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Background: Cancer immunotherapy via immune-checkpoint inhibition (ICI) by antibodies against cytotoxic T-lymphocyte-associated protein 4 (CTLA-4) and cell death protein 1 (PD-1) have significantly improved the outcome of metastasized melanoma and of a rapidly increasing number of other cancer types. The anti-tumor effect is often accompanied by immune-related adverse events (irAE). Hematological irAE, specifically neutropenia, are rarely observed. However, neutropenia is associated with high morbidity and mortality due to infection complications. Thus, early detection and treatment is crucial., Methods: We present the clinical course of two patients with severe neutropenia after ICI therapy and demonstrate the difficulty of the diagnosis when a comedication of metamizole, a well-known analgesic drug used to treat cancer pain, is present. Further, we provide a comprehensive descriptive and statistical analysis of published data on diagnostics, treatment and infection complication in patients with at least grade 4 neutropenia by a systematic database search., Results: Finally, 34 patients were analyzed, including the two case reports from our cohort. The median onset of neutropenia was 10.5 weeks after first ICI administration (interquartile range: 6 weeks). In 76% (N = 26), a normalization of the neutrophil count was achieved after a median duration of neutropenia of 13 days. In a subsample of 22 patients with detailed data, the infection rate was 13%, proven by positive blood culture in 3 cases, but 68% (N = 15) presented with fever > 38 °C. Treatment regime differed relevantly, but mainly included G-CSF and intravenous corticosteroids. Death was reported in 14 patients (41%), 3 of whom (9%) were associated with hematological irAE but only two directly associated with neutropenia., Conclusion: With an increasing number of cancer patients eligible to ICI therapy, the incidence of severe hematological toxicities may rise substantially over the next years. Clinicians working in the field of cancer immune therapies should be aware of neutropenia as irAE to provide immediate treatment.

As accessing, collecting, and storing personal information become increasingly easier, the secondary use of data has the potential to make healthcare research more cost and time effective. The widespread reuse of data, however, raises important ethical and policy issues, especially because of the sensitive nature of genetic and health-related information. Regulation is thus crucial to determine the conditions upon which data can be reused. In this respect, the question emerges whether it is appropriate to endorse genetic exceptionalism and grant genetic data an exceptional status with respect to secondary use requirements. Using Swiss law as a case study, it is argued that genetic exceptionalism in secondary use regulation is not justified for three reasons. First, although genetic data have particular features, also other non-genetic data can be extremely sensitive. Second, having different regulatory requirements depending on the nature of data hinders the creation of comprehensible consent forms. Third, empirical evidence about public preferences concerning data reuse suggests that exceptional protection for genetic data alone is not justified. In this sense, it is claimed that regulation concerning data reuse should treat genetic data as important, but not exceptional., (Copyright © 2019 Martani, Geneviève, Pauli-Magnus, McLennan and Elger.)

Biorespositories of formalin-fixed and paraffin-embedded (FFPE) or fresh frozen human tissues from malignant diseases generated as integral part of the diagnostic workup in many pathology departments have been pivotal resources for translational cancer studies. However, such tissue biobanks have traditionally contained only non-viable specimens and thus cannot enable functional assays for the discovery and validation of therapeutic targets or the assessment of drug responses and resistance to treatment. To overcome these limitations, we have developed a next-generation comprehensive biobanking platform that includes the generation of patient-derived in vitro cell models from colorectal, pancreatic and kidney cancers among others. As such patient-derived cell (PDC) models retain important features of the original human tumors, they have emerged as relevant tools for more dynamic clinical and experimental analyses of cancer. Here, we describe details of the complex processes of acquisition and processing of patient-derived samples, propagation, annotation, characterization and distribution of resulting cell models and emphasize the requirements of quality assurance, organizational considerations and investment into resources. Taken together, we show how clinical tissue collections can be taken to the next level thus promising major new opportunities for understanding and treating cancer in the context of precision medicine., (Copyright © 2019 Bolck, Pauli, Göbel, Mühlbauer, Dettwiler, Moch and Schraml.)

Terpenes are responsible for most or all of the odor and flavor properties of Cannabis sativa, and may also impact effects users experience either directly or indirectly. We report the diversity of terpene profiles across samples bound for the Washington dispensary market. The remarkable degree of variation in terpene profiles ultimately results from action of a family of terpene synthase genes, only some of which have been described. Using a recently available genome assembly we describe 55 terpene synthases with genomic context, and tissue specific expression. The family is quite diverse from a protein similarity perspective, and subsets of the family are expressed in all tissues in the plant, including a set of root specific monoterpene synthases that could well have agronomic importance. Ultimately understanding and breeding for specific terpene profiles will require a good understanding of the gene family that underlies it. We intend for this work to serve as a foundation for that., Competing Interests: I have read the journal's policy and the authors of this manuscript have the following competing interests: RG is a member of the boards for PDX, Biomedcan and Rylies Smile Foundation and the advisory board for the California Cannabis Industry Association, was given an honorarium for speaking at the Cannabis Science Conference East, 2019, and has a personal relationship with Greg Copenhaver, Editor-in-Chief for PLoS Genetics. KJM owns stock on Medicinal Genomics, a Cannabis DNA sequencing and Cannabis microbial focused company. KDA, CP, JR and AT declare no competing interests.This does not alter our adherence to PLOS ONE policies on sharing data and materials.

Excessive consumption of beverages sweetened with high-fructose corn syrup (HFCS) is associated with obesity and with an increased risk of colorectal cancer. Whether HFCS contributes directly to tumorigenesis is unclear. We investigated the effects of daily oral administration of HFCS in adenomatous polyposis coli (APC) mutant mice, which are predisposed to develop intestinal tumors. The HFCS-treated mice showed a substantial increase in tumor size and tumor grade in the absence of obesity and metabolic syndrome. HFCS increased the concentrations of fructose and glucose in the intestinal lumen and serum, respectively, and the tumors transported both sugars. Within the tumors, fructose was converted to fructose-1-phosphate, leading to activation of glycolysis and increased synthesis of fatty acids that support tumor growth. These mouse studies support the hypothesis that the combination of dietary glucose and fructose, even at a moderate dose, can enhance tumorigenesis., (Copyright © 2019 The Authors, some rights reserved; exclusive licensee American Association for the Advancement of Science. No claim to original U.S. Government Works.)

Background: The preparation of a randomized controlled trial (RCT) requires substantial resources and the administrative processes can be burdensome. To facilitate the conduct of RCTs it is important to better understand cost drivers. In January 2014 the enactment of the new Swiss Legislation on Human Research (LHR) considerably changed the regulatory framework in Switzerland. We assess if the new LHR was associated with change in (i) resource use and costs to prepare an RCT, and (ii) approval times with research ethics committees (RECs) and the regulatory authority Swissmedic., Methods: We surveyed investigators of RCTs which were approved by RECs in 2012 or in 2016 and asked for RCT preparation costs using a pre-specified item list. Additionally, we collected approval times from RECs and Swissmedic., Results: The response rates of the investigator survey were 8.3% (19/228) for 2012 and 16.5% (47/285) in 2016. The median preparation cost of an RCT was USD 72,400 (interquartile range [IQR]: USD 59,500-87,700; n = 18) in 2012 and USD 72,600 (IQR: USD 42,800-169,600; n = 35) in 2016. For single centre RCTs a median REC approval time of 82 (IQR: 49-107; n = 38) days in 2012 and 92 (IQR: 65-131; n = 63) days in 2016 was observed. The median Swissmedic approval time for any clinical trial was 27 (IQR: 19-51; n = 213) days in 2012 and 49 (IQR: 36-67; n = 179) days in 2016. The total duration for achieving RCT approval from both authorities (REC and Swissmedic) in the parallel submission procedure applied in 2016 could not be assessed., Conclusion: Based on limited data the costs to plan and prepare RCTs in Switzerland were approximately USD 72,000 in 2012 and 2016. For effective and valid research on costs and approval times of RCTs a greater willingness to share cost information among investigators and more collaboration between stakeholders with data linkage is necessary., Competing Interests: All authors have declared that no competing interests exist. The funder of this study (Swiss Federal Office of Public Health) has implemented the new law on research with human beings (Human Research Act, HRA) and its ordinances (Swiss Legislation on Human Research, LHR) which is evaluated within this study. This does not alter our adherence to PLOS ONE policies on sharing data and materials.

