Impact of clinical supervision on the mental health nursing workforce: a scoping review protocol

INTRODUCTION

Mental health nurses work in potentially unpredictable, stressful and complex environments that can lead to burn-out and high staff turnover. Clinical supervision is a formal and professional agreement between two or more people that aims to strengthen individuals' competencies and organisational strengths. Effective clinical supervision has been noted as a method of reducing workplace issues within mental health nursing, but there is not currently a synthesis of evidence in this area. The key objective of this scoping review is to identify, map and analyse the available evidence reporting on the impact of clinical supervision on workforce outcomes for mental health nurses.

METHODS

A scoping review following the Preferred Reporting Items for Systematic Reviews and Meta-Analyses-Scoping Review Extension method will be conducted exploring clinical supervision for mental health nurses. A search for academic literature from Medline, CINAHL, Embase and PsycINFO will be combined with grey literature sourced through Google to identify potentially relevant studies. Studies identified by the search strategy will be managed using Covidence, and two authors will screen all identified articles. Reference lists of included studies will be handsearched to identify any potentially relevant studies missed by the search strategy.

ANALYSIS

A summary tool including predefined categories (such as author, date published, workforce outcome measured) will be used to summarise the included studies in this scoping review. Additionally, a narrative synthesis approach will be used to report the outcomes of included studies and provide further analysis.

ETHICS AND DISSEMINATION

This scoping review protocol described research that will use secondary analysis of publicly available information, and therefore, does not require ethics approval. The findings of this research will be disseminated through publication in a peer-reviewed academic journal and relevant conference presentations.

The Effectiveness of the Safety Planning Intervention for Adults Experiencing Suicide-Related Distress: A Systematic Review

The safety planning intervention (SPI) is gaining momentum in suicide prevention practice and research. This systematic review sought to determine the effectiveness of the SPI for adults experiencing suicide-related distress. Systematic searches of international, peer-reviewed literature were conducted in six databases (Cochrane Trials, Embase, Emcare, Medline, PsycINFO and Web of Science), including terms for safety planning, suicide, and suicide-related outcomes. A total of 565 results were included for screening. Result screening (title/abstract and full-text), data extraction and critical appraisal were conducted in duplicate. Twenty-six studies met the inclusion criteria. Studies were primarily quantitative (n = 20), largely with general adult or veteran samples; a small number of studies explored the perspectives of staff and significant others. Half of the studies included the SPI as a standalone intervention, while the other half examined the SPI in combination with other interventions. Most interventions were delivered in-person, with a hard-copy safety plan created, while a smaller number explored internet-based interventions. Primary measures included: suicidality (ideation, behavior, deaths; 10 studies), suicide-related outcomes (depression, hopelessness; 5 studies) and treatment outcomes (hospitalizations, treatment engagement; 7 studies). The evidence supports improvements in each of these domains, with complementary findings from the remaining quantitative and qualitative studies suggesting that the SPI is a feasible and acceptable intervention. While positive, these findings are limited by the heterogeneity of interventions and study designs, making the specific impact of the SPI difficult to both determine and generalize. Conversely, this also points to the flexibility of the SPI.HighlightsThe Safety Planning Intervention (SPI) is a valuable indicated intervention for general adult and veteran populations experiencing suicide-related distress, primarily in face-to-face, clinical settings.Quantitative findings indicate associations between the SPI and improvements in suicidal ideation and behavior, decreases in depression and hopelessness, along with reductions in hospitalizations and improvements in treatment attendance.Qualitative studies suggest the SPI is acceptable and feasible, with areas for development.SPIs have been shown to be adaptable to the clinical area in its modality (digital or paper-based), delivery (face-to-face or online), facilitation (clinician or self-administered) and multiplicity (as stand-alone or combined intervention).

Abstract 112: Analytical performance of a cfDNA-based targeted methylation multi-cancer early detection test for population-scale screening

Introduction: cfDNA-based tests have the potential to facilitate earlier detection of cancer and provide greater opportunity for curative intervention. Previously, we demonstrated that a cfDNA-based targeted methylation multi-cancer early detection (MCED) test can detect multiple cancers across all stages with high specificity, and predict the signal origin (SO; ie, tissue of origin) with high accuracy; we also validated the repeatability and reproducibility of its performance. Here, we validate a recent version of this MCED test planned for use as a screening tool.

Methods: In the Circulating Cell-free Genome Atlas study (NCT02889978), cfDNA was analyzed using targeted methylation sequencing and machine learning to classify samples as cancer or non-cancer, and predict SO. Dilutions of cfDNA samples from participants with early-stage lung, head and neck, sarcoma, upper gastrointestinal, colorectal, or ovarian cancer into cfDNA from individuals without cancer were analyzed to establish the limit of detection (LOD95%) defined by the lowest variant allele frequency (VAF) at which accurate classification of cancer signals was attained in at least 95% of replicates. Analytical specificity was assessed by the true negative rate in 66 non-cancer cfDNA samples. Classification performance was evaluated as a function of cfDNA input (0.5-100 ng) using cancer samples (liver/bile duct, lung, head and neck, ovarian, breast, bladder/urothelial, uterine). Repeatability within-run and reproducibility between-runs were characterized by pairwise comparisons among 53 cancer samples (anorectal, breast, head and neck, uterine) and among 62 non-cancer samples processed across multiple reagent lots, instruments, and operators. The effects of high levels of potential interferents hemoglobin, bilirubin, triglycerides, and genomic DNA on classification when spiked into 88 plasma samples along with cfDNA from individuals with cancer (liver/bile duct or lung) or when spiked into 87 non-cancer samples were evaluated.

