Classification and risk stratification of invasive breast carcinomas using a real-time quantitative RT-PCR assay

INTRODUCTION: Predicting the clinical course of breast cancer is often difficult because it is a diverse disease comprised of many biological subtypes. Gene expression profiling by microarray analysis has identified breast cancer signatures that are important for prognosis and treatment. In the current article, we use microarray analysis and a real-time quantitative reverse-transcription (qRT)-PCR assay to risk-stratify breast cancers based on biological 'intrinsic' subtypes and proliferation. METHODS: Gene sets were selected from microarray data to assess proliferation and to classify breast cancers into four different molecular subtypes, designated Luminal, Normal-like, HER2+/ER-, and Basal-like. One-hundred and twenty-three breast samples (117 invasive carcinomas, one fibroadenoma and five normal tissues) and three breast cancer cell lines were prospectively analyzed using a microarray (Agilent) and a qRT-PCR assay comprised of 53 genes. Biological subtypes were assigned from the microarray and qRT-PCR data by hierarchical clustering. A proliferation signature was used as a single meta-gene (log(2 )average of 14 genes) to predict outcome within the context of estrogen receptor status and biological 'intrinsic' subtype. RESULTS: We found that the qRT-PCR assay could determine the intrinsic subtype (93% concordance with microarray-based assignments) and that the intrinsic subtypes were predictive of outcome. The proliferation meta-gene provided additional prognostic information for patients with the Luminal subtype (P = 0.0012), and for patients with estrogen receptor-positive tumors (P = 3.4 × 10(-6)). High proliferation in the Luminal subtype conferred a 19-fold relative risk of relapse (confidence interval = 95%) compared with Luminal tumors with low proliferation. CONCLUSION: A real-time qRT-PCR assay can recapitulate microarray classifications of breast cancer and can risk-stratify patients using the intrinsic subtype and proliferation. The proliferation meta-gene offers an objective and quantitative measurement for grade and adds significant prognostic information to the biological subtypes

Temporal scale‐dependence of plant–pollinator networks

The study of mutualistic interaction networks has led to valuable insights into ecological and evolutionary processes. However, our understanding of network structure may depend upon the temporal scale at which we sample and analyze network data. To date, we lack a comprehensive assessment of the temporal scale-dependence of network structure across a wide range of temporal scales and geographic locations. If network structure is temporally scale-dependent, networks constructed over different temporal scales may provide very different perspectives on the structure and composition of species interactions. Furthermore, it remains unclear how various factors – including species richness, species turnover, link rewiring and sampling effort – act in concert to shape network structure across different temporal scales. To address these issues, we used a large database of temporally-resolved plant–pollinator networks to investigate how temporal aggregation from the scale of one day to multiple years influences network structure. In addition, we used structural equation modeling to explore the direct and indirect effects of temporal scale, species richness, species turnover, link rewiring and sampling effort on network structural properties. We find that plant–pollinator network structure is strongly temporally-scale dependent. This general pattern arises because the temporal scale determines the degree to which temporal dynamics (i.e. phenological turnover of species and links) are included in the network, in addition to how much sampling effort is put into constructing the network. Ultimately, the temporal scale-dependence of our plant–pollinator networks appears to be mostly driven by species richness, which increases with sampling effort, and species turnover, which increases with temporal extent. In other words, after accounting for variation in species richness, network structure is increasingly shaped by its underlying temporal dynamics. Our results suggest that considering multiple temporal scales may be necessary to fully appreciate the causes and consequences of interaction network structure.Fil: Schwarz, Benjamin. Albert Ludwigs University of Freiburg; AlemaniaFil: Vazquez, Diego P.. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Mendoza. Instituto Argentino de Investigaciones de las Zonas Áridas. Provincia de Mendoza. Instituto Argentino de Investigaciones de las Zonas Áridas. Universidad Nacional de Cuyo. Instituto Argentino de Investigaciones de las Zonas Áridas; ArgentinaFil: Cara Donna, Paul J.. Chicago Botanic Garden; Estados UnidosFil: Knight, Tiffany M.. German Centre for Integrative Biodiversity Research; AlemaniaFil: Benadi, Gita. Albert Ludwigs University of Freiburg; AlemaniaFil: Dormann, Carsten F.. Albert Ludwigs University of Freiburg; AlemaniaFil: Gauzens, Benoit. German Centre for Integrative Biodiversity Research; AlemaniaFil: Motivans, Elena. German Centre for Integrative Biodiversity Research; AlemaniaFil: Resasco, Julian. University of Colorado; Estados UnidosFil: Blüthgen, Nico. Universitat Technische Darmstadt; AlemaniaFil: Burkle, Laura A.. Montana State University; AlemaniaFil: Fang, Qiang. Henan University of Science and Technology; ChinaFil: Kaiser Bunbury, Christopher N.. University of Exeter; Reino UnidoFil: Alarcón, Ruben. California State University; Estados UnidosFil: Bain, Justin A.. Chicago Botanic Garden; Estados UnidosFil: Chacoff, Natacha Paola. Universidad Nacional de Tucumán. Instituto de Ecología Regional. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Tucumán. Instituto de Ecología Regional; ArgentinaFil: Huang, Shuang Quan. Central China Normal University; ChinaFil: LeBuhn, Gretchen. San Francisco State University; Estados UnidosFil: MacLeod, Molly. Rutgers University; Estados UnidosFil: Petanidou, Theodora. Univversity of the Aegean; Estados UnidosFil: Rasmussen, Claus. University Aarhus; DinamarcaFil: Simanonok, Michael P.. Montana State University; Estados UnidosFil: Thompson, Amibeth H.. German Centre for Integrative Biodiversity Research; AlemaniaFil: Fründ, Jochen. Albert Ludwigs University of Freiburg; Alemani