Purpose: We developed a precision medicine program for patients with advanced cancer using integrative whole-exome sequencing and transcriptome analysis., Patients and Methods: Five hundred fifteen patients with locally advanced/metastatic solid tumors were prospectively enrolled, and paired tumor/normal sequencing was performed. Seven hundred fifty-nine tumors from 515 patients were evaluated., Results: Most frequent tumor types were prostate (19.4%), brain (16.5%), bladder (15.4%), and kidney cancer (9.2%). Most frequently altered genes were TP53 (33%), CDKN2A (11%), APC (10%), KTM2D (8%), PTEN (8%), and BRCA2 (8%). Pathogenic germline alterations were present in 10.7% of patients, most frequently CHEK2 (1.9%), BRCA1 (1.5%), BRCA2 (1.5%), and MSH6 (1.4%). Novel gene fusions were identified, including a RBM47-CDK12 fusion in a metastatic prostate cancer sample. The rate of clinically relevant alterations was 39% by whole-exome sequencing, which was improved by 16% by adding RNA sequencing. In patients with more than one sequenced tumor sample (n = 146), 84.62% of actionable mutations were concordant., Conclusion: Integrative analysis may uncover informative alterations for an advanced pan-cancer patient population. These alterations are consistent in spatially and temporally heterogeneous samples., Competing Interests: AUTHORS’ DISCLOSURES OF POTENTIAL CONFLICTS OF INTEREST The following represents disclosure information provided by authors of this manuscript. All relationships are considered compensated. Relationships are self-held unless noted. I = Immediate Family Member, Inst = My Institution. Relationships may not relate to the subject matter of this manuscript. For more information about ASCO’s conflict of interest policy, please refer to www.asco.org/rwc or ascopubs.org/po/author-center. Alexandros Sigaras Employment: Weill Cornell Medical College Loredana Puca Employment: Petra Pharma Corporation Bishoy M. Faltas Honoraria: Digital Science Press publications Research Funding: Eli Lilly David Rickman Research Funding: Janssen Oncology Eleni Andreopoulou Honoraria: AstraZeneca, Sirtex, SVB Leerink, AbbVie, Eisai, NanoString Technologies Consulting or Advisory Role: AstraZeneca, Sirtex, SVB Leerink, AbbVie, Eisai, NanoString Technologies Speakers’ Bureau: R-Pharm US Travel, Accommodations, Expenses: AstraZeneca, Sirtex, SVB Leerink, AbbVie, Eisai, NanoString Technologies Kevin Holcomb Research Funding: Fujirebio Diagnostics Expert Testimony: Johnson & Johnson Linda T. Vahdat Honoraria: Polyphor, R-Pharm, Athenex, Seattle Genetics, Osmol Therapeutics Consulting or Advisory Role: Berg Pharma Speakers’ Bureau: Eisai Research Funding: Polyphor (Inst), Immunomedics (Inst), Seattle Genetics (Inst) Patents, Royalties, Other Intellectual Property: Patent pending on the application for BMD progenitor cells (Inst) Douglas S. Scherr Research Funding: Urogen Pharma (Inst), Cepheid (Inst), Anchiano (Inst), CryoLife (Inst) Koen van Besien Stock and Other Ownership Interests: Hemogenyx Consulting or Advisory Role: Hemogenyx, Actinium Pharmaceuticals, Cellectis, Tessa Therapeutics Research Funding: Miltenyi Biotec, Actinium Pharmaceuticals, Juno Therapeutics, Fate Therapeutics Christopher E. Barbieri Patents, Royalties, Other Intellectual Property: Coinventor on a patent application filed regarding SPOP mutations in prostate cancer by Weill Cornell Medicine Brian D. Robinson Consulting or Advisory Role: Bristol-Myers Squibb Patents, Royalties, Other Intellectual Property: Methods for diagnosing and treating prostate cancer Allyson J. Ocean Consulting or Advisory Role: Celgene, Tyme Speakers’ Bureau: Daiichi Sankyo Travel, Accommodations, Expenses: Daiichi Sankyo Ana Molina Honoraria: American Society of Clinical Oncology Consulting or Advisory Role: Eisai, Exelixis, Novartis, Janssen Oncology Manish A. Shah Consulting or Advisory Role: Astellas Pharma, Eli Lilly Research Funding: Gilead Sciences (Inst), Merck (Inst), Boston Biomedical (Inst), Oncolys BioPharma (Inst), Bristol-Myers Squibb (Inst) David M. Nanus Consulting or Advisory Role: Genentech Research Funding: Novartis (Inst), Boehringer Ingelheim (Inst), Zenith Epigenetics (Inst) Qiulu Pan Employment: Caris Life Sciences Stock and Other Ownership Interests: Caris Life Sciences Francesca Demichelis Patents, Royalties, Other Intellectual Property: Co-inventor on a patent filed by the University of Michigan and Brigham and Women’s Hospital covering the diagnostic and therapeutic fields for ETS fusions in prostate cancer, diagnostic field licensed to Gen-Probe Scott T. Tagawa Consulting or Advisory Role: Medivation, Astellas Pharma, Dendreon, Janssen Oncology, Bayer, Genentech, Endocyte, Immunomedics, Karyopharm Therapeutics, AbbVie, Tolmar, QED, Amgen, Sanofi, Pfizer Research Funding: Eli Lilly (Inst), Sanofi (Inst), Janssen Oncology (Inst), Astellas Pharma (Inst), Progenics (Inst), Millennium Pharmaceuticals (Inst), Amgen (Inst), Bristol-Myers Squibb (Inst), Dendreon (Inst), Rexahn Pharmaceuticals (Inst), Bayer (Inst), Genentech (Inst), Newlink Genetics (Inst), Inovio Pharmaceuticals (Inst), AstraZeneca (Inst), Immunomedics (Inst), Novartis (Inst), AVEO (Inst), Boehringer Ingelheim (Inst), Merck (Inst), Stem CentRx (Inst), Karyopharm Therapeutics (Inst), AbbVie (Inst), Medivation (Inst), Endocyte (Inst), Exelixis (Inst), Clovis Oncology (Inst) Travel, Accommodations, Expenses: Sanofi, Immunomedics, Amgen Wei Song Employment: Genentech (I), Cytokinetics (I) Honoraria: Foundation Medicine, Loxo Consulting or Advisory Role: Foundation Medicine, Loxo Juan Miguel Mosquera Research Funding: Personal Genome Diagnostics Travel, Accommodations, Expenses: Personal Genome Diagnostics Mark A. Rubin Honoraria: F Hoffmann-La Roche, Novartis, Astellas Pharma Research Funding: Eli Lilly, Janssen Oncology, Millennium Pharmaceuticals, Sanofi Patents, Royalties, Other Intellectual Property: US Patent (7,767,393 and 7,229,774), Expression Profile of Prostate Cancer, 2007; US Patent (7,332,290), Detection of AMACR Cancer Markers in Urine, 2008; US Patent (7,718,369), Recurrent Gene Fusions in Prostate Cancer, 2010; US Patent (7,803,552 and 7,666,595), Biomarkers for Predicting Prostate Cancer Progression, 2010; US Patent (7,981,609 B2), Methods for Identifying and Using SNP Panels, 2011; US Patent (8,106,037 B2), Identification and Treatment of Estrogen Responsive PCa, 2012; US Patent (9,090,899 B2), Methods of Diagnosing and Treating Prostate Cancer Characterized by NDRG1-ERG Fusion, 2015; US Patent (9,458,213 B2), Compositions and Methods for Diagnosing Prostate Cancer Based on Detection of SLC45A3-ELK4 Fusion Transcript, 2016; US Patent (9,568,483 B2), Molecular Subtyping, Prognosis and Treatment of Prostate Cancer, 2017; US Patent (9,678,077 B2), ERG/TFF3/HMWCK Triple Immunostain for Detection of Prostate Cancer, 2017; US Patent (61,408,341), Exploration of Novel Gene Fusion in Prostate Cancer by RNA-Seq Travel, Accommodations, Expenses: F Hoffmann-La Roche, Novartis, Astellas Pharma Olivier Elemento Stock and Other Ownership Interests: Volastra, Owkin, One Three Biotech Himisha Beltran Consulting or Advisory Role: Janssen Oncology, Genzyme, GlaxoSmithKline, AbbVie, Astellas Pharma, AstraZeneca Research Funding: Janssen Oncology (Inst), AbbVie (Inst), Stemcentrx (Inst), Eli Lilly (Inst) Travel, Accommodations, Expenses: Janssen Oncology No other potential conflicts of interest were reported.

Background: Biomedical research has recently moved through three stages in digital healthcare: (1) data collection; (2) data sharing; and (3) data analytics. With the explosion of stored health data (HD), dental medicine is edging into its fourth stage of digitization using artificial intelligence (AI). This narrative literature review outlines the challenge of managing HD and anticipating the potential of AI in oral healthcare and dental research by summarizing the current literature., Summary: The basis of successful management of HD is the establishment of a generally accepted data standard that will guide its implementation within electronic health records (EHR) and health information technology ecosystems (HIT Eco). Thereby continuously adapted (self-) learning health systems (LHS) can be created. The HIT Eco of the future will combine (i) the front-end utilization of HD in clinical decision-making by providers using supportive diagnostic tools for patient-centered treatment planning, and (ii) back-end algorithms analyzing the standardized collected data to inform population-based policy decisions about resource allocations and research directions. Cryptographic methods in blockchain enable a safe, more efficient, and effective dental care within a global perspective. Key Message: The interoperability of HD with accessible digital health technologies is the key to deliver value-based dental care and exploit the tremendous potential of AI., (© 2019 S. Karger AG, Basel.)

In this Letter, author Xing Du was incorrectly listed as Du Xing; this has been corrected online.

