted analyses, significant findings were observed for only two exposures. Injured children were significantly less likely to live in a household without furniture corner covers (adjusted OR (AOR) 0.72, 95% CI 0.55 to 0.95), or without rugs and carpets firmly fixed to the floor (AOR 0.76, 95% CI 0.59 to 0.98).

CONCLUSIONS

We did not find any safety practices, use of safety equipment or home hazards associated with a reduced risk of fall on one level. Our findings do not provide evidence to support changes to current injury prevention practice.

Pilot study to assess measures to be used in the prospective audit of the management of foot ulcers in people with diabetes

AIM

To design and test a methodology for assessing aspects of the management of foot disease in diabetes.

METHODS

A national working group devised pilot datasets that may be used to document the process of management of active ulceration. Participating volunteer specialist units throughout England were required to characterize newly presenting people with diabetic foot ulcers using a standard questionnaire comprising the dataset and to document outcomes at 6 and 12 months. Semi-structured interviews were later conducted with the volunteers at the units.

RESULTS

A total of 23 units recorded baseline data on 652 people with incident foot ulcers; valid outcome data were available for 541 people (83.0%). Of the 541 index ulcers, 351 (64.9%) healed within 24 weeks, with a median time to healing of 63 days. Ulcer site and depth and peripheral arterial disease were associated with differing ulcer healing rates. By contrast, baseline demographic characteristics were not independently associated with healing. These were used to calculate a standardized case-mix adjusted healing ratio. In most units data collection took < 10 min per person, but participants reported that the burden of local data collection was still excessive.

CONCLUSION

This study confirmed the feasibility of routine multi-unit comparative assessment of care of the foot in diabetes, including the generation of meaningful service reports, but for general use the burden of local data collection will need to be reduced (e.g. by using linkage to existing national data collections).