Results: LOD95% was 0.11% VAF. No false positives were detected in non-cancer samples (100% analytical specificity). Across all input cfDNA levels tested, in 50/50 (100%) cancer samples, a cancer signal was detected with a correct SO prediction. All sample pairs in within-run (n=110) and between-run (n=696) analyses were concordant with respect to cancer/non-cancer classification and SO prediction (100% repeatability and reproducibility). None of the tested interferents affected cancer signal detection (100% correct) or SO prediction (100% accuracy).

Conclusions: These results suggest that the analytical performance of a cfDNA-based targeted methylation MCED screening test is robust for clinical implementation. This MCED test can be a complementary tool to the existing repertoire of cancer screening options currently available for clinical use.

Citation Format: Gregory E. Alexander, Byoungsok Jung, Lijuan Ji, Ekaterina Revenkova, Payal Shah, Jacqueline Brooks, Jeremy Carter, Zhao Dong, Lane Eubank, Maryam Hosseini, Xinyi Hou, Hannah Kiarie, Neda Ronaghi, Fabian E. Ortega, Madhuvanthi Ramaiah, Kate Rhodes, Rita Shaknovich, Seyedmehdi Shojaee, Sonya Parpart-Li, Nathan Hunkapiller. Analytical performance of a cfDNA-based targeted methylation multi-cancer early detection test for population-scale screening [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2021; 2021 Apr 10-15 and May 17-21. Philadelphia (PA): AACR; Cancer Res 2021;81(13_Suppl):Abstract nr 112.

Frequentist rules for regulatory approval of subgroups in phase III trials: A fresh look at an old problem

Background

The number of Phase III trials that include a biomarker in design and analysis has increased due to interest in personalised medicine. For genetic mutations and other predictive biomarkers, the trial sample comprises two subgroups, one of which, say B+ is known or suspected to achieve a larger treatment effect than the other B−. Despite treatment effect heterogeneity, trials often draw patients from both subgroups, since the lower responding B− subgroup may also gain benefit from the intervention. In this case, regulators/commissioners must decide what constitutes sufficient evidence to approve the drug in the B− population.

Methods and Results

Assuming trial analysis can be completed using generalised linear models, we define and evaluate three frequentist decision rules for approval. For rule one, the significance of the average treatment effect in B− should exceed a pre-defined minimum value, say ZB−>L. For rule two, the data from the low-responding group B− should increase statistical significance. For rule three, the subgroup-treatment interaction should be non-significant, using type I error chosen to ensure that estimated difference between the two subgroup effects is acceptable. Rules are evaluated based on conditional power, given that there is an overall significant treatment effect. We show how different rules perform according to the distribution of patients across the two subgroups and when analyses include additional (stratification) covariates in the analysis, thereby conferring correlation between subgroup effects.

Conclusions

When additional conditions are required for approval of a new treatment in a lower response subgroup, easily applied rules based on minimum effect sizes and relaxed interaction tests are available. Choice of rule is influenced by the proportion of patients sampled from the two subgroups but less so by the correlation between subgroup effects.

The impact of suicide prevention education programmes for nursing students: A systematic review

The purpose of this systematic review was to locate and synthesize peer-reviewed evidence regarding the effectiveness of providing suicide prevention education to nursing students. Systematic searches were conducted in seven databases (EMBASE, EmCare, Joanna Briggs, MEDLINE, PsycINFO, Scopus, and Web of Science). Results were screened in duplicate at two stages: title and abstract, and full text. Critical appraisal and data extraction were also completed in duplicate. Initial database searching yielded 303 results. Following the addition of seven records from relevant reference lists, and the removal of duplicates, a total of 118 results were included for screening. Eight articles were deemed eligible for inclusion in this review; most (n = 5) were quantitative. While all were conducted within university settings, half were stand-alone education sessions, while the remaining were integrated with existing programmes/courses. The types of education programmes varied considerably across studies, with only three being established, evidence-based programmes. The studies explore a range of outcomes, which have been narratively categorized as enhanced skills, abilities, and self-confidence; development of positive attitudes and beliefs; acquisition of knowledge; and programme experience and evaluation. While there is a small body of evidence indicating that suicide prevention education programmes contribute to improvements in skills, abilities, self-confidence, and attitudes among nursing students, the variability in educational interventions and outcomes, coupled with short-term evaluation time frames, makes it difficult to fully understand the impact of this important suicide prevention strategy.

