Advancing brain barriers RNA sequencing: guidelines from experimental design to publication

Background: RNA sequencing (RNA-Seq) in its varied forms has become an indispensable tool for analyzing differential gene expression and thus characterization of specific tissues. Aiming to understand the brain barriers genetic signature, RNA seq has also been introduced in brain barriers research. This has led to availability of both, bulk and single-cell RNA-Seq datasets over the last few years. If appropriately performed, the RNA-Seq studies provide powerful datasets that allow for significant deepening of knowledge on the molecular mechanisms that establish the brain barriers. However, RNA-Seq studies comprise complex workflows that require to consider many options and variables before, during and after the proper sequencing process.Main body: In the current manuscript, we build on the interdisciplinary experience of the European PhD Training Network BtRAIN (https://www.btrain-2020.eu/) where bioinformaticians and brain barriers researchers collaborated to analyze and establish RNA-Seq datasets on vertebrate brain barriers. The obstacles BtRAIN has identified in this process have been integrated into the present manuscript. It provides guidelines along the entire workflow of brain barriers RNA-Seq studies starting from the overall experimental design to interpretation of results. Focusing on the vertebrate endothelial blood–brain barrier (BBB) and epithelial blood-cerebrospinal-fluid barrier (BCSFB) of the choroid plexus, we provide a step-by-step description of the workflow, highlighting the decisions to be made at each step of the workflow and explaining the strengths and weaknesses of individual choices made. Finally, we propose recommendations for accurate data interpretation and on the information to be included into a publication to ensure appropriate accessibility of the data and reproducibility of the observations by the scientific community.Conclusion: Next generation transcriptomic profiling of the brain barriers provides a novel resource for understanding the development, function and pathology of these barrier cells, which is essential for understanding CNS homeostasis and disease. Continuous advancement and sophistication of RNA-Seq will require interdisciplinary approaches between brain barrier researchers and bioinformaticians as successfully performed in BtRAIN. The present guidelines are built on the BtRAIN interdisciplinary experience and aim to facilitate collaboration of brain barriers researchers with bioinformaticians to advance RNA-Seq study design in the brain barriers community

Are patient-reported outcomes useful in post-treatment follow-up care for women with early breast cancer? A scoping review

Cathrine Lundgaard Riis,1–3 Troels Bechmann,1,2 Pernille Tine Jensen,4,5 Angela Coulter,2,3,6 Karina Dahl Steffensen1–3 1Department of Oncology, Vejle Hospital, Vejle, Denmark; 2Institute of Regional Health Research, Faculty of Health Sciences, University of Southern Denmark, Odense, Denmark; 3Center for Shared Decision Making, Vejle, Denmark; 4Department of Gynecology and Obstetrics, Odense University Hospital, Odense, Denmark; 5Department of Clinical Research, University of Southern Denmark, Odense, Denmark; 6Nuffield Department of Population Health, University of Oxford, Oxford, UK Background: Patient-reported outcomes (PROs) are frequently used to evaluate treatment effects and quality of life in clinical trials. The application of PROs in breast cancer clinics is evolving but their use to generate real-time information for use in follow-up care is uncommon. This proactive use might help to shift healthcare delivery toward a more patient-centered approach by acting as a screening tool for unmet needs or a dialogue tool to discuss issues proposed by the patient.Aims: This review aims to determine the effects and feasibility of using PROs proactively during follow-up care in early breast cancer.Materials and methods: A systematic search was conducted in January 2019 in PubMed, Cochrane Library, Embase, and CINAHL. Studies that exclusively concerned women treated for early breast cancer where PROs were used as a proactive tool during follow-up were included.Results: The search revealed a total of 653 records and four eligible studies were identified; three of which concerned the use of PROs both as a screening tool and as a dialogue tool, and one study in which PROs were used solely as a screening tool. The studies explored the feasibility of collecting and integrating PROs in the clinic and their ability to detect otherwise unrecognized problems. All of the included studies were prone to bias, but they point to potential benefits in respect of better symptom management in follow-up care.Conclusion: Our search identified a small number of low to moderate quality studies of the proactive use of PROs during follow-up after treatment for early stage breast cancer. The limited evidence available suggests that PROs may be useful for providing a more complete picture of the patient’s symptoms and problems, possibly leading to improvements in symptom management. Keywords: proactive, patient-reported outcome, PRO, breast cancer, follow-u