Meeting report: discussions and preliminary findings on extracellular RNA measurement methods from laboratories in the NIH Extracellular RNA Communication Consortium
Extracellular RNAs (exRNAs) have been identified in all tested biofluids and have been associated with a variety of extracellular vesicles, ribonucleoprotein complexes and lipoprotein complexes. Much of the interest in exRNAs lies in the fact that they may serve as signalling molecules between cells, their potential to serve as biomarkers for prediction and diagnosis of disease and the possibility that exRNAs or the extracellular particles that carry them might be used for therapeutic purposes. Among the most significant bottlenecks to progress in this field is the lack of robust and standardized methods for collection and processing of biofluids, separation of different types of exRNA‐containing particles and isolation and analysis of exRNAs. The Sample and Assay Standards Working Group of the Extracellular RNA Communication Consortium is a group of laboratories funded by the U.S. National Institutes of Health to develop such methods. In our first joint endeavour, we held a series of conference calls and in‐person meetings to survey the methods used among our members, placed them in the context of the current literature and used our findings to identify areas in which the identification of robust methodologies would promote rapid advancements in the exRNA field.
Improvements in Health Behaviors, Eating Self-Efficacy, and Goal-Setting Skills Following Participation in Wellness Coaching
Purpose: This project examined potential changes in health behaviors following wellness coaching. Design: In a single cohort study design, wellness coaching participants were recruited in 2011, data were collected through July 2012, and were analyzed through December 2013. Items in the study questionnaire used requested information about 11 health behaviors, self-efficacy for eating, and goalsetting skills. Setting: Worksite wellness center. Participants: One-hundred employee wellness center members with an average age of 42 years; 90% were female and most were overweight or obese. Intervention: Twelve weeks of in-person, one-on-one wellness coaching. Method: Participants completed study questionnaires when they started wellness coaching (baseline), after 12 weeks of wellness coaching, and at a 3-month follow-up. Results: From baseline to week 12, these 100 wellness coaching participants improved their self-reported health behaviors (11 domains, 0- to 10-point scale) from an average of 6.4 to 7.7 ( p < .001), eating selfefficacy from an average of 112 to 142 (on a 0- to 180-point scale; p < .001), and goal-setting skills from an average of 49 to 55 (on a 16- to 80-point scale; p < .001). Conclusion: These results suggest that participants improved their current health behaviors and learned skills for continued healthy living. Future studies that use randomized controlled trials are needed to establish causality for wellness coaching.
Literature has long suggested that collaboration and interprofessional communication are associated with improved provider satisfaction, patient satisfaction, and the provision of individualized care. More recent literature has documented the favorable influence of a collaborative culture on patient outcomes. In response to the growing need for enhanced nurse–physician partnership and recognition of its impact on the patient experience, nurses are designing unit-based programs to bring the two professions together for opportunities to enhance partnership. This article discusses two approaches to enhancing nurse–resident physician partnership introduced by Benike and Clark (2013) and identifies common elements that were critical to the programs ‘success.
Abstract 3899: Integrating RNA/DNA analysis with a comprehensive cancer panel to improve interpretations of stage four metastatic renal cell carcinoma
Abstract Next-generation sequencing is now commonly applied to measure genomic modifications, providing the opportunity for a more accurate view of cancer progression. That being said, several challenges including tumor purity, heterogeneity and the broad set of cancer associated cellular functions, increase the difficulty of interpreting cancer genomes and make analyzing them distinct from analysis of germline diseases. The ability to detect low allelic mutations in the broad set of cancer-associated genes is critically important. To address these issues, we developed an extended cancer panel, a targeted enrichment sequencing platform that includes over 1,300 cancer genes and 200 miRNAs that improves coverage in traditionally difficult to sequence NGS regions. In this study, we apply an integrated RNA/DNA analysis approach as well as our extended cancer panel to explore mutations in metastatic renal cell carcinoma (RCC) tissue samples before and after treatment. Our goal with this study was to test the importance of integrating DNA and RNA analysis, which allows for detection of mutational events that cannot be observed by either method alone. With RNA analysis it is possible to detect gene fusion events, expression of small variants (SNVs/indels), and gene expression levels while DNA analysis allows for detection of loss of heterozygosity (LOH), copy number variants (CNVs), and small variants. By integrating both the RNA and DNA analysis, it is possible to identify unique variant classes, such as unexpressed variants, allele specific expression (ASE), effects of CNVs on gene expression levels, and how fusion gene integration sites affect CNVs. In our study, each variant class was interpreted pre- and post-treatment, allowing for optimal analysis of treatment effectiveness. By applying both our RNA/DNA integration approach and our extended cancer panel to investigate metastatic RCC samples, we were able to classify many genomic alterations that drive cancer progression. For example, we found that anywhere from 5% to 30% of small variant mutations in driver genes called in the DNA reside in genes that are unexpressed in the RNA. Likewise, we noted multiple cases of ASE, where high profile variants observed in DNA were entirely