Dynamic genetic regulation of gene expression during cellular differentiation

Genetic regulation of gene expression is dynamic, as transcription can change during cell differentiation and across cell types. We mapped expression quantitative trait loci (eQTLs) throughout differentiation to elucidate the dynamics of genetic effects on cell type-specific gene expression. We generated time-series RNA sequencing data, capturing 16 time points during the differentiation of induced pluripotent stem cells to cardiomyocytes, in 19 human cell lines. We identified hundreds of dynamic eQTLs that change over time, with enrichment in enhancers of relevant cell types. We also found nonlinear dynamic eQTLs, which affect only intermediate stages of differentiation and cannot be found by using data from mature tissues. These fleeting genetic associations with gene regulation may explain some of the components of complex traits and disease. We highlight one example of a nonlinear eQTL that is associated with body mass index.

Correct cell- and differentiation-specific expression of a murine alpha 1 (I) collagen minigene in vitro differentiating embryonal carcinoma cells

An in vitro differentiation system utilizing retinoic acid (RA) treatment of pluripotent murine P19 embryonal carcinoma (EC) cells, which can be induced to differentiate into various cell types, was optimized for maximal induction of alpha 1 type I collagen (Col1a1) gene expression. Differentiation was associated with apoptotic death of the majority of cells, indicating that this in vitro system faithfully mimics the in vivo differentiation process. Col1a1 mRNA became detectable by RNase protection assay after 3 days of RA treatment and, after 6 days, reached a level comparable to that in NIH 3T3 fibroblasts. After induction of differentiation the Col1a1 gene remained transcriptionally active for extended periods of time even in the absence of RA. A minigene version of the murine Col1a1 gene was constructed that contains all of the so far known Col1a1 regulatory elements. This construct exhibited the correct expression pattern in stable transfection experiments: it was expressed in fibroblasts, but not in undifferentiated P19 EC cells, and it was transcriptionally activated after induction of differentiation. This experimental system should be a useful tool for dissecting the molecular mechanisms involved in the developmental activation and stage- and tissue-specific expression of the murine Col1a1 gene.

Performance and Side Effects of Supplementation with N-Acetylcysteine: A Systematic Review and Meta-Analysis

BACKGROUND

N-Acetylcysteine (NAC) is a promising antioxidant supplement with potential as an acute strategy to enhance performance in elite sport, but there are concerns about its side effects with high doses.

OBJECTIVE

To review the current literature and evaluate the effects of NAC supplementation on sport performance and the risk of adverse effects.

METHODS

The literature up to May 2016 was searched on MEDLINE (PubMed), EMBASE, SPORTDiscus, Google Scholar and Scopus databases to identify all studies investigating the effects of NAC supplementation on exercise performance and/or side effects experienced. Performance outcomes from each study were converted to the percent effect equivalent to mean power output in a time trial. All pooled analyses were based on random-effects models generated by Review Manager (RevMan) [Computer program], version 5.3 (The Nordic Cochrane Centre, The Cochrane Collaboration, Copenhagen, 2014).

RESULTS

A total of seven studies met criteria for inclusion in the sport performance meta-analysis, and 17 for inclusion in the side effects meta-analysis. The typical daily dose of NAC reported was 5.8 g·d^-1; with a range between 1.2 and 20.0 g·d^-1. The mean increase in performance was 0.29% (95% confidence interval -0.67 to 1.25). The difference in the odds ratio of side effects on NAC compared with placebo was 1.11 (95% confidence interval 0.88-1.39). The sub-analysis of NAC dose suggested an increase in side effects as the dosage of NAC increased; however, this observation requires further investigation.

CONCLUSIONS

Despite initial research publications reporting positive performance effects with NAC, at this stage it cannot be recommended further. The risk of side effects from NAC supplementation also remains unclear owing to significant variations in effects. Suboptimal reporting and documentation in the literature creates difficulties when meta-analysing outcomes and generating conclusions.

Goldspotted spinefoot Siganus punctatus (Siganidae) age-based reproductive life history and fisheries vulnerability

Between February 2015 and 2016, samples of the Indo-Pacific goldspotted spinefoot Siganus punctatus were taken from local fish markets, feeding sites and nursery grounds on the main island of Pohnpei, Micronesia, to ascertain sexual pattern, reproductive seasonality, age, growth and mortality. Microscopic examinations of gonads identified two seasonal peaks in reproduction: February to May and September to December, with evidence of some spawning activity in most months. Ripe females were observed 4 days on either side of the new moon. Females first matured at c. 180 mm fork length (L_F ) and 1 year of age, which coincides with their entry into the fishery. Ninety five per cent of individuals were less than 3 years and the oldest fish were 8 years. To examine the species vulnerability to fishing, a tag-and-recapture study was conducted over 4 months in 2015 in a locally managed marine area and at an unprotected site. Findings suggest high residency and high vulnerability to fishing at shallow-water feeding sites and restricted migration overall. The placement of marine protected areas within critical habitat appears to be an effective conservation strategy for this species, particularly when combined with gear and seasonal market restrictions during vulnerable life-history phases.

