The Brain Protein Atlas: A conglomerate of proteomics datasets of human neural tissue.

The human brain represents one of the most complex biological structures with significant spatiotemporal molecular plasticity occurring through early development, learning, aging, and disease. While much progress has been made in mapping its transcriptional architecture, more downstream phenotypic readouts are relatively scarce due to limitations with tissue heterogeneity and accessibility, as well as an inability to amplify protein species prior to global -OMICS analysis. To address some of these barriers, our group has recently focused on using mass-spectrometry workflows compatible with small amounts of formalin-fixed paraffin-embedded tissue samples. This has enabled exploration into spatiotemporal proteomic signatures of the brain and disease across otherwise inaccessible neurodevelopmental timepoints and anatomical niches. Given the similar theme and approaches, we introduce an integrated online portal, "The Brain Protein Atlas (BPA)" (www.brainproteinatlas.org), representing a public resource that allows users to access and explore these amalgamated datasets. Specifically, this portal contains a growing set of peer-reviewed mass-spectrometry-based proteomic datasets, including spatiotemporal profiles of human cerebral development, diffuse gliomas, clinically aggressive meningiomas, and a detailed anatomic atlas of glioblastoma. One barrier to entry in mass spectrometry-based proteomics data analysis is the steep learning curve required to extract biologically relevant data. BPA, therefore, includes several built-in analytical tools to generate relevant plots (e.g., volcano plots, heatmaps, boxplots, and scatter plots) and evaluate the spatiotemporal patterns of proteins of interest. Future iterations aim to expand available datasets, including those generated by the community at large, and analytical tools for exploration. Ultimately, BPA aims to improve knowledge dissemination of proteomic information across the neuroscience community in hopes of accelerating the biological understanding of the brain and various maladies.

Mass Spectrometry-Based Assay for Targeting Fifty-Two Proteins of Brain Origin in Cerebrospinal Fluid.

Cerebrospinal fluid (CSF) is a circulatory fluid of the central nervous system and it can reflect the biochemical changes occurring in the brain. Although CSF retrieval through lumbar puncture is invasive, it remains the most commonly used fluid in exploring brain pathology as it is less complex and contains a higher concentration of brain-derived proteins than plasma (Reiber, H. Clin. Chim. Acta 2001, 310, 173-186; Macron et al. J. Proteome Res. 2018, 17, 4315-4319). We hypothesize that proteins produced by the brain will have diagnostic significance for brain pathologies. Hence, we expanded the previously in-house-developed 31-protein panel with more proteins classified as brain-specific by the Human Protein Atlas (HPA). Using the HPA, we selected 76 protein coding genes and screened CSF using liquid chromatography-mass spectrometry (LC-MS) and narrowed the protein list to candidates identified endogenously in CSF. Next, we developed a parallel reaction monitoring (PRM) assay for the 21 new proteins and merged it with the 31-protein assay developed earlier. In the process, we evaluated different screening strategies and optimized MS collision energies and ion isolation windows to achieve the highest possible analyte signal resulting in the PRM assay with an average linear dynamic range of 4.3 × 103. We also assessed the extent of Asn (N)-Gln (Q) deamidation, N-terminal pyro-Glu (E) conversion, and Met (M) oxidation and found that deamidation can be misassigned without high mass accuracy and high-resolution settings. We also assessed how many of these proteins could be reliably measured in 10 individual patient CSF samples. Our approach allows us to measure the relative levels of 52 brain-derived proteins in CSF by a single LC-MS method. This new assay may have important applications in discovering CSF biomarkers for various neurological diseases.

Mutations in normal tissues-some diagnostic and clinical implications.

BACKGROUND: It has long been known that mutations are at the core of many diseases, most notably cancer. Mutational analysis of tissues and fluids is useful for cancer and other disease diagnosis and management. MAIN BODY: The prevailing cancer development hypothesis posits that cancer originates from mutations in cancer-driving genes that accumulate in tissues over time. These mutations then confer special characteristics to cancer cells, known as the hallmarks of cancer. Mutations in specific driver genes can lead to the formation of cancerous subclones and mutation risk increases with age. New research has revealed an unexpectedly large number of mutations in normal tissues; these findings could have significant implications to the understanding of the pathobiology of cancer and for disease diagnosis and therapy. Here, we discuss how the prevalence of mutations in normal tissues provides novel and relevant insights about clonal development in cancer and other diseases. Specifically, this review will focus on discussing mutations in normal tissues in the context of developing specific, circulating tumor DNA (ctDNA) tests for cancer, and evaluating clonal hematopoiesis as a predictor of blood cancers and cardiovascular pathology, as well as their implications to the phenomena of neural mosaicism in the context of Alzheimer's disease. CONCLUSIONS: In view of these new findings, the fundamental differences between the accumulation of genetic alterations in healthy, aging tissues compared to cancer and cardiovascular or neural diseases will need to be better delineated in the future.