A high-resolution map of human evolutionary constraint using 29 mammals.

The comparison of related genomes has emerged as a powerful lens for genome interpretation. Here we report the sequencing and comparative analysis of 29 eutherian genomes. We confirm that at least 5.5% of the human genome has undergone purifying selection, and locate constrained elements covering ∼4.2% of the genome. We use evolutionary signatures and comparisons with experimental data sets to suggest candidate functions for ∼60% of constrained bases. These elements reveal a small number of new coding exons, candidate stop codon readthrough events and over 10,000 regions of overlapping synonymous constraint within protein-coding exons. We find 220 candidate RNA structural families, and nearly a million elements overlapping potential promoter, enhancer and insulator regions. We report specific amino acid residues that have undergone positive selection, 280,000 non-coding elements exapted from mobile elements and more than 1,000 primate- and human-accelerated elements. Overlap with disease-associated variants indicates that our findings will be relevant for studies of human biology, health and disease

A High-Resolution Map of Human Evolutionary Constraint Using 29 Mammals

The comparison of related genomes has emerged as a powerful lens for genome interpretation. Here we report the sequencing and comparative analysis of 29 eutherian genomes. We confirm that at least 5.5% of the human genome has undergone purifying selection, and locate constrained elements covering ~4.2% of the genome. We use evolutionary signatures and comparisons with experimental data sets to suggest candidate functions for ~60% of constrained bases. These elements reveal a small number of new coding exons, candidate stop codon readthrough events and over 10,000 regions of overlapping synonymous constraint within protein-coding exons. We find 220 candidate RNA structural families, and nearly a million elements overlapping potential promoter, enhancer and insulator regions. We report specific amino acid residues that have undergone positive selection, 280,000 non-coding elements exapted from mobile elements and more than 1,000 primate- and human-accelerated elements. Overlap with disease-associated variants indicates that our findings will be relevant for studies of human biology, health and disease.National Human Genome Research Institute (U.S.)National Institute of General Medical Sciences (U.S.) (Grant number GM82901)National Science Foundation (U.S.). Postdoctural Fellowship (Award 0905968)National Science Foundation (U.S.). Career (0644282)National Institutes of Health (U.S.) (R01-HG004037)Alfred P. Sloan Foundation.Austrian Science Fund. Erwin Schrodinger Fellowshi

Trans-ethnic Meta-analysis and Functional Annotation Illuminates the Genetic Architecture of Fasting Glucose and Insulin

Knowledge of the genetic basis of the type 2 diabetes (T2D)-related quantitative traits fasting glucose (FG) and insulin (FI) in African ancestry (AA) individuals has been limited. In non-diabetic subjects of AA (n = 20,209) and European ancestry (EA; n = 57,292), we performed trans-ethnic (AA+EA) fine-mapping of 54 established EA FG or FI loci with detailed functional annotation, assessed their relevance in AA individuals, and sought previously undescribed loci through trans-ethnic (AA+EA) meta-analysis. We narrowed credible sets of variants driving association signals for 22/54 EA-associated loci; 18/22 credible sets overlapped with active islet-specific enhancers or transcription factor (TF) binding sites, and 21/22 contained at least one TF motif. Of the 54 EA-associated loci, 23 were shared between EA and AA. Replication with an additional 10,096 AA individuals identified two previously undescribed FI loci, chrX FAM133A (rs213676) and chr5 PELO (rs6450057). Trans-ethnic analyses with regulatory annotation illuminate the genetic architecture of glycemic traits and suggest gene regulation as a target to advance precision medicine for T2D. Our approach to utilize state-of-the-art functional annotation and implement trans-ethnic association analysis for discovery and fine-mapping offers a framework for further follow-up and characterization of GWAS signals of complex trait loc