Somatic mutation burden in cancer samples determined by targeted next generation sequencing

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Background: High somatic mutation burden in tumor tissues is associated with the presentation of neoantigens that promote immune responses particularly in the context of immune checkpoint therapies. Herein, we characterize the ability of targeted cancer research panels to generate estimates of somatic mutation burden. Methods: Somatic mutation data from > 8000 cancer samples obtained from The Cancer Genome Atlas (TCGA) was curated and standardized, and the number of single nucleotide variants (SNVs) in exonic regions of each sample determined. Next, the number of SNVs associated with target regions of two Ion AmpliSeq cancer panels (Oncomine Comprehensive Assay [OCA, 146 genes, 0.35 MB]; Comprehensive Cancer Panel [CCP, 409 genes, 1.7 MB]) was likewise determined and the frequency of mutation counts in the exome and the panel target regions was compared. Mutation counts of samples containing truncating mutations in mismatch repair (MMR) and other DNA repair genes were characterized. A facile workflow with less than 60 minutes of hands-on time was developed to estimate mutation counts for a batch of 8 samples using the Ion Chef for automated library preparation and templating followed by sequencing on the Ion S5. Results: The sensitivity of targeted panels in estimating somatic mutation burden was positively correlated with panel size. The area under the Receiver Operating Characteristic (ROC) curve showed that CCP had > 90% sensitivity and > 95% specificity to differentiate high and low mutation burden based on informatics analysis of TCGA data. As expected, truncating mutations in MMR genes were associated with higher somatic mutation counts in colorectal tumor tissue. Using data generated from OCA and CCP, we characterized a set of filters that provided a good estimate of somatic mutation counts when applied to a tumor-only workflow. Conclusions: A simple workflow was developed on the Ion Torrent sequencing platform to estimate somatic mutation burden in cancer samples. The methods described herein will help advance research in immuo-oncology.

Intergenerational transmission of dietary behaviours: A qualitative study of Anglo-Australian, Chinese-Australian and Italian-Australian three-generation families

Family food choice is complex with a number of people within the family sharing food choice and preparation responsibilities. Differences in dietary behaviours also exist between various ethnic groups worldwide, and are apparent within multicultural nations such as Australia. This study examined the intergenerational transmission of eating behaviour through semi-structured family interviews with 27 three generation families (Anglo-Australian: n = 11, Chinese-Australian: n = 8, Italian-Australian: n = 8; N = 114). The influence of generation (grandparent, parent, child), role (grandmother, grandfather, mother, father, daughter, son), and ethnic background were considered. Thematic analysis identified that regardless of ethnic background, grandmothers and mothers dominated family food choice decisions even in families where fathers were primarily responsible for the preparation of family meals. The women in each generation influenced fruit and vegetable intake by controlling purchasing decisions (e.g., by shopping for food or editing family grocery shopping lists), insisting on consumption, monitoring and reminding, utilizing food as a prerequisite for conditional treats (e.g., eating fruit before being allowed snacks), instigating and enforcing food rules (e.g., fast food only on weekends), and restricting others' food choices. Grandparents and children shared a relationship that skipped the parent generation and influenced dietary behaviours bi-directionally. These findings have implications for the delivery of dietary health messages used in disease prevention interventions designed to successfully reach culturally and linguistically diverse populations and all members of multigenerational families.

Abstract 3627: Automated, purification-free, Ion AmpliSeq™ library preparation from FFPE samples using the Ion Torrent™ Ion Chef™ System

The ability to produce high quality libraries from FFPE samples is ever more important for next-generation sequencing. Quick turnaround time from sample to answer and simple protocols are critical components for this process. The Ion Chef and Ion AmpliSeq Kit for Chef DL8 is an automated system that has proven to reliably generate quality libraries from purified high molecular weight genomic DNA, in addition to formalin-fixed paraffin embedded (FFPE) DNA samples. We have further developed a simple and robust protocol for preparing DNA libraries from FFPE samples with no nucleic acid purification required. Our protocol is compatible with all Ion AmpliSeq panels and generates eight balanced libraries on the Ion Chef Instrument in under 8 hours, with less than 1 hour hands-on time. We observed equivalent or better sequencing performance using this method compared to a 16-hour manual FFPE DNA extraction protocol. This method has shown to work with low, medium, and high input FFPE samples from different tissue types on a single run. We evaluated a variety of FFPE samples using 1 or 2 pool Ion AmpliSeq DNA research panels containing assays designed to known oncogenes. We were able to generate and successfully sequence DNA libraries from a single FFPE slice as small as 2 mm X 2 mm. Minimal sample handling is an advantage for the NGS platform with this robust protocol.

For Research Use Only. Not for use in diagnostic procedures.

Citation Format: Tanya Biorac, Michael Allen, Francis B. Peters, Cristina Van Loy, Kate Rhodes, Mark Andersen. Automated, purification-free, Ion AmpliSeq™ library preparation from FFPE samples using the Ion Torrent™ Ion Chef™ System. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 3627.

Rapid outbreak sequencing of Ebola virus in Sierra Leone identifies transmission chains linked to sporadic cases

To end the largest known outbreak of Ebola virus disease (EVD) in West Africa and to prevent new transmissions, rapid epidemiological tracing of cases and contacts was required. The ability to quickly identify unknown sources and chains of transmission is key to ending the EVD epidemic and of even greater importance in the context of recent reports of Ebola virus (EBOV) persistence in survivors. Phylogenetic analysis of complete EBOV genomes can provide important information on the source of any new infection. A local deep sequencing facility was established at the Mateneh Ebola Treatment Centre in central Sierra Leone. The facility included all wetlab and computational resources to rapidly process EBOV diagnostic samples into full genome sequences. We produced 554 EBOV genomes from EVD cases across Sierra Leone. These genomes provided a detailed description of EBOV evolution and facilitated phylogenetic tracking of new EVD cases. Importantly, we show that linked genomic and epidemiological data can not only support contact tracing but also identify unconventional transmission chains involving body fluids, including semen. Rapid EBOV genome sequencing, when linked to epidemiological information and a comprehensive database of virus sequences across the outbreak, provided a powerful tool for public health epidemic control efforts.