Circulating tumor DNA (ctDNA) is not a good proxy for liquid biopsies of tumor tissues for early detection.

The important conclusion that ctDNA is a mediocre proxy for liquid biopsies of tumor tissues for early detection was reached after new data were published recently in Nature Genetics. These data have shown that most mutations found in ctDNA are not related to tumor tissues but rather to the precancerous condition clonal hematopoiesis. Previously, our group has analyzed the sensitivity of the ctDNA test for early detection of cancer and concluded that the achievable sensitivity, especially for small tumors, is not enough to have clinical value. Now, the new data have shown a serious compromise in specificity. We believe that scientists who are interested in early cancer diagnostics should be aware of the limitations of this test, in both sensitivity and specificity. Our work may prompt further work aiming to alleviate these important issues in the cancer diagnostics field.

The democratization of scientific publishing.

Where should I submit my paper? This is a question that young scientists and trainees frequently ask. In this Commentary, we advise on how to make such a decision whilst balancing the risks and benefits. We argue that trying to publish in top tier journals may not always be the best option and that publishing in indexed, open access journals may expose research to the same or larger audiences. The value of research should not be judged according to the publishing journal's name, but rather from other measures of impact such as successful commercialization of new technologies, number of citations, and downloads. We also highlight the role of mentors, who have the responsibility to protect the long-term interests of their trainees by balancing the consequences of acceptances and rejections.

Benefits and harms of wellness initiatives.

Wellness projects are large scale studies of healthy individuals through extensive laboratory and other testing. The "Hundred Person Wellness Study", was one of the first to report results and lessons from its approach and these lessons can be applied to other wellness projects which are being undertaken by major companies and other organizations. In the "Hundred Person Wellness Study", investigators from the Institute for Systems Biology (ISB) sequenced the genome, and analyzed the blood, saliva, urine and microbiome of 108 healthy participants every 3 months, for 9 months, to look for subtle changes signifying the transition to disease. We discuss some of the possible shortcomings of this approach; questioning the need to "improve" biomarker levels, excessive testing leading to over-diagnosis and over-treatment, expected results and improvements, selection of tests, problems with whole genome sequencing and speculations on therapeutic measures. We hope this discussion will lead to a continued evaluation of wellness interventions, leading to strategies that truly benefit patients within the constraint of limited health care resources.

Utility of circulating tumor DNA in cancer diagnostics with emphasis on early detection.

Various recent studies have focused on analyzing tumor genetic material released into the blood stream, known as circulating tumor DNA (ctDNA). Herein, we describe current research on the application of ctDNA to cancer management, including prognosis determination, monitoring for treatment efficacy/relapse, treatment selection, and quantification of tumor size and disease burden. Specifically, we examine the utility of ctDNA for early cancer diagnostics focusing on the development of a blood test to detect cancer in asymptomatic individuals by sequencing and analyzing mutations in ctDNA. Next, we discuss the prospect of using ctDNA to test for cancer, and present our calculations based on previously published empirical findings in cancer and prenatal diagnostics. We show that very early stage (asymptomatic) tumors are not likely to release enough ctDNA to be detectable in a typical blood draw of 10 mL. Data are also presented showing that mutations in circulating free DNA can be found in healthy individuals and will likely be very difficult to distinguish from those associated with cancer.We conclude that the ctDNA test, in addition to its high cost and complexity, will likely suffer from the same issues of low sensitivity and specificity as traditional biomarkers when applied to population screening and early (asymptomatic) cancer diagnosis.

The meteoric rise and dramatic fall of Theranos: lessons learned for the diagnostic industry.

In this piece we discuss and reflect on the conclusion of the Theranos saga in the light of its fraud conviction. Theranos (founded in 2003 by Elizabeth Holmes) was supposed to disrupt the diagnostic testing industry by developing technology which could perform dozens of tests using a tiny amount of blood from a finger-prick. As a result, Ms. Holmes rose to fame, becoming the world's youngest female self-made billionaire and was plastered across magazine covers. However, in 2014, Theranos began to fall apart following increasingly damaging revelations regarding its lack of expertise, technology, framework, extreme secrecy and inaccurate test results. This led to the closure of two of its laboratories, investor and patient lawsuits and the devaluation of Ms. Holmes's wealth to nothing. In March 2018, the United States Security Exchange Commission ordered Ms. Holmes to pay $500,000 to settle the charge of massive fraud and barred her from being a director of a publicly owned company for 10 years, likely concluding Theranos's endeavors. We conclude our series of articles on this topic by reflecting on the lessons the laboratory medicine community can learn from Theranos.