Population-based linkage of patient-level information opens new strategies for dental research to identify unknown correlations of diseases, prognostic factors, novel treatment concepts and evaluate healthcare systems. As clinical trials have become more complex and inefficient, register-based controlled (clinical) trials (RC(C)T) are a promising approach in dental research. RC(C)Ts provide comprehensive information on hard-to-reach populations, allow observations with minimal loss to follow-up, but require large sample sizes with generating high level of external validity. Collecting data is only valuable if this is done systematically according to harmonized and inter-linkable standards involving a universally accepted general patient consent. Secure data anonymization is crucial, but potential re-identification of individuals poses several challenges. Population-based linkage of big data is a game changer for epidemiological surveys in Public Health and will play a predominant role in future dental research by influencing healthcare services, research, education, biotechnology, insurance, social policy and governmental affairs.

Mutations in PIK3CA, which encodes the p110α subunit of the insulin-activated phosphatidylinositol-3 kinase (PI3K), and loss of function mutations in PTEN, which encodes a phosphatase that degrades the phosphoinositide lipids generated by PI3K, are among the most frequent events in human cancers 1,2 . However, pharmacological inhibition of PI3K has resulted in variable clinical responses, raising the possibility of an inherent mechanism of resistance to treatment. As p110α mediates virtually all cellular responses to insulin, targeted inhibition of this enzyme disrupts glucose metabolism in multiple tissues. For example, blocking insulin signalling promotes glycogen breakdown in the liver and prevents glucose uptake in the skeletal muscle and adipose tissue, resulting in transient hyperglycaemia within a few hours of PI3K inhibition. The effect is usually transient because compensatory insulin release from the pancreas (insulin feedback) restores normal glucose homeostasis 3 . However, the hyperglycaemia may be exacerbated or prolonged in patients with any degree of insulin resistance and, in these cases, necessitates discontinuation of therapy 3-6 . We hypothesized that insulin feedback induced by PI3K inhibitors may reactivate the PI3K-mTOR signalling axis in tumours, thereby compromising treatment effectiveness 7,8 . Here we show, in several model tumours in mice, that systemic glucose-insulin feedback caused by targeted inhibition of this pathway is sufficient to activate PI3K signalling, even in the presence of PI3K inhibitors. This insulin feedback can be prevented using dietary or pharmaceutical approaches, which greatly enhance the efficacy/toxicity ratios of PI3K inhibitors. These findings have direct clinical implications for the multiple p110α inhibitors that are in clinical trials and provide a way to increase treatment efficacy for patients with many types of tumour.

Avascular (Avas) meniscus regeneration remains a challenge, which is partly a consequence of our limited knowledge of the cells that maintain this tissue region. In this study, we utilized microarrays to characterize gene expression profiles of intact human Avas meniscus tissue and of cells following culture expansion. Using these data, we examined various 3D culture conditions to redifferentiate Avas cells toward the tissue phenotype. RNA was isolated from either the tissue directly or following cell isolation and 2 weeks in monolayer culture. RNA was hybridized on human genome arrays. Differentially expressed (DE) genes were identified by ranking analysis. DAVID pathway analysis was performed and visualized using STRING analysis. Quantitative PCR (qPCR) on additional donor menisci (tissues and cells) were used to validate array data. Avas cells cultured in 3D were subjected to qPCR to compare with the array-generated data. A total of 387 genes were DE based on differentiation state (>3-fold change; p < 0.01). In Avas-cultured cells, the upregulated pathways included focal adhesion, ECM-receptor interaction, regulation of actin cytoskeleton, and PDGF Signaling. In 3D-cultured Avas cells, TGFβ1 or combinations of TGFβ1 and BMP6 were most effective to promote an Avas tissue phenotype. THBS2 and THBS4 expression levels were identified as a means to denote meniscus cell phenotype status. We identified the key gene expression profiles, new markers and pathways involved in characterizing the Avas meniscus phenotype in the native state and during in vitro dedifferentiation and redifferentiation. These data served to screen 3D conditions to generate meniscus-like neotissues. © 2018 Orthopaedic Research Society. Published by Wiley Periodicals, Inc. J Orthop Res 36:1947-1958, 2018., (© 2018 Orthopaedic Research Society. Published by Wiley Periodicals, Inc.)

A major hurdle in the study of rare tumors is a lack of existing preclinical models. Neuroendocrine prostate cancer is an uncommon and aggressive histologic variant of prostate cancer that may arise de novo or as a mechanism of treatment resistance in patients with pre-existing castration-resistant prostate cancer. There are few available models to study neuroendocrine prostate cancer. Here, we report the generation and characterization of tumor organoids derived from needle biopsies of metastatic lesions from four patients. We demonstrate genomic, transcriptomic, and epigenomic concordance between organoids and their corresponding patient tumors. We utilize these organoids to understand the biologic role of the epigenetic modifier EZH2 in driving molecular programs associated with neuroendocrine prostate cancer progression. High-throughput organoid drug screening nominated single agents and drug combinations suggesting repurposing opportunities. This proof of principle study represents a strategy for the study of rare cancer phenotypes.

Background: Compelling evidence has demonstrated that a large proportion of investment in biomedical research is wasted; this waste is avoidable. Academic institutions have, thus far, shown limited response to recommendations for increasing value and reducing waste. We formulated an academic response by (i) achieving consensus across a wide range of stakeholder groups on a comprehensive framework for quality of patient-oriented clinical research and (ii) highlighting first successful examples of its operationalization to facilitate waste-reducing strategies at academic institutions., Methods and Findings: Based on a systematic review of quality definitions, concepts, and criteria in the medical literature (systematic MEDLINE search up to February 15, 2015, with independent and in duplicate article selection) and on stakeholder websites from 13 countries (Australia, Austria, Canada, France, Germany, Italy, Japan, Norway, Spain, Sweden, Switzerland, United Kingdom, and United States), we systematically developed a comprehensive framework for the quality of clinical research. We identified websites through personal contacts with experts in clinical research or public health who also suggested, for each country, websites of the following 7 stakeholder groups: patient organizations; academic research infrastructures; governmental bodies; regulatory agencies; ethics committees; the pharmaceutical industry; and funding agencies. In addition, we searched websites of inter- or supranational bodies involved in clinical research until no further insights emerged. After consolidation of the identified definitions, concepts, and criteria of quality in a basic framework structure, we conducted 4 rounds of an adapted online Delphi process among the same 7 stakeholder groups from 16 countries. The Delphi process ultimately achieved consensus on structure and content. The framework addresses 5 study stages (concept, planning and feasibility, conduct, analysis and interpretation, and reporting and knowledge translation) and includes the following dimensions: (i) protection of patient safety and rights, (ii) relevance/patient centeredness and involvement, (iii) minimization of bias (internal validity), (iv) precision, (v) transparency/access to data, and (vi) generalizability (external validity) of study results. These dimensions interact with 2 promoters-infrastructure and sustainability through education-that include a set of factors that may enhance all listed quality dimensions. Each quality dimension contains specific questions and explanatory items that guide quality assessment at each research stage from conceptualization of the research question through reporting and knowledge translation of study results. In the last survey round, Delphi participants from 9 countries (Austria, Australia, Canada, Germany, Italy, the Netherlands, Switzerland, UK, and US) agreed on the structure, content, and wording of the research stages, quality dimensions, specific questions, and descriptive examples of the final framework. In Switzerland, INQUIRE has resulted in a roadmap that guides initiatives to increase value within the Swiss Clinical Trial Organization network and through affiliated researchers., Conclusions: We present a framework based on a consensus of different stakeholder groups guiding the practical assessment of clinical research quality at all stages of a research project. Operationalization of this common structure will support the increase of value by guiding academic institutions and researchers in developing quality enhancement initiatives, from posing the right research question to the transparent publication of results., Competing Interests: The authors have declared that no competing interests exist.

While the majority of phosphatidylinositol-4, 5-bisphosphate (PI-4, 5-P 2 ) in mammalian cells is generated by the conversion of phosphatidylinositol-4-phosphate (PI-4-P) to PI-4, 5-P 2 , a small fraction can be made by phosphorylating phosphatidylinositol-5-phosphate (PI-5-P). The physiological relevance of this second pathway is not clear. Here, we show that deletion of the genes encoding the two most active enzymes in this pathway, Pip4k2a and Pip4k2b, in the liver of mice causes a large enrichment in lipid droplets and in autophagic vesicles during fasting. These changes are due to a defect in the clearance of autophagosomes that halts autophagy and reduces the supply of nutrients salvaged through this pathway. Similar defects in autophagy are seen in nutrient-starved Pip4k2a -/- Pip4k2b -/- mouse embryonic fibroblasts and in C. elegans lacking the PI5P4K ortholog. These results suggest that this alternative pathway for PI-4, 5-P 2 synthesis evolved, in part, to enhance the ability of multicellular organisms to survive starvation., (Copyright © 2018 Elsevier Inc. All rights reserved.)