Development and validation of a scalable next-generation sequencing system for assessing relevant somatic variants in solid tumors

Next-generation sequencing (NGS) has enabled genome-wide personalized oncology efforts at centers and companies with the specialty expertise and infrastructure required to identify and prioritize actionable variants. Such approaches are not scalable, preventing widespread adoption. Likewise, most targeted NGS approaches fail to assess key relevant genomic alteration classes. To address these challenges, we predefined the catalog of relevant solid tumor somatic genome variants (gain-of-function or loss-of-function mutations, high-level copy number alterations, and gene fusions) through comprehensive bioinformatics analysis of >700,000 samples. To detect these variants, we developed the Oncomine Comprehensive Panel (OCP), an integrative NGS-based assay [compatible with < 20 ng of DNA/RNA from formalin-fixed paraffin-embedded (FFPE) tissues], coupled with an informatics pipeline to specifically identify relevant predefined variants and created a knowledge base of related potential treatments, current practice guidelines, and open clinical trials. We validated OCP using molecular standards and more than 300 FFPE tumor samples, achieving >95% accuracy for KRAS, epidermal growth factor receptor, and BRAF mutation detection as well as for ALK and TMPRSS2:ERG gene fusions. Associating positive variants with potential targeted treatments demonstrated that 6% to 42% of profiled samples (depending on cancer type) harbored alterations beyond routine molecular testing that were associated with approved or guideline-referenced therapies. As a translational research tool, OCP identified adaptive CTNNB1 amplifications/mutations in treated prostate cancers. Through predefining somatic variants in solid tumors and compiling associated potential treatment strategies, OCP represents a simplified, broadly applicable targeted NGS system with the potential to advance precision oncology efforts.

Abstract A1-43: Targeted amplicon-based next-generation sequencing of routine solid tumor specimens to detect clinically relevant somatic alterations

Background: Although precision medicine approaches have revolutionized oncology, widespread adoption requires robust, inexpensive approaches enabling the targeted assessment of all relevant alteration classes from routine tissue samples.

Methods: Here we interrogated &gt;7,000 cancer exomes and transcriptomes, along with &gt;30,000 array based cancer genomes to identify recurrent somatic alterations (mutations, copy number alterations [CNAs] and gene fusions) across solid tumors. From this analysis, we developed and validated an integrated multiplexed PCR based Ion Torrent next generation sequencing panel (Oncomine Cancer Research Panel [OCP]) targeting the actionable somatic cancer genome optimized for 20ng of formalin-fixed, paraffin-embedded (FFPE) tissue isolated DNA/RNA.

Results: We validated the OCP using FFPE cell line mixtures, as well as a prospective cohort of 104 FFPE tumor specimens sent for concurrent clinical molecular testing, with &gt;97% sensitivity and specificity for the presence/absence of KRAS, EGFR, BRAF and ALK point mutations, indels or gene fusions in this molecular testing cohort. We also applied the OCP to 100 lung cancers, identifying known and novel alterations, including ALK and ROS1 gene fusions. Lastly, applying the OCP to 116 prostate cancers, including 50 previously treated samples, we recapitulated known molecular subtypes, observed distinct profiles according to previous treatment and obtained 100% concordance for isoform specific TMPRSS2:ERG gene fusion detection compared to qPCR. Additionally, OCP profiling supports a novel molecular subtype of prostate cancer defined by IDH1 R132 hotspot mutations and informed on resistance mechanisms in a pre- and post-treatment sample pair. Importantly, 44%, 35% and 9% of patients in the molecular testing, lung and prostate cancer cohorts, respectively, harbored additional alterations (beyond routine molecular testing) associated with FDA approved or NCCN guideline referenced therapies.

Conclusions: Through analysis of both DNA and RNA to assess the actionable somatic cancer genome, the validated OCP panel may have utility in both clinical and research settings.

Citation Format: Daniel H. Hovelson, Andrew S. McDaniel, Bryan Johnson, Andi K. Cani, Kate Rhodes, Paul D. Williams, Chia-Jen Liu, Santhoshi Bandla, Catherine S. Grasso, Michael J. Quist, Seth Sadis, Daniel R. Rhodes, Scott A. Tomlins. Targeted amplicon-based next-generation sequencing of routine solid tumor specimens to detect clinically relevant somatic alterations. [abstract]. In: Proceedings of the AACR Special Conference on Translation of the Cancer Genome; Feb 7-9, 2015; San Francisco, CA. Philadelphia (PA): AACR; Cancer Res 2015;75(22 Suppl 1):Abstract nr A1-43.