Circulating tumor DNA for personalized lung cancer monitoring.

Advances in deep sequencing technology have led to developments in personalized medicine. Here, we describe the implications of a recent investigation that sequenced ctDNA from the plasma of non-small cell lung cancer patients to develop personalized ctDNA tests. These 'liquid biopsies' have shown promise in monitoring tumor growth and response to treatment, providing a timely overview of mutations present in the tumor. We discuss the advantages of this budding approach, as well as its challenges and drawbacks, while also providing areas for further investigation and an outlook for the future.

How to reduce scientific irreproducibility: the 5-year reflection.

We discuss in depth six causes of scientific irreproducibility and their ramifications for the clinical sciences: fraud, unfounded papers published by prominent authorities, bias, technical deficiencies, fragmented science and problems with big data. Some proposed methods to combat this problem are briefly described, including an effort to replicate results from some high impact papers and a proposal that authors include detailed preclinical data in papers with supposedly high translational value. We here advocate for a 5-year reflection on papers with seemingly high clinical/translational potential, published alongside the original paper where authors reflect on the quality, reproducibility and impact of their findings. These reflections can be used as a benchmark for credibility, and begin a virtuous cycle of improving the quality of published findings in the literature.

Evaluating ExpandED: Evaluating the effectiveness of a serious game expansion pack in teaching health professional students about interprofessional care.

Background: The emergency department (ED) is a challenging fast-paced environment with high-acuity, undifferentiated patients who often require extensive interdisciplinary care. This paper introduces ExpandED, an expansion pack to the serious board game GridlockED, designed to enhance players' understanding of interprofessional collaboration in the ED and the diverse scope of practice of different ED professionals including physicians, residents, registered nurses, registered practical nurses, social workers, occupational therapists, and physiotherapists. This investigation evaluates the effectiveness of ExpandED as a teaching tool for medical and allied health professions students about interprofessional collaboration in the ED. Methods: A program evaluation harnessing a playtest framework was employed. Participants completed pre- and postgame surveys including quantitative measures (e.g., Likert scales) and qualitative free-text feedback that focused on participant familiarity with ED functioning, valuation of interprofessional collaboration before and after playing, and feedback on game usability and effectiveness. Results: Recruitment was open to students in all health care and allied health professional programs at the institution. Forty-five participants were recruited from medical doctor, nursing, physiotherapy, and speech language pathology programs. ExpandED enhances participants' understanding of ED workflow (p < 0.001) and provides an enjoyable playing experience. However, participants' valuation of interdisciplinary teamwork did not change significantly before and after game play (p = 0.17). Participants expressed satisfaction with the game's accuracy in simulating the ED environment and appreciated the opportunity to collaborate with peers from different disciplines. Challenges reported included some tension among players, potential biases, and limitations of fidelity to a real-life ED. Conclusions: While this study has limitations regarding participant sampling and duration of gameplay sessions, it highlights the potential of ExpandED for teaching interprofessional collaboration in the ED. These findings will guide further development to optimize the expansion pack's effectiveness and its implementation into health care curricula.

Parenting and Childbearing in Neurosurgical Residency: Perspectives from the United States and Canada.

BACKGROUND: Despite growing interest in family planning alongside surgical training, significant barriers exist including time constraints, stigma, and lack of paid leave and formal policies. We currently lack a deep understanding of the challenges residents face and how practice cultures may prohibit successful policy enactment. OBJECTIVE: To investigate residents' perspectives surrounding parenting and childbearing during neurosurgical residency in the United States and Canada. METHODS: A cross-sectional, qualitative study methodology was used, including focus groups with neurosurgical residents. Purposive sampling was employed to capture a broad range of perspectives including stage of training, geographical location, and gender. Data collection and analysis occurred in parallel, using a thematic analysis approach. Data collection continued until no new themes relating to the research questions were identified. RESULTS: Notable challenges included lack of formal family leave policies, time constraints, insufficient clinical human resources, physical health concerns, lack of lactation accommodations, and lack of mentorship. A subset of barriers were uncovered that stem specifically from workplace cultures, including gender norms, difficulty in asking for help, concerns for inconveniencing others, and pressures to time parental leave during research blocks. Several positive changes were identified including growing awareness and female representation, and benefits of the dual surgeon-parent identity. CONCLUSION: While parenting during neurosurgery residency is becoming increasingly common, significant practical and cultural barriers persist including a marked absence of formal policies. Culture shifts are essential in ensuring opportunities for life outside of medicine for all residents, irrespective of family status.