A prominent 2014 series by The Lancet on "Increasing value, reducing waste in biomedical research" provided recommendations on how to optimise precious resources, including in clinical research. Despite being ideally placed to lead the movement in patient-oriented clinical research, academia struggles to take corresponding measures and find ways to evaluate their impact. A decade ago, Swiss stakeholders established constructive initiatives to improve the quality of clinical research, including a national Clinical Trial Unit (CTU) Network, predominantly rooted in university hospitals. At the 10th anniversary of this network (2007-2017), we reflect on the CTUs' trajectory and review whether - and how - they have been successful in improving the value of clinical research conducted in Switzerland. Anonymised surveys with involved clinical research stakeholder institutions and CTU customers at university hospitals suggest that the CTU Network has positively influenced the quality of academic clinical research. Future goals should include standardised education on Good Clinical Practice; the establishing of an audit function; the positioning of the network as an "entrance gate" for international trials; and support for young scientists launching their careers. Although stakeholder feedback has been very positive, praise does not constitute a standardised measure of the actual impact of CTU services. Beyond that, a broad understanding and practical guidance on how to increase value in academic clinical research are still lacking. We conclude with ways forward, including "INcreasing QUality In clinical Research" (INQUIRE), a comprehensive framework for the practical assessment of quality in academia developed by the CTU Basel. INQUIRE, founded on consensus across international and Swiss stakeholders, outlines six key quality dimensions to be fulfilled study-wide and is available for all relevant parties involved. INQUIRE encourages academic institutions to adopt waste-reducing strategies and strives to build an evidence-based clinical research landscape in Switzerland, with national and international influence.

Objectives: Randomized clinical trials (RCTs) are costly and published information on resource requirements for their conduct is limited. To identify key factors for making RCTs more sustainable, empirical data on resource use and associated costs are needed. We aimed to retrospectively assess resource use and detailed costs of two academic, investigator-initiated RCTs using a comprehensive list of cost items., Study Design and Setting: The resource use of two investigator-initiated RCTs (Prednisone-Trial [NCT00973154] and Oxantel-Trial [ISRCTN54577342]) was empirically assessed in a standardized manner through semistructured interviews and a systematically developed cost item list. Using information about yearly salaries, resource use was translated into costs. In addition, we collected all "other costs" including fixed priced items. Overall costs as well as cost of different study phases were calculated., Results: The personnel time used in the Prednisone-Trial trial was approximately 2,897 working days and the overall costs were calculated to be USD 2.3 million, which was USD 700,000 more than planned. In the Oxantel-Trial 798 working days were spent and the overall costs were as originally planned USD 100,000. Cost drivers were similar between the two RCTs with recruitment delays explaining the additional costs in the Prednisone-Trial., Conclusion: This case study provides an example of how to transparently assess resources and costs of RCTs and presents detailed empirical data on type and magnitude of expenses. In the future, this model approach may serve others to plan, assess, or monitor resource use and costs of RCTs., (Copyright © 2017 Elsevier Inc. All rights reserved.)

Objectives: Randomized clinical trials (RCTs) are costly. We aimed to provide a systematic overview of the available evidence on resource use and costs for RCTs to support budget planning., Study Design and Setting: We systematically searched MEDLINE, EMBASE, and HealthSTAR from inception until November 30, 2016 without language restrictions. We included any publication reporting empirical data on resource use and costs of RCTs and categorized them depending on whether they reported (i) resource and costs of all aspects at all study stages of an RCT (including conception, planning, preparation, conduct, and all tasks after the last patient has completed the RCT); (ii) on several aspects, (iii) on a single aspect (e.g., recruitment); or (iv) on overall costs for RCTs. Median costs of different recruitment strategies were calculated. Other results (e.g., overall costs) were listed descriptively. All cost data were converted into USD 2017., Results: A total of 56 articles that reported on cost or resource use of RCTs were included. None of the articles provided empirical resource use and cost data for all aspects of an entire RCT. Eight articles presented resource use and cost data on several aspects (e.g., aggregated cost data of different drug development phases, site-specific costs, selected cost components). Thirty-five articles assessed costs of one specific aspect of an RCT (i.e., 30 on recruitment; five others). The median costs per recruited patient were USD 409 (range: USD 41-6,990). Overall costs of an RCT, as provided in 16 articles, ranged from USD 43-103,254 per patient, and USD 0.2-611.5 Mio per RCT but the methodology of gathering these overall estimates remained unclear in 12 out of 16 articles (75%)., Conclusion: The usefulness of the available empirical evidence on resource use and costs of RCTs is limited. Transparent and comprehensive resource use and cost data are urgently needed to support budget planning for RCTs and help improve sustainability., (Copyright © 2017 Elsevier Inc. All rights reserved.)

Background: Metastatic biopsies are increasingly being performed in patients with advanced prostate cancer to search for actionable targets and/or to identify emerging resistance mechanisms. Due to a predominance of bone metastases and their sclerotic nature, obtaining sufficient tissue for clinical and genomic studies is challenging., Methods: Patients with prostate cancer bone metastases were enrolled between February 2013 and March 2017 on an institutional review board-approved protocol for prospective image-guided bone biopsy. Bone biopsies and blood clots were collected fresh. Compact bone was subjected to formalin with a decalcifying agent for diagnosis; bone marrow and blood clots were frozen in optimum cutting temperature formulation for next-generation sequencing. Frozen slides were cut from optimum cutting temperature cryomolds and evaluated for tumor histology and purity. Tissue was macrodissected for DNA and RNA extraction, and whole-exome sequencing and RNA sequencing were performed., Results: Seventy bone biopsies from 64 patients were performed. Diagnostic material confirming prostate cancer was successful in 60 of 70 cases (85.7%). The median DNA/RNA yield was 25.5 ng/μL and 16.2 ng/μL, respectively. Whole-exome sequencing was performed successfully in 49 of 60 cases (81.7%), with additional RNA sequencing performed in 20 of 60 cases (33.3%). Recurrent alterations were as expected, including those involving the AR, PTEN, TP53, BRCA2, and SPOP genes., Conclusions: This prostate cancer bone biopsy protocol ensures a valuable source for high-quality DNA and RNA for tumor sequencing and may be used to detect actionable alterations and resistance mechanisms in patients with bone metastases. Cancer 2018;124:1008-15. © 2017 American Cancer Society., (© 2017 American Cancer Society.)

Background/aim: An evaluation if radiomic features of CT perfusion (CTP) can predict tumor grade and aggressiveness in prostate cancer was performed., Materials and Methods: Forty-seven patients had biopsy-confirmed prostate cancer, and received a CTP. Blood volume (BV), blood flow (BF) and mean transit time (MTT) maps were derived and 1,701 radiomic features were determined per patient. Regression models were built to estimate post-surgical Gleason score (GS), microvessel density (MVD) and distinguish between the different risk groups., Results: Six out of the 47 patients had to be excluded from further analysis. A weak relationship between postsurgical GS and one radiomic parameter was found (R 2 =0.21, p=0.01). The same parameter combined with MTT inter-quartile range was prognostic for the risk group categorisation (AUC=0.81). Two different radiomic parameters were able to distinguish between low-intermediate risk and high-intermediate risk (AUC=0.77). Four parameters correlated with MVD (R2=0.53, p<0.02)., Conclusion: This exploratory study shows the potential of radiomics to classify prostate cancer., (Copyright© 2018, International Institute of Anticancer Research (Dr. George J. Delinasios), All rights reserved.)

Chromosomal instability is a hallmark of cancer that results from ongoing errors in chromosome segregation during mitosis. Although chromosomal instability is a major driver of tumour evolution, its role in metastasis has not been established. Here we show that chromosomal instability promotes metastasis by sustaining a tumour cell-autonomous response to cytosolic DNA. Errors in chromosome segregation create a preponderance of micronuclei whose rupture spills genomic DNA into the cytosol. This leads to the activation of the cGAS-STING (cyclic GMP-AMP synthase-stimulator of interferon genes) cytosolic DNA-sensing pathway and downstream noncanonical NF-κB signalling. Genetic suppression of chromosomal instability markedly delays metastasis even in highly aneuploid tumour models, whereas continuous chromosome segregation errors promote cellular invasion and metastasis in a STING-dependent manner. By subverting lethal epithelial responses to cytosolic DNA, chromosomally unstable tumour cells co-opt chronic activation of innate immune pathways to spread to distant organs.

The cancer anorexia cachexia syndrome is a systemic metabolic disorder characterized by the catabolism of stored nutrients in skeletal muscle and adipose tissue that is particularly prevalent in nonsmall cell lung cancer (NSCLC). Loss of skeletal muscle results in functional impairments and increased mortality. The aim of the present study was to characterize the changes in systemic metabolism in a genetically engineered mouse model of NSCLC. We show that a portion of these animals develop loss of skeletal muscle, loss of adipose tissue, and increased inflammatory markers mirroring the human cachexia syndrome. Using noncachexic and fasted animals as controls, we report a unique cachexia metabolite phenotype that includes the loss of peroxisome proliferator-activated receptor-α (PPARα) -dependent ketone production by the liver. In this setting, glucocorticoid levels rise and correlate with skeletal muscle degradation and hepatic markers of gluconeogenesis. Restoring ketone production using the PPARα agonist, fenofibrate, prevents the loss of skeletal muscle mass and body weight. These results demonstrate how targeting hepatic metabolism can prevent muscle wasting in lung cancer, and provide evidence for a therapeutic strategy., Competing Interests: The authors declare no conflict of interest.