absent in the RNA despite high expression levels. Strong correlations between CNVs observed in DNA and gene expression changes found in RNA were also detected. We also observed that about half of the RCC samples we tested were biallelic for VHL mutations, suggesting inherited predisposition combined with second hit somatic mutations, facilitating cancer progression. This analysis demonstrates how combining an integrated RNA/DNA approach with a cancer focused augmented enrichment panel allows for detection of both low allelic representation variants and unique variant classes, both of which are critical for accurate interpretation of cancer samples. Citation Format: Sean M. Boyle, Michael J. Clark, Elena Helman, Alexander S. Parker, Thai Ho, Shujun Luo, Scott Kirk, Parin Sripakdeevong, Mirian Karbelashvili, Deanna M. Church, Michael Snyder, John West, Rich Chen. Integrating RNA/DNA analysis with a comprehensive cancer panel to improve interpretations of stage four metastatic renal cell carcinoma. [abstract]. In: Proceedings of the 106th Annual Meeting of the American Association for Cancer Research; 2015 Apr 18-22; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2015;75(15 Suppl):Abstract nr 3899. doi:10.1158/1538-7445.AM2015-3899
Tumor Cell Adhesion As a Risk Factor for Sentinel Lymph Node Metastasis in Primary Cutaneous Melanoma
Purpose Less than 20% of patients with melanoma who undergo sentinel lymph node (SLN) biopsy based on American Society of Clinical Oncology/Society of Surgical Oncology recommendations are SLN positive. We present a multi-institutional study to discover new molecular risk factors associated with SLN positivity in thin and intermediate-thickness melanoma. Patients and Methods Gene clusters with functional roles in melanoma metastasis were discovered by next-generation sequencing and validated by quantitative polymerase chain reaction using a discovery set of 73 benign nevi, 76 primary cutaneous melanoma, and 11 in-transit melanoma metastases. We then used polymerase chain reaction to quantify gene expression in a model development cohort of 360 consecutive thin and intermediate-thickness melanomas and a validation cohort of 146 melanomas. Outcome of interest was SLN biopsy metastasis within 90 days of melanoma diagnosis. Logic and logistic regression analyses were used to develop a model for the likelihood of SLN metastasis from molecular, clinical, and histologic variables. Results ITGB3, LAMB1, PLAT, and TP53 expression were associated with SLN metastasis. The predictive ability of a model that included these molecular variables in combination with clinicopathologic variables (patient age, Breslow depth, and tumor ulceration) was significantly greater than a model that only considered clinicopathologic variables and also performed well in the validation cohort (area under the curve, 0.93; 95% CI, 0.87 to 0.97; false-positive and false-negative rates of 22% and 0%, respectively, using a 10% cutoff for predicted SLN metastasis risk). Conclusion The addition of cell adhesion–linked gene expression variables to clinicopathologic variables improves the identification of patients with SLN metastases within 90 days of melanoma diagnosis.
Characteristics of participants consenting versus declining follow-up for up to 10 years in a randomized clinical trial
Background: With patients living a decade or longer post-procedure, long-term data are needed to assess the durability of carotid artery stenting versus carotid endarterectomy. Identifying characteristics of those consenting or declining to continue in long-term follow-up may suggest strategies to improve retention in clinical trials. Purpose: This report describes differences between patients choosing or declining to continue follow-up for up to 10 years in the Carotid Revascularization Endarterectomy versus Stenting Trial. Methods: Following completion of the primary outcome, patients who were in active Carotid Revascularization Endarterectomy versus Stenting Trial follow-up were asked to continue beyond their original 4-year commitment for a maximum of 10 years. The characteristics of those who consented were compared with those who declined. Univariate and multivariable logistic regression were used for analysis, and backwards stepwise logistic regression (the most parsimonious model) was used to determine the factors associated with continuation. Results: Of the 1921 active Carotid Revascularization Endarterectomy versus Stenting Trial participants for whom consent to extend follow-up was requested, 1695 (88%; mean age: 68.4) consented; 226 (12%; mean age: 69.6) declined. Of those who did not consent versus those who consented, 66% versus 48% were symptomatic at baseline (p < 0.0001), at follow-up 28% versus 20% were smokers (p = 0.009), 85% versus 90% were hypertensive (p = 0.01), and 84% versus 94% were dyslipidemic (p < 0.0001). Additional factors that differed between those who did not consent and those who consented included the mean number of years in the study at time of consent (4.8 years vs 3.7 years (p = <0.0001)) and patients from sites that enrolled <30 patients compared to sites randomizing 30 or more (70% vs 52% (p < 0.0001)). Multivariable logistic regression indicated that those with lesser odds of consenting to the extended follow-up were older (odds ratio: 0.80; 95% confidence interval: 0.67, 0.96), more likely to be symptomatic (odds ratio: 0.58; 95% confidence interval: 0.42, 0.80), smokers (odds ratio: 0.48; 95% confidence interval: 0.34, 0.70), were in the study 5+ years versus <3 (odds ratio: 0.21; 95% confidence interval: 0.13, 0.34), and at a site that randomized <30 patients (odds ratio: 0.46; 95% confidence interval: 0.33, 0.63), while patients with dyslipidemia at follow-up had increased odds of consenting (odds ratio: 2.28 (1.47, 3.54)). Conclusion: Symptomatic status, increasing age, randomized at lower volume centers, and longer time in follow-up were associated with reduced odds of consenting to long-term follow-up. Identifying factors associated with reduced willingness to extend participation long-term can suggest targeted strategies to improve retention in future clinical trials.