Impact of Optimized Breastfeeding on the Costs of Necrotizing Enterocolitis in Extremely Low Birthweight Infants

To estimate risk of NEC for ELBW infants as a function of preterm formula and maternal milk (MM) intake and calculate the impact of suboptimal feeding on NEC incidence and costs

Omecamtiv mecarbil in chronic heart failure with reduced ejection fraction, GALACTIC‐HF: baseline characteristics and comparison with contemporary clinical trials

Aims: The safety and efficacy of the novel selective cardiac myosin activator, omecamtiv mecarbil, in patients with heart failure with reduced ejection fraction (HFrEF) is tested in the Global Approach to Lowering Adverse Cardiac outcomes Through Improving Contractility in Heart Failure (GALACTIC‐HF) trial. Here we describe the baseline characteristics of participants in GALACTIC‐HF and how these compare with other contemporary trials. Methods and Results: Adults with established HFrEF, New York Heart Association functional class (NYHA) ≥ II, EF ≤35%, elevated natriuretic peptides and either current hospitalization for HF or history of hospitalization/ emergency department visit for HF within a year were randomized to either placebo or omecamtiv mecarbil (pharmacokinetic‐guided dosing: 25, 37.5 or 50 mg bid). 8256 patients [male (79%), non‐white (22%), mean age 65 years] were enrolled with a mean EF 27%, ischemic etiology in 54%, NYHA II 53% and III/IV 47%, and median NT‐proBNP 1971 pg/mL. HF therapies at baseline were among the most effectively employed in contemporary HF trials. GALACTIC‐HF randomized patients representative of recent HF registries and trials with substantial numbers of patients also having characteristics understudied in previous trials including more from North America (n = 1386), enrolled as inpatients (n = 2084), systolic blood pressure < 100 mmHg (n = 1127), estimated glomerular filtration rate < 30 mL/min/1.73 m2 (n = 528), and treated with sacubitril‐valsartan at baseline (n = 1594). Conclusions: GALACTIC‐HF enrolled a well‐treated, high‐risk population from both inpatient and outpatient settings, which will provide a definitive evaluation of the efficacy and safety of this novel therapy, as well as informing its potential future implementation

An integrated digital/clinical approach to smoking cessation in lung cancer screening: study protocol for a randomized controlled trial

Abstract Background Delivering effective tobacco dependence treatment that is feasible within lung cancer screening (LCS) programs is crucial for realizing the health benefits and cost savings of screening. Large-scale trials and systematic reviews have demonstrated that digital cessation interventions (i.e. web-based and text message) are effective, sustainable over the long-term, scalable, and cost-efficient. Use of digital technologies is commonplace among older adults, making this a feasible approach within LCS programs. Use of cessation treatment has been improved with models that proactively connect smokers to treatment rather than passive referrals. Proactive referral to cessation treatment has been advanced through healthcare systems changes such as modifying the electronic health record to automatically link smokers to treatment. Methods This study evaluates the impact of a proactive enrollment strategy that links LCS-eligible smokers with an evidence-based intervention comprised of a web-based (WEB) program and integrated text messaging (TXT) in a three-arm randomized trial with repeated measures at one, three, six, and 12 months post randomization. The primary outcome is biochemically confirmed abstinence at 12 months post randomization. We will randomize 1650 smokers who present for a clinical LCS to: (1) a usual care control condition (UC) which consists of Ask–Advise–Refer; (2) a digital (WEB + TXT) cessation intervention; or (3) a digital cessation intervention combined with tobacco treatment specialist (TTS) counseling (WEB + TXT + TTS). Discussion The scalability and sustainability of a digital intervention may represent the most cost-effective and feasible approach for LCS programs to proactively engage large numbers of smokers in effective cessation treatment. We will also evaluate the impact and cost-effectiveness of adding proven clinical intervention provided by a TTS. We expect that a combined digital/clinical intervention will yield higher quit rates than digital alone, but that it may not be as cost-effective or feasible for LCS programs to implement. This study is innovative in its use of interoperable, digital technologies to deliver a sustainable, scalable, high-impact cessation intervention and to facilitate its integration within clinical practice. It will add to the growing knowledge base about the overall effectiveness of digital interventions and their role in the healthcare delivery system. Trial registration ClinicalTrials.gov, NCT03084835 . Registered on 9 March 2017