Background: Clinical studies in children are necessary yet conducting multiple visits at study centers remains challenging. The success of "care-at-home" initiatives and remote clinical trials suggests their potential to facilitate conduct of pediatric studies. This pilot aimed to study the feasibility of remotely collecting valid (i.e. complete and correct) saliva samples and clinical data utilizing mobile technology., Methods: Single-center, prospective pilot study in children undergoing elective tonsillectomy at the University of Basel Children's Hospital. Data on pain scores and concomitant medication and saliva samples were collected by caregivers on two to four inpatient study days and on three consecutive study days at home. A tailored mobile application developed for this study supported data collection. The primary endpoint was the proportion of complete and correct caregiver-collected data (pain scale) and saliva samples in the at-home setting. Secondary endpoints included the proportion of complete and correct saliva samples in the inpatient setting, subjective feasibility for caregivers, and study cost., Results: A total number of 23 children were included in the study of which 17 children, median age 6.0 years (IQR 5.0, 7.4), completed the study. During the at-home phase, 71.9% [CI = 64.4, 78.6] of all caregiver-collected pain assessments and 53.9% [CI = 44.2, 63.4] of all saliva samples were complete and correct. Overall, 64.7% [CI = 58.7, 70.4] of all data collected by caregivers at home was complete and correct. The predominant reason for incorrectness of data was adherence to the timing of predefined patient actions. Participating caregivers reported high levels of satisfaction and willingness to participate in similar trials in the future. Study costs for a potential sample size of 100 patients were calculated to be 20% lower for the at-home than for a traditional in-patient study setting., Conclusions: Mobile device supported studies conducted at home may provide a cost-effective approach to facilitate conduct of clinical studies in children. Given findings in this pilot study, data collection at home may focus on electronic data capture rather than biological sampling.

Purpose: To investigate the effect of sample orientation on T1rho and T2 values of articular cartilage in histologically confirmed normal and abnormal regions using a whole-body 3T scanner., Materials and Methods: Eight human cadaveric patellae were evaluated using a 2D CPMG sequence for T2 measurement as well as a 2D spin-locking prepared spiral sequence and a 3D magnetization-prepared angle-modulated partitioned-k-space spoiled gradient echo snapshots (3D MAPSS) sequence for T1rho measurement. Each sample was imaged at six angles from 0° to 100° relative to the B 0 field. T2 and T1rho values were measured for three regions (medial, apex and lateral) with three layers (10% superficial, 60% middle, 30% deep). Multiple histopathologically confirmed normal and abnormal regions were used to evaluate the angular dependence of T2 and T1rho relaxation in articular cartilage., Results: Our study demonstrated a strong magic angle effect for T1rho and T2 relaxation in articular cartilage, especially in the deeper layers of cartilage. On average, T2 values were increased by 231.8% (72.2% for superficial, 237.6% for middle, and 187.9% for deep layers) while T1rho values were increased by 92% (31.7% for superficial, 69% for middle, and 140% for deep layers) near the magic angle. Both normal and abnormal cartilage showed similar T1rho and T2 magic angle effect., Conclusions: Changes in T1rho and T2 values due to the magic angle effect can be several times more than that caused by degeneration, and this may significantly complicate the clinical application of T1rho and T2 as an early surrogate marker for degeneration., (Copyright © 2017 Osteoarthritis Research Society International. Published by Elsevier Ltd. All rights reserved.)

Background: Precision oncology is a clinical approach aimed towards tailoring treatment strategies for patients based on the genetic profile of each patient's cancer. The integration of a living biobank, consisting of patient-derived tumor organoids and PDXs, with next generation sequencing approaches and high-throughput drug screening help to guide clinical decision-making and clinical trial development., Methods: Tumor organoids derived from fresh tumor samples were used for in vitro and in vivo high-throughput drug testing., Results: Over a period of two years we established 56 in vitro tumor organoids and 19 in vivo xenografts from 18 different solid tumor types. Tumor morphology and molecular profiles show good concordance between the in vitro and in vivo models compared to their native tumor. High-throughput drug screening (up to 160 drugs) has been tested on eight tumor organoid lines. Seven of them underwent an additional combination drug screen. We nominated several targeted small molecules and novel combinations that have been validated in corresponding xenograft models., Conclusion: This precision medicine approach outlines the integration of genomic data with drug screening from personalized preclinical cancer models to guide precision cancer care. It also fuels next generation research and has been implemented for clinical trial development.

Purpose: The purpose of this study was to investigate the following: i) the objective impairment in neuropsychological tests that were associated with the subjective perception of cognitive function decline in Brazilian patients who underwent mesial temporal lobe epilepsy (MTLE) surgery and ii) the predictive variables for those impaired objective neuropsychological tests., Methods: Forty-eight adults with MTLE (27 right HS and 23 male) were divided according to their perception of changes (Decline or No-decline) of cognitive function domain of the QOLIE-31 questionnaire applied before and 1year after the ATL. The mean (SD) of changes in the raw score difference of the neuropsychological tests before and after the ATL was compared between Decline and No-decline groups. Receiver Operating Characteristic curves, sensitivity, specificity, and predictive values were used to assess the optimum cutoff points of neuropsychological test score changes to predict patient-reported subjective cognitive decline., Key Findings: Six (12.5%) patients reported a perception of cognitive function decline after ATL. Among the 25 cognitive tests analyzed, only changes in the Boston Naming Test (BNT) were associated with subjective cognitive decline reported by patients. A reduction of ≥8 points in the raw score of BNT after surgery had 91% of sensitivity and 45% specificity for predicting subjective perception of cognitive function decline by the patient. Left side surgery and age older than 40years were more associated with an important BNT reduction with overall accuracy of 91.7%, 95% predictive ability for no impairment, and 75% for impairment of cognitive function., Significance: Impairment in word-finding seems to be the objective cognitive finding most relevant to Brazilian patients after mesial temporal lobe epilepsy surgery. Similar to American patients, the side of surgery and age are good predictors for no decline in the BNT, but shows a lower accuracy to predict its decline. If replicated in other populations, the results may have wider implications for the surgical management of patients with drug-resistant MTLE., (Copyright © 2017 Elsevier Inc. All rights reserved.)

Objective: To systematically survey existing definitions, concepts, and criteria of clinical research quality, both developed by stakeholder groups as well as in the medical literature. This study serves as a first step in the development of a comprehensive framework for the quality of clinical research., Study Design and Setting: We systematically and in duplicate searched definitions, concepts and criteria of clinical research quality on websites of stakeholders in clinical research until no further insights emerged and in MEDLINE up to February 2015. Stakeholders included governmental bodies, regulatory agencies, the pharmaceutical industry, academic and commercial contract research organizations, initiatives, research ethics committees, patient organizations and funding agencies from 13 countries. Data synthesis involved descriptive and qualitative analyses following the Framework Method on definitions, concepts, and criteria of clinical research quality. Descriptive codes were applied and grouped into clusters to identify common and stakeholder-specific quality themes., Results: Stakeholder concepts on how to assure quality throughout study conduct or articles on quality assessment tools were common, generally with no a priori definition of the term quality itself. We identified a total of 20 explicit definitions of clinical research quality including varying quality dimensions and focusing on different stages in the clinical research process. Encountered quality dimensions include ethical conduct, patient safety/rights/priorities, internal validity, precision of results, generalizability or external validity, scientific and societal relevance, transparency and accessibility of information, research infrastructure and sustainability. None of the definitions appeared to be comprehensive either in terms of quality dimensions, research stages, or stakeholder perspectives., Conclusion: Clinical research quality is often discussed but rarely defined. A framework defining clinical research quality across stakeholders' individual perspectives is desirable to facilitate discussion, assessment, and improvement of quality at all stages of clinical research.

Leukaemogenesis requires enhanced self-renewal, which is induced by oncogenes. The underlying molecular mechanisms remain incompletely understood. Here, we identified C/D box snoRNAs and rRNA 2'-O-methylation as critical determinants of leukaemic stem cell activity. Leukaemogenesis by AML1-ETO required expression of the groucho-related amino-terminal enhancer of split (AES). AES functioned by inducing snoRNA/RNP formation via interaction with the RNA helicase DDX21. Similarly, global loss of C/D box snoRNAs with concomitant loss of rRNA 2'-O-methylation resulted in decreased leukaemia self-renewal potential. Genomic deletion of either C/D box snoRNA SNORD14D or SNORD35A suppressed clonogenic potential of leukaemia cells in vitro and delayed leukaemogenesis in vivo. We further showed that AML1-ETO9a, MYC and MLL-AF9 all enhanced snoRNA formation. Expression levels of C/D box snoRNAs in AML patients correlated closely with in vivo frequency of leukaemic stem cells. Collectively, these findings indicate that induction of C/D box snoRNA/RNP function constitutes an important pathway in leukaemogenesis.