Next-Gen Sequencing Exposes Frequent MED12 Mutations and Actionable Therapeutic Targets in Phyllodes Tumors

Phyllodes tumors are rare fibroepithelial tumors with variable clinical behavior accounting for a small subset of all breast neoplasms, yet little is known about the genetic alterations that drive tumor initiation and/or progression. Here, targeted next-generation sequencing (NGS) was used to identify somatic alterations in formalin-fixed paraffin-embedded (FFPE) patient specimens from malignant, borderline, and benign cases. NGS revealed mutations in mediator complex subunit 12 (MED12) affecting the G44 hotspot residue in the majority (67%) of cases spanning all three histologic grades. In addition, loss-of-function mutations in p53 (TP53) as well as deleterious mutations in the tumor suppressors retinoblastoma (RB1) and neurofibromin 1 (NF1) were identified exclusively in malignant tumors. High-level copy-number alterations (CNA) were nearly exclusively confined to malignant tumors, including potentially clinically actionable gene amplifications in IGF1R and EGFR. Taken together, this study defines the genomic landscape underlying phyllodes tumor development, suggests potential molecular correlates to histologic grade, expands the spectrum of human tumors with frequent recurrent MED12 mutations, and identifies IGF1R and EGFR as potential therapeutic targets in malignant cases.

IMPLICATIONS

Integrated genomic sequencing and mutational profiling provides insight into the molecular origin of phyllodes tumors and indicates potential druggable targets in malignant disease. Visual Overview: http://mcr.aacrjournals.org/content/early/2015/04/02/1541-7786.MCR-14-0578/F1.large.jpg.

Abstract 5076: Rapid assessment of AML genes for mutation detection and copy number variation

Targeted sequencing using the Ion AmpliSeq™ Library kit combined with the Ion PGM™ sequencing instrument is a fast and effective method to identify genetic variants in cancer samples. A new targeted primer panel for amplification of genes involved in Acute Myeloid Leukemia (AML) has been developed by Life Technologies. The panel covers 19 genes characterized using over 300 specific primer pairs in two highly multiplexed PCRs. To demonstrate the coverage efficiency, we evaluated libraries prepared from whole blood and isolated genomic DNA. When libraries from 4 individuals were run on a single Ion 318™ Chip, the average coverage depth was &gt;3000x, with &gt;97% of the target bases covered &gt;500X. Additionally, &gt;90% of reads were on-target. The panel was tested on control samples and analyzed using the Ion Reporter™ Software, and expected variants, including copy number variations (CNVs) were detected with high sensitivity and specificity.

Citation Format: Mark Andersen, Kate Rhodes, Steve Roman, Cristina VanLoy, Adam Broomer, Michael Allen, Denise Topacio, Guoying Liu, Fiona Hyland. Rapid assessment of AML genes for mutation detection and copy number variation. [abstract]. In: Proceedings of the 105th Annual Meeting of the American Association for Cancer Research; 2014 Apr 5-9; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2014;74(19 Suppl):Abstract nr 5076. doi:10.1158/1538-7445.AM2014-5076

gammadeltaT cell-mediated regulation of chemokine producing macrophages during Listeria monocytogenes infection-induced inflammation

Infection of gammadeltaT cell-deficient (TcRdelta-/-) mice with the intracellular bacterium Listeria monocytogenes (Lm) results in an exacerbated inflammatory response characterized by the accumulation of activated macrophages and necrotic liver lesions. Here we investigated whether changes in chemokine production by Lm-elicited macrophages contribute to this abnormal inflammatory response. In response to Lm infection, activated macrophages accumulate in the primary sites of infection in TcRdelta-/- mice and express high amounts of mRNA encoding the chemokines CCL3 (MIP-1alpha), CCL4 (MIP-1beta), CXCL2 (MIP-2) and CXCL10 (IP-10). In the infected tissues of TcRdelta-/- the number of chemokine-synthesizing macrophages was higher than in wild-type (WT) mice, with the amount of MIP-1alpha and MIP-1beta secreted by individual macrophages in the spleen of TcRdelta-/- mice also being significantly higher than in WT mice. By contrast, protease activity and NO production in individual splenic macrophages of Lm-infected TcRdelta-/- and WT mice were comparable. Pathogen-elicited macrophages in TcRdelta-/- mice also expressed high levels of the CCL3 and CCL4 receptor, CCR5. In macrophage-gammadeltaT cell co-cultures, chemokine-producing macrophages were killed by cytotoxic Vgamma1+ T cells in a Fas-FasL-dependent manner consistent with the high levels of chemokine-producing macrophages seen in infected TcRdelta-/- mice being due to the absence of Vgamma1+ T cells. Together these findings highlight the importance of gammadeltaT cells in regulating macrophage anti-microbial responses.

Cancer Care Ontario Colonoscopy Standards: standards and evidentiary base

Colorectal cancer (CRC) is the most common cause of non-tobacco-related cancer deaths in Canadian men and women, accounting for 10% of all cancer deaths. An estimated 7800 men and women will be diagnosed with CRC, and 3250 will die from the disease in Ontario in 2007. Given that CRC incidence and mortality rates in Ontario are among the highest in the world, the best opportunity to reduce this burden of disease would be through screening. The present report describes the findings and recommendations of Cancer Care Ontario's Colonoscopy Standards Expert Panel, which was convened in March 2006 by the Program in Evidence-Based Care. The recommendations will form the basis of the quality assurance program for colonoscopy delivered in support of Ontario's CRC screening program.

