Stability in Ecosystem Functioning across a Climatic Threshold and Contrasting Forest Regimes

Classical ecological theory predicts that changes in the availability of essential resources such as nitrogen should lead to changes in plant community composition due to differences in species-specific nutrient requirements. What remains unknown, however, is the extent to which climate change will alter the relationship between plant communities and the nitrogen cycle. During intervals of climate change, do changes in nitrogen cycling lead to vegetation change or do changes in community composition alter the nitrogen dynamics? We used long-term ecological data to determine the role of nitrogen availability in changes of forest species composition under a rapidly changing climate during the early Holocene (16k to 8k cal. yrs. BP). A statistical computational analysis of ecological data spanning 8,000 years showed that secondary succession from a coniferous to deciduous forest occurred independently of changes in the nitrogen cycle. As oak replaced pine under a warming climate, nitrogen cycling rates increased. Interestingly, the mechanism by which the species interacted with nitrogen remained stable across this threshold change in climate and in the dominant tree species. This suggests that changes in tree population density over successional time scales are not driven by nitrogen availability. Thus, current models of forest succession that incorporate the effects of available nitrogen may be over-estimating tree population responses to changes in this resource, which may result in biased predictions of future forest dynamics under climate warming

Genomic activation of the EGFR and HER2-neu genes in a significant proportion of invasive epithelial ovarian cancers

<p>Abstract</p> <p>Background</p> <p>The status of the EGFR and HER2-neu genes has not been fully defined in ovarian cancer. An integrated analysis of both genes could help define the proportion of patients that would potentially benefit from targeted therapies.</p> <p>Methods</p> <p>We determined the tumour mutation status of the entire tyrosine kinase (TK) domain of the EGFR and HER2-neu genes in a cohort of 52 patients with invasive epithelial ovarian cancer as well as the gene copy number and protein expression of both genes in 31 of these patients by DGGE and direct sequecing, immunohistochemistry and Fluorescent in Situ Hybridisation (FISH).</p> <p>Results</p> <p>The EGFR was expressed in 59% of the cases, with a 2+/3+ staining intensity in 38%. HER2-neu expression was found in 35%, with a 2/3+ staining in 18%. No mutations were found in exons 18–24 of the TK domains of EGFR and HER2-neu. High polysomy of the EGFR gene was observed in 13% of the invasive epthelial cancers and amplification of the HER2-neu gene was found in 10% and correlated with a high expression level by immunohistochemistry.</p> <p>Mutations within the tyrosine kinase domain were not found in the entire TK domain of both genes, but have been found in very rare cases by others.</p> <p>Conclusion</p> <p>Genomic alteration of the HER2-neu and EGFR genes is frequent (25%) in ovarian cancer. EGFR/HER2-neu targeted therapies should be investigated prospectively and specifically in that subset of patients.</p

imPlatelet classifier: image-converted RNA biomarker profiles enable blood-based cancer diagnostics

Liquid biopsies offer a minimally invasive sample collection, outperforming traditional biopsies employed for cancer evaluation. The widely used material is blood, which is the source of tumor-educated platelets. Here, we developed the imPlatelet classifier, which converts RNA-sequenced platelet data into images in which each pixel corresponds to the expression level of a certain gene. Biological knowledge from the Kyoto Encyclopedia of Genes and Genomes was also implemented to improve accuracy. Images obtained from samples can then be compared against standard images for specific cancers to determine a diagnosis. We tested imPlatelet on a cohort of 401 non-small cell lung cancer patients, 62 sarcoma patients, and 28 ovarian cancer patients. imPlatelet provided excellent discrimination between lung cancer cases and healthy controls, with accuracy equal to 1 in the independent dataset. When discriminating between noncancer cases and sarcoma or ovarian cancer patients, accuracy equaled 0.91 or 0.95, respectively, in the independent datasets. According to our knowledge, this is the first study implementing an image-based deep-learning approach combined with biological knowledge to classify human samples. The performance of imPlatelet considerably exceeds previously published methods and our own alternative attempts of sample discrimination. We show that the deep-learning image-based classifier accurately identifies cancer, even when a limited number of samples are available.publishedVersio

Correlation of EGFR expression, gene copy number and clinicopathological status in NSCLC

Background: Epidermal Growth Factor Receptor (EGFR) targeting therapies are currently of great relevance for the treatment of lung cancer. For this reason, in addition to mutational analysis immunohistochemistry (IHC) of EGFR in lung cancer has been discussed for the decision making of according therapeutic strategies. The aim of this study was to obtain standardization of EGFR-expression methods for the selection of patients who might benefit of EGFR targeting therapies. Methods: As a starting point of a broad investigation, aimed at elucidating the expression of EGFR on different biological levels, four EGFR specific antibodies were analyzed concerning potential differences in expression levels by Immunohistochemistry (IHC) and correlated with fluorescence in situ hybridization (FISH) analysis and clinicopathological data. 206 tumor tissues were analyzed in a tissue microarray format employing immunohistochemistry with four different antibodies including Dako PharmDx kit (clone 2-18C9), clone 31G7, clone 2.1E1 and clone SP84 using three different scoring methods. Protein expression was compared to FISH utilizing two different probes. Results: EGFR protein expression determined by IHC with Dako PharmDx kit, clone 31G7 and clone 2.1E1 (≤ 0.05) correlated significantly with both FISH probes independently of the three scoring methods; best correlation is shown for 31G7 using the scoring method that defined EGFR positivity when ≥ 10% of the tumor cells show membranous staining of moderate and severe intensity (p = 0.001). Conclusion: Overall, our data show differences in EGFR expression determined by IHC, due to the applied antibody. Highest concordance with FISH is shown for antibody clone 31G7, evaluated with score B (p = 0.001). On this account, this antibody clone might by utilized for standard evaluation of EGFR expression by IHC

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

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