Objective: The role of computed tomography perfusion (CTP) in characterizing primary prostate cancer (PCa) is not definitely known. The aim of the present study was to investigate the relationship between CTP parameters and histopathological features of PCa tissue, using a sector-wise approach., Material and Methods: Fifty-one patients with biopsy-proven PCa underwent prospectively a CTP scan prior to radical prostatectomy. Blood flow (BF), mean blood volume (BV) and mean transit time (MTT) were calculated, with the prostate being divided into eight sectors. Corresponding sector-wise histopathological analysis of whole-mount prostatectomy specimens was performed to determine tumoral area (mm 2 ), mean microvessel density (MVD), Gleason patterns (primary, secondary) and total Gleason score. Spearman's rank correlation coefficient was used to analyze the association between CTP and histopathological parameters., Results: BF correlated weakly with tumoral area [ρs coefficient (p-value): 0.25 (0.00)] and MVD [ρs coefficient (p-value): 0.23 (0.00)]. No valuable correlation was found between CTP parameters and primary and secondary Gleason patterns, whereas total Gleason score was weakly correlated with BV [ρs coefficient (p-value): 0.22 (0.00)] and MTT [ρs coefficient (p-value): 0.25 (0.00)]., Conclusion: BF correlates weakly with size and vascularity of PCa. There is a need for further studies to elucidate the association between CTP parameters and other histopathological parameters., Competing Interests: Conflict of Interest: No conflict of interest was declared by the authors.

Colorectal cancer (CRC) is a leading cause of death in the developed world, yet facile preclinical models that mimic the natural stages of CRC progression are lacking. Through the orthotopic engraftment of colon organoids we describe a broadly usable immunocompetent CRC model that recapitulates the entire adenoma-adenocarcinoma-metastasis axis in vivo. The engraftment procedure takes less than 5 minutes, shows efficient tumor engraftment in two-thirds of mice, and can be achieved using organoids derived from genetically engineered mouse models (GEMMs), wild-type organoids engineered ex vivo, or from patient-derived human CRC organoids. In this model, we describe the genotype and time-dependent progression of CRCs from adenocarcinoma (6 weeks), to local disseminated disease (11-12 weeks), and spontaneous metastasis (>20 weeks). Further, we use the system to show that loss of dysregulated Wnt signaling is critical for the progression of disseminated CRCs. Thus, our approach provides a fast and flexible means to produce tailored CRC mouse models for genetic studies and pre-clinical investigation.

Precision medicine is an approach that takes into account the influence of individuals' genes, environment, and lifestyle exposures to tailor interventions. Here, we describe the development of a robust precision cancer care platform that integrates whole-exome sequencing with a living biobank that enables high-throughput drug screens on patient-derived tumor organoids. To date, 56 tumor-derived organoid cultures and 19 patient-derived xenograft (PDX) models have been established from the 769 patients enrolled in an Institutional Review Board-approved clinical trial. Because genomics alone was insufficient to identify therapeutic options for the majority of patients with advanced disease, we used high-throughput drug screening to discover effective treatment strategies. Analysis of tumor-derived cells from four cases, two uterine malignancies and two colon cancers, identified effective drugs and drug combinations that were subsequently validated using 3-D cultures and PDX models. This platform thereby promotes the discovery of novel therapeutic approaches that can be assessed in clinical trials and provides personalized therapeutic options for individual patients where standard clinical options have been exhausted. Significance: Integration of genomic data with drug screening from personalized in vitro and in vivo cancer models guides precision cancer care and fuels next-generation research. Cancer Discov; 7(5); 462-77. ©2017 AACR. See related commentary by Picco and Garnett, p. 456 This article is highlighted in the In This Issue feature, p. 443 ., (©2017 American Association for Cancer Research.)

Objectives: To investigate prospectively the independent predictors of a minimum clinically important change (MCIC) in quality of life (QOL) after anterior temporal lobectomy (ATL) for drug-resistant mesial temporal lobe epilepsy related to hippocampal sclerosis (MTLE-HS) in Brazilian patients., Methods: Multiple binary logistic regression analysis was performed to identify the clinical, demographic, radiologic, and electrophysiologic variables independently associated with MCIC in the Quality of Life in Epilepsy-31 Inventory (QOLIE-31) overall score 1 year after ATL in 77 consecutive patients with unilateral MTLE-HS., Results: The overall QOLIE-31 score and all its subscale scores increased significantly (p < 0.0001) 1 year after ATL. In the final logistic regression model, absence of presurgical diagnosis of depression (adjusted odds ratio [OR] 4.4, 95% confidence interval [CI] 1.1-16.1, p = 0.02) and a complete postoperative seizure control (adjusted OR 4.1, 95% CI 1.2-14.5, p = 0.03) were independently associated with improvement equal to or greater than the MCIC in QOL after ATL. The overall model accuracy for MCIC improvement in the QOL was 85.6%, with a 95.2% of sensitivity and 46.7% of specificity., Significance: These results in Brazilian patients reinforce the external validation of previous findings in Canadian patients showing that presurgical depression and complete seizure control after surgery are independent predictors for meaningful improvement in QOL after ATL, and have implications for the surgical management of MTLE patients., (Wiley Periodicals, Inc. © 2017 International League Against Epilepsy.)

Purpose: Meniscus contains heterogeneous populations of cells that have not been fully characterized. Cell phenotype is often lost during culture; however, culture expansion is typically required for tissue engineering. We examined and compared cell-surface molecule expression levels on human meniscus cells from the vascular and avascular regions and articular chondrocytes while documenting changes during culture-induced dedifferentiation., Materials and Methods: Expressions of 16 different surface molecules were examined by flow cytometry after monolayer culture for 24 h, 1 week, and 2 weeks. Menisci were also immunostained to document the spatial distributions of selected surface molecules., Results: Meniscus cells and chondrocytes exhibited several similarities in surface molecule profiles with dynamic changes during culture. A greater percentage of meniscal cells were positive for CD14, CD26, CD49c, and CD49f compared to articular chondrocytes. Initially, more meniscal cells from the vascular region were positive for CD90 compared to cells from the avascular region or chondrocytes. Cells from the vascular region also expressed higher levels of CD166 and CD271 compared to cells from the avascular region. CD90, CD166, and CD271-positive cells were predominately perivascular in location. However, CD166-positive cells were also located in the superficial layer and in the adjacent synovial and adipose tissue., Conclusions: These surface marker profiles provide a target phenotype for differentiation of progenitors in tissue engineering. The spatial location of progenitor cells in meniscus is consistent with higher regenerative capacity of the vascular region, while the surface progenitor subpopulations have potential to be utilized in tears created in the avascular region.

Background/aim: Development of patient-derived three-dimensional (3D) organoid cultures is an emerging technique in the field of precision oncology. We aimed to integrate on-site adequacy evaluation using cytology into the tumor organoid development workflow to ensure precise characterization and growth of these cultures., Patients and Methods: Cancer patients were consented to a Precision Medicine trial. Fresh tissue was procured for genomic analyses as well as organoid development. Fresh tissue destined for organoid development was evaluated by preparing on-site cytology smears to ensure that only lesional tissue would be submitted for further cell culture work., Results: Cytology preparations were made from 64 different tumor samples and evaluated prior to tissue submission for organoid development. In 53 (82.2%) of those tumor samples, the cytology preparation was diagnostic, thus providing adequate material for organoid development., Conclusion: Characterizing the tissue prior to submission for organoid development ensures submission of lesional tissue only. Furthermore, it is a cost-effective method that can help document patient diagnosis. This can be of importance in biopsies, since the tissue submitted for organoid development cannot be retrieved for clinical diagnosis afterwards. Our findings in this pilot study led to the implementation of on-site cytological evaluation in the tumor organoid development workflow at the Englander Institute for Precision Medicine, NY, USA., (Copyright© 2017, International Institute of Anticancer Research (Dr. George J. Delinasios), All rights reserved.)

Background: In spite of efforts to employ risk-based strategies to increase monitoring efficiency in the academic setting, empirical evidence on their effectiveness remains sparse. This mixed-methods study aimed to evaluate the risk-based on-site monitoring approach currently followed at our academic institution., Methods: We selected all studies monitored by the Clinical Trial Unit (CTU) according to Risk ADApted MONitoring (ADAMON) at the University Hospital Basel, Switzerland, between 01.01.2012 and 31.12.2014. We extracted study characteristics and monitoring information from the CTU Enterprise Resource Management system and from monitoring reports of all selected studies. We summarized the data descriptively. Additionally, we conducted semi-structured interviews with the three current CTU monitors., Results: During the observation period, a total of 214 monitoring visits were conducted in 43 studies resulting in 2961 documented monitoring findings. Our risk-based approach predominantly identified administrative (46.2%) and patient right findings (49.1%). We identified observational study design, high ADAMON risk category, industry sponsorship, the presence of an electronic database, experienced site staff, and inclusion of vulnerable study population to be factors associated with lower numbers of findings. The monitors understand the positive aspects of a risk-based approach but fear missing systematic errors due to the low frequency of visits., Conclusions: We show that the factors mostly increasing the risk for on-site monitoring findings are underrepresented in the current risk analysis scheme. Our risk-based on-site approach should further be complemented by centralized data checks, allowing monitors to transform their role towards partners for overall trial quality, and success.