Post-ischemic treatment with erythropoietin or carbamylated erythropoietin reduces infarction and improves neurological outcome in a rat model of focal cerebral ischemia

BACKGROUND AND PURPOSE

Recombinant human erythropoietin (rhEPO; Epoetin-alpha; PROCRITtrade mark) has been shown to exert neuroprotective and restorative effects in a variety of CNS injury models. However, limited information is available regarding the dose levels required for these beneficial effects or the neuronal responses that may underlie them. Here we have investigated the dose-response to rhEPO and compared the effects of rhEPO with those of carbamylated rhEPO (CEPO) in a model of cerebral stroke in rats.

EXPERIMENTAL APPROACH

Rats subjected to embolic middle cerebral artery occlusion (MCAo) were treated with rhEPO or CEPO, starting at 6 h and repeated at 24 and 48 h, after MCAo. Cerebral infarct volumes were assessed at 28 days and neurological impairment at 7, 14, 21 and 28 days, post-MCAo.

KEY RESULTS

rhEPO at dose levels of 500, 1150 or 5000 IU kg(-1) or CEPO at a dose level of 50 microg kg(-1) significantly reduced cortical infarct volume and reduced neurologic impairment. All doses of rhEPO, but not CEPO, produced a transient increase in haematocrit, while rhEPO and CEPO substantially reduced the number of apoptotic cells and activated microglia in the ischemic boundary region.

CONCLUSIONS AND IMPLICATIONS

These data indicate that rhEPO and CEPO have anti-inflammatory and anti-apoptotic effects, even with administration at 6 h following embolic MCAo in rats. Taken together, these actions of rhEPO and CEPO are likely to contribute to their reduction of neurologic impairment following cerebral ischemia.

Cellular laserfection

Many studies in modern biology often rely on the introduction of a foreign molecule (i.e., transfection), be it DNA plasmids, siRNA molecules, protein biosensors, labeled tracers, and so on, into cells in order to answer the important questions of today's science. Many different methods have been developed over time to facilitate cellular transfection, but most of these methods were developed to work with a specific type of molecule (usually DNA plasmids) and none work well enough with difficult, sensitive, or primary cells to meet the needs of current life science researchers. A novel procedure that uses laser light to gently permeabilize large number of cells in a very short time has been developed and is described in detail in this chapter. This method allows difficult cells to be efficiently transfected in a high-throughput manner, with a wide variety of molecules, with extremely low toxicity.

Evidence for the opposing roles of different gamma delta T cell subsets in macrophage homeostasis

To ensure invading pathogens are eliminated with minimal damage to host tissues it is essential that macrophage activation be tightly regulated. Previously we demonstrated that a subset of gammadelta T cells (Vgamma1(+)) contributes to resolving pathogen-induced immune responses by killing activated macrophages. However, the exaggerated macrophage response seen in infected Vgamma1(+) T cell-deficient mice suggests that gammadelta T cells play a broader role in macrophage homeostasis and other subsets might promote macrophage activation. Using a macrophage:gammadelta T cell co-culture system we have shown that gammadelta T cells increase the activity of macrophages activated in vivo by Listeria monocytogenes infection. In a dose-dependent manner, gammadelta T cells up-regulated production of cytokines (TNF-alpha, IL-6, IL-10) and chemokines (MIP-1alpha, MIP-1beta) by Listeria-elicited macrophages. The ability to increase macrophage cytokine production was prominent among Vgamma4(+) gammadelta T cells. Reciprocally, Vgamma4(+) gammadelta T cells were activated by Listeria-elicited macrophages, resulting in production of the anti-inflammatory cytokine, IL-10. gammadelta T cell adoptive transfer experiments showed that Vgamma4(+) T cells protected TCRdelta(-/-) mice against Listeria-induced liver injury and necrosis. These findings identify distinct and non-overlapping roles for gammadelta T cell subsets in regulating macrophage function during pathogen-induced immune responses.

Composition of perineuronal net extracellular matrix in rat brain: a different disaccharide composition for the net-associated proteoglycans

We developed a method to extract differentially chondroitin sulfate proteoglycans (CSPGs) that are diffusely present in the central nervous system (CNS) matrix and CSPGs that are present in the condensed matrix of perineuronal nets (PNNs). Adult rat brain was sequentially extracted with Tris-buffered saline (TBS), TBS-containing detergent, 1 m NaCl, and 6 m urea. Extracting tissue sections with these buffers showed that the diffuse and membrane-bound CSPGs were extracted in the first three buffers, but PNN-associated CSPGs remained and were only removed by 6 m urea. Most of the CSPGs were extracted to some degree with all the buffers, with neurocan, brevican, aggrecan, and versican particularly associated with the stable urea-extractable PNNs. The CSPGs in stable complexes only extractable in urea buffer are found from postnatal day 7-14 coinciding with PNN formation. Disaccharide composition analysis indicated a different glycosaminoglycan (GAG) composition for PGs strongly associated with extracellular matrix (ECM). For CS/dermatan sulfate (DS)-GAG the content of nonsulfated, 6-O-sulfated, 2,6-O-disulfated, and 4,6-O-disulfated disaccharides were higher and for heparan sulfate (HS)-GAG, the content of 6-O-sulfated, 2-N-, 6-O-disulfated, 2-O-, 2-N-disulfated, and 2-O-, 2-N-, 6-O-trisulfated disaccharides were higher in urea extract compared with other buffer extracts. Digestions with chondroitinase ABC and hyaluronidase indicated that aggrecan, versican, neurocan, brevican, and phosphacan are retained in PNNs through binding to hyaluronan (HA). A comparison of the brain and spinal cord ECM with respect to CSPGs indicated that the PNNs in both parts of the CNS have the same composition.