Purpose: Patients with cancer who graciously consent for autopsy represent an invaluable resource for the study of cancer biology. To advance the study of tumor evolution, metastases, and resistance to treatment, we developed a next-generation rapid autopsy program integrated within a broader precision medicine clinical trial that interrogates pre- and postmortem tissue samples for patients of all ages and cancer types., Materials and Methods: One hundred twenty-three (22%) of 554 patients who consented to the clinical trial also consented for rapid autopsy. This report comprises the first 15 autopsies, including patients with metastatic carcinoma (n = 10), melanoma (n = 1), and glioma (n = 4). Whole-exome sequencing (WES) was performed on frozen autopsy tumor samples from multiple anatomic sites and on non-neoplastic tissue. RNA sequencing (RNA-Seq) was performed on a subset of frozen samples. Tissue was also used for the development of preclinical models, including tumor organoids and patient-derived xenografts., Results: Three hundred forty-six frozen samples were procured in total. WES was performed on 113 samples and RNA-Seq on 72 samples. Successful cell strain, tumor organoid, and/or patient-derived xenograft development was achieved in four samples, including an inoperable pediatric glioma. WES data were used to assess clonal evolution and molecular heterogeneity of tumors in individual patients. Mutational profiles of primary tumors and metastases yielded candidate mediators of metastatic spread and organotropism including CUL9 and PIGM in metastatic ependymoma and ANKRD52 in metastatic melanoma to the lung. RNA-Seq data identified novel gene fusion candidates., Conclusion: A next-generation sequencing-based autopsy program in conjunction with a pre-mortem precision medicine pipeline for diverse tumors affords a valuable window into clonal evolution, metastasis, and alterations underlying treatment. Moreover, such an autopsy program yields robust preclinical models of disease.

Precision medicine is an emerging field in medicine for disease prevention and treatment that takes into account the individual variability in genes, environment, and lifestyle for each individual patient. The authors have developed a special program as part of the Englander Institute for Precision Medicine to grow patient-derived, 3-dimensional tumor organoids for tumor-specific drug testing, tailoring treatment strategies, and as models for studying drug resistance. Routine cytology preparations represent a cost-effective and powerful tool to aid in performing molecular testing in the age of personalized medicine. In this commentary, the platforms used for the characterization and validation of patient-derived, 3-dimensional tumor organoids are outlined and discussed, and the role of cytology as a cost-effective and powerful quality-control measure is illustrated., (© 2015 American Cancer Society.)

Objectives: To determine T2* relaxation in articular cartilage using ultrashort echo time (UTE) imaging and bi-component analysis, with an emphasis on the deep radial and calcified cartilage., Methods: Ten patellar samples were imaged using two-dimensional (2D) UTE and Car-Purcell-Meiboom-Gill (CPMG) sequences. UTE images were fitted with a bi-component model to calculate T2* and relative fractions. CPMG images were fitted with a single-component model to calculate T2. The high signal line above the subchondral bone was regarded as the deep radial and calcified cartilage. Depth and orientation dependence of T2*, fraction and T2 were analyzed with histopathology and polarized light microscopy (PLM), confirming normal regions of articular cartilage. An interleaved multi-echo UTE acquisition scheme was proposed for in vivo applications (n = 5)., Results: The short T2* values remained relatively constant across the cartilage depth while the long T2* values and long T2* fractions tended to increase from subchondral bone to the superficial cartilage. Long T2*s and T2s showed significant magic angle effect for all layers of cartilage from the medial to lateral facets, while the short T2* values and T2* fractions are insensitive to the magic angle effect. The deep radial and calcified cartilage showed a mean short T2* of 0.80 ± 0.05 ms and short T2* fraction of 39.93 ± 3.05% in vitro, and a mean short T2* of 0.93 ± 0.58 ms and short T2* fraction of 35.03 ± 4.09% in vivo., Conclusion: UTE bi-component analysis can characterize the short and long T2* values and fractions across the cartilage depth, including the deep radial and calcified cartilage. The short T2* values and T2* fractions are magic angle insensitive., (Copyright © 2015 Osteoarthritis Research Society International. Published by Elsevier Ltd. All rights reserved.)

Background: To determine if off-saturation ratio (OSR) measured with the ultrashort echo time magnetization transfer (UTE-MT) sequence could differentiate between tendons under different states of tensile load and to compare these changes between normal versus degenerated tendons., Methods: Fourteen tendons were imaged at 3 Tesla before and during the application of 0.5-1 kg tension. A two-dimensional (2D) -UTE-MT sequence with 1.5, 3, and 5 kHz frequency offsets was used on nine tendons and a 3D-UTE-MT sequence with 1.5 kHz frequency offset was used on five tendons. OSR was calculated and compared for each condition. Histologic correlation was performed using light microscopy., Results: In general, OSR increased after the application of tension. Mean increase of 2D OSR was 0.035 (95% confidence interval [CI], 0.013-0.056) at 1.5 kHz offset (P < 0.01), 0.031 (95% CI, 0.023-0.040) at 3 kHz offset (P < 0.01), and 0.013 (95% CI, -0.013-0.027) at 5 kHz offset (P = 0.07) from pre- to posttension states. Mean increase of 3D OSR was 0.026 (95% CI, 0.008-0.044) at a 1.5 kHz offset (P = 0.02) from pre- to posttension states. Mean decrease of 2D OSR at 1.5 kHz offset was 0.074-0.087 when comparing normal versus degenerated tendons (P < 0.01)., Conclusion: OSR as measured with 2D or 3D UTE-MT sequences can detect the changes in hydration seen when tendons are placed under two different states of tensile load, but these changes are smaller than those encountered when comparing between normal versus pathologic tendons. Lower off-resonance saturation frequencies (3 kHz or less) are more sensitive to these changes than higher off-resonance saturation frequencies., (© 2015 Wiley Periodicals, Inc.)

Introduction: the aim of this pilot study was to implement ultrashort echo time (UTE) MRI with bi-component analysis on grossly normal Achilles tendons with histologic correlation., Materials and Methods: six tendon samples which were grossly normal on visual inspection and palpation were harvested. A 2D UTE pulse sequence was implemented on a 3T MR scanner and bi-component and single-component T2* analysis was performed. Tendon samples were histologically processed and evaluated., Results: mean short T2* fraction was 79.2% (95% confidence interval [CI], 70.1 - 88.3%), mean short T2* was 1.8 ms (95% CI, 1.3 - 2.3 ms), mean long T2* fraction was 20.8% (95% CI, 11.7 - 29.9%), mean long T2* was 9.2 ms (95% CI, 5.1 - 13.3 ms), and mean single-component T2* was 2.5 ms (95% CI, 1.8 - 3.1 ms)., Discussion: 2D UTE MRI with bi-component and single-component T2* analysis was successfully implemented. Inter-individual variation can be demonstrated in grossly and histologically normal Achilles tendons.

Six multidisciplinary competence centres (Clinical Trial Units, CTUs) in Basel, Berne, Geneva, Lausanne, St. Gallen and Zurich provide professional support to clinical researchers in the planning, implementation, conduct and evaluation of clinical studies. Through their coordinated network, these units promote high-quality, nationally harmonised and internationally standardised clinical research conduct in Switzerland. We will describe why this network has been established, how it has been successful in stilling the growing need for clinical research support, which training and education opportunities it offers, and how it created national awareness for the still-existing hurdles towards clinical research excellence in Switzerland. Taking the CTU Basel as an example, we show that a considerable number (25%) of the studies submitted for regulatory approval in 2013 were supported by the CTU, decreasing the number of findings in ethics reviews by about one-third. We conclude that these achievements, together with a Swiss national funding model for clinical research, and improved national coordination, will be critical factors to successfully position Swiss clinical research at the international forefront.

Importance: Understanding molecular mechanisms of response and resistance to anticancer therapies requires prospective patient follow-up and clinical and functional validation of both common and low-frequency mutations. We describe a whole-exome sequencing (WES) precision medicine trial focused on patients with advanced cancer., Objective: To understand how WES data affect therapeutic decision making in patients with advanced cancer and to identify novel biomarkers of response., Design, Setting, and Patients: Patients with metastatic and treatment-resistant cancer were prospectively enrolled at a single academic center for paired metastatic tumor and normal tissue WES during a 19-month period (February 2013 through September 2014). A comprehensive computational pipeline was used to detect point mutations, indels, and copy number alterations. Mutations were categorized as category 1, 2, or 3 on the basis of actionability; clinical reports were generated and discussed in precision tumor board. Patients were observed for 7 to 25 months for correlation of molecular information with clinical response., Main Outcomes and Measures: Feasibility, use of WES for decision making, and identification of novel biomarkers., Results: A total of 154 tumor-normal pairs from 97 patients with a range of metastatic cancers were sequenced, with a mean coverage of 95X and 16 somatic alterations detected per patient. In total, 16 mutations were category 1 (targeted therapy available), 98 were category 2 (biologically relevant), and 1474 were category 3 (unknown significance). Overall, WES provided informative results in 91 cases (94%), including alterations for which there is an approved drug, there are therapies in clinical or preclinical development, or they are considered drivers and potentially actionable (category 1-2); however, treatment was guided in only 5 patients (5%) on the basis of these recommendations because of access to clinical trials and/or off-label use of drugs. Among unexpected findings, a patient with prostate cancer with exceptional response to treatment was identified who harbored a somatic hemizygous deletion of the DNA repair gene FANCA and putative partial loss of function of the second allele through germline missense variant. Follow-up experiments established that loss of FANCA function was associated with platinum hypersensitivity both in vitro and in patient-derived xenografts, thus providing biologic rationale and functional evidence for his extreme clinical response., Conclusions and Relevance: The majority of advanced, treatment-resistant tumors across tumor types harbor biologically informative alterations. The establishment of a clinical trial for WES of metastatic tumors with prospective follow-up of patients can help identify candidate predictive biomarkers of response.

Background: Primary bone cancers are among the deadliest cancer types in adolescents, with osteosarcomas being the most prevalent form. Osteosarcomas are commonly treated with multi-drug neoadjuvant chemotherapy and therapy success as well as patient survival is affected by the presence of tumor suppressors. In order to assess the prognostic value of tumor-suppressive biomarkers, primary osteosarcoma tissues were analyzed prior to and after neoadjuvant chemotherapy., Methods: We constructed a tissue microarray from high grade osteosarcoma samples, consisting of 48 chemotherapy naïve biopsies (BXs) and 47 tumor resections (RXs) after neoadjuvant chemotherapy. We performed immunohistochemical stainings of P53, P16, maspin, PTEN, BMI1 and Ki67, characterized the subcellular localization and related staining outcome with chemotherapy response and overall survival. Binary logistic regression analysis was used to analyze chemotherapy response and Kaplan-Meier-analysis as well as the Cox proportional hazards model was applied for analysis of patient survival., Results: No significant associations between biomarker expression in BXs and patient survival or chemotherapy response were detected. In univariate analysis, positive immunohistochemistry of P53 (P = 0.008) and P16 (P16; P = 0.033) in RXs was significantly associated with poor survival prognosis. In addition, presence of P16 in RXs was associated with poor survival in multivariate regression analysis (P = 0.003; HR = 0.067) while absence of P16 was associated with good chemotherapy response (P = 0.004; OR = 74.076). Presence of PTEN on tumor RXs was significantly associated with an improved survival prognosis (P = 0.022)., Conclusions: Positive immunohistochemistry (IHC) of P16 and P53 in RXs was indicative for poor overall patient survival whereas positive IHC of PTEN was prognostic for good overall patient survival. In addition, we found that P16 might be a marker of osteosarcoma chemotherapy resistance. Therefore, our study supports the use of tumor RXs to assess the prognostic value of biomarkers.

Objectives: To analyze the correlation of computed tomography (CT) perfusion parameters blood flow (BF), blood volume (BV), and mean transit time (MTT) with presurgical prostate cancer data., Methods: Ninety-eight patients with biopsy-proven prostate cancer underwent a CT-perfusion scan of the prostate. MTT, BF, and BV were determined and correlated with prostate-specific antigen (PSA) level, tumor load and Gleason score of transrectal ultrasonography-guided biopsy specimens., Results: Mean BF was 41.3 ml/100 ml*min(-1), BV 5.2 ml/100 ml, MTT 8.7 s. Moderate correlations were observed between Gleason score and BF (0.35) and between PSA and BF (0.33) and BV (0.30)., Conclusions: CT-perfusion shows no valuable correlation with presurgical prostate cancer data., (Copyright © 2014 Elsevier Inc. All rights reserved.)

Objectives: The aim of this study was to assess the performance of dynamic contrast-enhanced computed tomography of the prostate in patients with biopsy-proven prostate cancer., Material and Methods: A total of 46 male patients (median age, 65 years; range, 49-73 years) with biopsy-proven prostate cancer underwent an en bloc computed tomography perfusion (CTP) scan of the prostate before surgery. The perfusion parameters mean transit time (MTT), blood flow (BF), and blood volume (BV), as well as the microvessel density (MVD) of surgical specimens were determined. Differences in CTP parameters and MVD among postsurgical Gleason score (sGS) and postsurgical combined Gleason grade (sGG) groups were analyzed. Spearman correlation coefficients were determined between CTP parameters and presurgical biopsy-derived Gleason score (bGS), presurgical biopsy-derived combined Gleason grade (bGG), sGS, sGG, MVD, and pathological tumor stage. A linear regression analysis was carried out for exogenous variables BF, BV, MTT, bGS, and presurgical biopsy-derived combined Gleason grade and endogenous variables sGS, sGG, MVD, and T stage. A receiver operating characteristics analysis was performed to analyze the discriminating performance of CTP parameters and bGS between intermediate- and high-grade tumors., Results: The mean perfusion parameters within the prostate tissue were as follows: BF, 39.1 ± 13.4 mL/100 mL min; BV, 4.9 ± 2.4 mL/100 mL; and MTT, 8.9 ± 3.7 seconds. The mean MVD of the tumor tissue was 144.3 ± 55.6/mm. Computed tomography perfusion parameters and MVD were significantly higher in patients with high-grade tumors compared with those with intermediate-grade tumors (P < 0.01 for BF, BV, and MVD). Only BV and MVD were significantly different among sGS and sGG groups. Moderate correlations were found between BF and sGS (0.38) and between BV and sGS (0.43). Linear relations of BV to sGS and to sGG were found. Blood volume (area under the curve, 0.86) was superior to bGS (area under the curve, 0.75) in discriminating high-grade from intermediate-grade tumors., Conclusion: Computed tomography perfusion parameters derived by en bloc perfusion of the prostate are higher in high-grade tumors compared with intermediate-grade tumors. Blood flow and BV correlate with the definitive Gleason score. Blood volume predicts high-grade tumors better than does the Gleason score of biopsy specimens. Further studies are needed to determine a potential role for CTP in prostate cancer patients.

Many studies in the field of cell-based cartilage repair have focused on identifying markers associated with the differentiation status of human articular chondrocytes (HAC) that could predict their chondrogenic potency. A previous study from our group showed a correlation between the expression of S100 protein in HAC and their chondrogenic potential. The aims of the current study were to clarify which S100 proteins are associated with HAC differentiation status and to provide an S100-based assay for measuring HAC chondrogenic potential. The expression patterns of S100A1 and S100B were investigated in cartilage and in HAC cultured under conditions promoting dedifferentiation (monolayer culture) or redifferentiation (pellet culture or BMP4 treatment in monolayer culture), using characterized antibodies specifically recognizing S100A1 and S100B, by immunohistochemistry, immunocytochemistry, Western blot, and gene expression analysis. S100A1 and S100B were expressed homogeneously in all cartilage zones, and decreased during dedifferentiation. S100A1, but not S100B, was re-expressed in pellets and co-localized with collagen II. Gene expression analysis revealed concomitant modulation of S100A1, S100B, collagen type II, and aggrecan: down-regulation during monolayer culture and up-regulation upon BMP4 treatment. These results strongly support an association of S100A1, and to a lesser extent S100B, with the HAC differentiated phenotype. To facilitate their potential application, we established an S100A1/B-based flow cytometry assay for accurate assessment of HAC differentiation status. We propose S100A1 and S100B expression as a marker to develop potency assays for cartilage regeneration cell therapies, and as a redifferentiation readout in monolayer cultures aiming to investigate stimuli for chondrogenic induction., (© 2013 Wiley Periodicals, Inc.)

Objectives: To compare dual-energy CT images (DECT) directly with gold standard histology., Methods: A 85-year-old woman with chronic recurrent gouty arthritis and macroscopically visible tophi was assessed with DECT-scans of her feet. When she died 7 days later, three tophi in different regions and in different tissues of her left foot were processed for histological examination., Results: Of the selected tophi, two were almost completely missed by the color-coding DECT sequences. The tophi remained in most of their volume below the detection threshold value of 150HU (default value)., Conclusions: It could be demonstrated that DECT only highlights the dense tophi (corresponding of approximately 15-20vol% urate in the tophus). Less dense tophi, despite considerable size, will be missed in the color-coded images., (© 2013 Published by Elsevier Inc.)

Background: The purpose of this study was to assess the relationship of CT-perfusion (CTP), 18F-FDG-PET/CT and histological parameters, and the possible added value of CTP to FDG-PET/CT in the initial staging of lung cancer., Methods: Fifty-four consecutive patients (median age 65 years, 15 females, 39 males) with suspected lung cancer were evaluated prospectively by CT-perfusion scan and 18F-FDG-PET/CT scan. Overall, 46 tumors were identified. CTP parameters blood flow (BF), blood volume (BV), and mean transit time (MTT) of the tumor tissue were calculated. Intratumoral microvessel density (MVD) was assessed quantitatively. Differences in CTP parameters concerning tumor type, location, PET positivity of lymph nodes, TNM status, and UICC stage were analyzed. Spearman correlation analyses between CTP and 18F-FDG-PET/CT parameters (SUVmax, SUVmean, PETvol, and TLG), MVD, tumor size, and tumor stage were performed., Results: The mean BF (mL/100 mL min-1), BV (mL/100 mL), and MTT (s) was 35.5, 8.4, and 14.2, respectively. The BF and BV were lower in tumors with PET-positive lymph nodes (p = 0.02). However, the CTP values were not significantly different among the N stages. The CTP values were not different, depending on tumor size and location. No significant correlation was found between CTP parameters and MVD., Conclusions: Overall, the CTP information showed only little additional information for the initial staging compared with standard FDG-PET/CT. Low perfusion in lung tumors might possibly be associated with metabolically active regional lymph nodes. Apart from that, both CTP and 18F-FDG-PET/CT parameter sets may reflect different pathophysiological mechanisms in lung cancer.