Choosing a silicone adhesive and treatment system

As devices become smaller and bonds more critical, choosing the right adhesive system may be essential to the success of the device. This article investigates some adhesives and primers used to adhere difficult substrates.

Baby walkers: paediatricians' knowledge, attitudes, and health promotion

Paediatricians were surveyed about baby walker knowledge, attitudes, and practice. Advising about walkers was associated with working in community paediatrics, treating walker related injuries, knowledge about walkers, and positive attitudes towards walker health promotion. Greater knowledge about walkers was associated with more negative attitudes to walkers. Educating paediatricians and parents about the risks of, and alternatives to using walkers is important.

A herpesvirus vector can transduce axotomized brain neurons

If gene therapy is to be used to promote axon regeneration after spinal cord injury, a suitable vector for transgene delivery must be obtained. Replication-defective herpes simplex virus (HSV) vectors are promising candidates. We have examined whether they can express a LacZ transgene in injured neurons of adult rat brain. We transected the medial forebrain bundle, injected replication-defective HSV/LacZ vectors close to the lesion site, and looked for transgene expression at 2-14 days after the lesion. The vectors carried the LacZ transgene controlled either by the cytomegalovirus immediate-early promoter (vector CS5) or the HSV latency-associated promoter (vector CS1). CS5 transfected many cells near the lesion at 2 days, but did not give persistent expression at 5 days. CS1, in contrast, labeled many neurons in midbrain regions remote from the injection site at 5 days, and much of this expression remained at 12-14 days. The neurons of most interest were in the substantia nigra pars compacta and parabrachial nuclei, which were axotomized by the lesion. Vector-driven beta-galactosidase expression was detected in neurons in both regions. These were confirmed as axotomized by double immunofluorescence for c-Jun. By 12-14 days, many substantia nigra neurons had disappeared but some transduced neurons remained; there was no net loss of transduced neurons from the parabrachial nuclei. These results show that an HSV vector is capable of transducing axotomized cells in the central nervous system and producing transgene expression in them for at least 2 weeks after injection.

Matrix metalloproteases and their inhibitors are produced by overlapping populations of activated astrocytes

Matrix metalloproteases (MMPs) and tissue inhibitors of metalloproteases (TIMPs) are involved in many cell migration phenomena and produced by many cell types, including neurons and glia. To assess their possible roles in brain injury and regeneration, we investigate their production by glial cells, after brain injury and in tissue culture, and we investigate whether they are capable of digesting known axon-inhibitory proteoglycans. To determine the action of MMPs, we incubated astrocyte conditioned medium with activated MMPs, then did western blots for several chondroitin sulphate proteoglycans. MMP-3 digested all five proteoglycans tested, whereas MMP-2 digested only two and MMP-9 none. To determine whether MMPs or TIMPs are produced by astrocytes in vitro, we tested both primary cultures and astrocyte cell lines by western blotting, and compared them with Schwann cells. All cultures produced at least some MMPs and TIMPs, with no obvious correlation with the ability of axons to grow on those cells. Both MMP-9 and TIMP-3 were regulated by various cytokines. To determine which cells produce MMPs and TIMPs after brain injury, we made lesions of adult rat cortex, and did immunohistochemistry. MMP-2 was seen to be induced in activated astrocytes through the whole thickness of the cortex but not deeper, but MMP-3 was not seen in the injured brain. TIMP-2 and TIMP-3 immunoreactivities were induced in activated astrocytes in deep cortex and the underlying white matter. In situ hybridisation confirmed induction of TIMP-2 in glia as well as neurons, but showed no expression of TIMP-4. These results show that both MMPs and TIMPs are produced by some astrocytes, but TIMP production is particularly strong, especially in deep cortex and white matter which is more inhibitory for axon regeneration. Conversely the MMPs produced may not be adequate to promote migration of cells and axons within the glial scar.

Mesenchymal/epithelial induction mediates olfactory pathway formation

In the olfactory pathway, as in the limbs, branchial arches, and heart, mesenchymal/epithelial induction, mediated by retinoic acid (RA), FGF8, sonic hedgehog (shh), and the BMPs, defines patterning, morphogenesis, and differentiation. Neuronal differentiation in the olfactory epithelium and directed growth of axons in the nascent olfactory nerve depend critically upon this inductive interaction. When RA, FGF8, shh, or BMP signaling is disrupted, distinct aspects of olfactory pathway patterning and differentiation are compromised. Thus, a cellular and molecular mechanism that facilitates musculoskeletal and vascular development elsewhere in the embryo has been adapted to guide the differentiation of the olfactory pathway in the developing forebrain.