The human protein atlas: Implications for human biology, drug development, and precision medicine

The Human Protein Atlas (HPA) is a Swedish-based program with the aim to map of all the human proteins in cells, tissues and organs using integration of various omics technologies, including genomics, transcriptomics, antibody-based imaging, mass spectrometry-based proteomics and systems biology. A Tissue Atlas was launch in 2015 (1) followed by a Cell Atlas in 2016 (2) and a Pathology Atlas in 2017 (3). This open access knowledge-base can be used to explore targets for next generation antibody therapeutics, as well as a discovery tool to find potential biomarkers and drug targets for disease (4,5). A focus has been to use a new drug development platform based on the affibody molecule developed in our group and use this concept for applications in cancer, autoimmune diseases and neurodegenerative diseases. Recently, we have set-up an animal cell factory using CHO cells with the aim to produce full-length proteins representing all the 2,000 secreted proteins encoded in human genome. The Human Protein Atlas program has already contributed to several thousands of publications in the field of human biology and disease and it was recently selected by the organization ELIXIR as a European core resource, due to its fundamental importance for a wider life science community. All the data in the knowledge resource is open access to allow scientists both in academia and industry to freely access the data for exploration of the human proteome. Selected recent references: 1. Uhlen et al (2015) Science 347: 394 2. Thul et al (2017), Science 356:6340 3. Uhlen et al (2017) Science (August 18) 4. Uhlen et al (2016) Mol Systems Biol. 12: 862 5. Lee et al (2016) Cell Metabolism 12;24(1):172-8

International Law and State Socialization: Conceptual, Empirical, and Normative Challenges

This article reports the results from the implementation and testing of a Wide-Area Power Oscillation Damper (WAPOD) controlling a 180 Mvar TCR Static Var Compensator (SVC) installed in the Hasle substation of Norwegian 420 kV transmission grid. The WAPOD uses voltage phase angle signals from two distant locations in the Norwegian grid as inputs to the damping controller. The damping controller modulates the voltage reference set point used by the SVC’s voltage controller, thereby creating a damping effect. The WAPOD is an extension to the existing Power Oscillation Damping (POD) controller that uses local measurements. A switch-over logic allows for the use of no damping control, local damping control or wide-area control. Field tests were performed during November 2011, and involved the disconnection and re-connection of a 420 kV transmission line. The performance of the WAPOD is compared to that of state-of-the-art local Phasor POD, and when no damping control is enabled. The testing results show that the WAPOD performed satisfactorily and according to the design expectations. These results show that the potential flexibility of the WAPOD to choose, among the different PMU signals, those that have the good observability of inter-area modes can be an advantage to the use of local feedback signals for damping control, as it is current practice today. Further testing of this WAPOD with other PMU signals from locations with stronger observability will be helpful to illustrate the advantage of this flexibility.QC 20140512Invited Paper for the Panel Session: “Synchrophasor Measurement Applications in Power Industry to Enhance Power System Reliability”, IEEE PES General Meeting 2012, San Diego, CA.</p

Human protein secretory pathway genes are expressed in a tissue-specific pattern to match processing demands of the secretome

Protein secretory pathway in eukaryal cells is responsible for delivering functional secretory proteins. The dysfunction of this pathway causes a range of important human diseases from congenital disorders to cancer. Despite the piled-up knowledge on the molecular biology and biochemistry level, the tissue-specific expression of the secretory pathway genes has not been analyzed on the transcriptome level. Based on the recent RNA-sequencing studies, the largest fraction of tissue-specific transcriptome encodes for the secretome (secretory proteins). Here, the question arises that if the expression levels of the secretory pathway genes have a tissue-specific tuning. In this study, we tackled this question by performing a meta-analysis of the recently published transcriptome data on human tissues. As a result, we detected 68 as called “extreme genes” which show an unusual expression pattern in specific gene families of the secretory pathway. We also inspected the potential functional link between detected extreme genes and the corresponding tissues enriched secretome. As a result, the detected extreme genes showed correlation with the enrichment of the nature and number of specific post-translational modifications in each tissue’s secretome. Our findings conciliate both the housekeeping and tissue-specific nature of the protein secretory pathway, which we attribute to a fine-tuned regulation of defined gene families to support the diversity of secreted proteins and their modifications

Scheffersomyces stipitis: a comparative systems biology study with the Crabtree positive yeast Saccharomyces cerevisiae

<p>Abstract</p> <p>Background</p> <p><it>Scheffersomyces stipitis</it> is a Crabtree negative yeast, commonly known for its capacity to ferment pentose sugars. Differently from Crabtree positive yeasts such as <it>Saccharomyces cerevisiae</it>, the onset of fermentation in <it>S. stipitis</it> is not dependent on the sugar concentration, but is regulated by a decrease in oxygen levels. Even though <it>S. stipitis</it> has been extensively studied due to its potential application in pentoses fermentation, a limited amount of information is available about its metabolism during aerobic growth on glucose. Here, we provide a systems biology based comparison between the two yeasts, uncovering the metabolism of <it>S. stipitis</it> during aerobic growth on glucose under batch and chemostat cultivations.</p> <p>Results</p> <p>Starting from the analysis of physiological data, we confirmed through ¹³C-based flux analysis the fully respiratory metabolism of <it>S. stipitis</it> when growing both under glucose limited or glucose excess conditions. The patterns observed showed similarity to the fully respiratory metabolism observed for <it>S. cerevisiae</it> under chemostat cultivations however, intracellular metabolome analysis uncovered the presence of several differences in metabolite patterns. To describe gene expression levels under the two conditions, we performed RNA sequencing and the results were used to quantify transcript abundances of genes from the central carbon metabolism and compared with those obtained with <it>S. cerevisiae</it>. Interestingly, genes involved in central pathways showed different patterns of expression, suggesting different regulatory networks between the two yeasts. Efforts were focused on identifying shared and unique families of transcription factors between the two yeasts through <it>in silico</it> transcription factors analysis, suggesting a different regulation of glycolytic and glucoenogenic pathways.</p> <p>Conclusions</p> <p>The work presented addresses the impact of high-throughput methods in describing and comparing the physiology of Crabtree positive and Crabtree negative yeasts. Based on physiological data and flux analysis we identified the presence of one metabolic condition for <it>S. stipitis</it> under aerobic batch and chemostat cultivations, which shows similarities to the oxidative metabolism observed for <it>S. cerevisiae</it> under chemostat cultivations. Through metabolome analysis and genome-wide transcriptomic analysis several differences were identified. Interestingly, <it>in silico</it> analysis of transciption factors was useful to address a different regulation of mRNAs of genes involved in the central carbon metabolism. To our knowledge, this is the first time that the metabolism of <it>S. stiptis</it> is investigated in details and is compared to <it>S. cerevisiae</it>. Our study provides useful results and allows for the possibility to incorporate these data into recently developed genome-scaled metabolic, thus contributing to improve future industrial applications of <it>S. stipitis</it> as cell factory.</p

Discovery of dachshund 2 protein as a novel biomarker of poor prognosis in epithelial ovarian cancer

<p>Abstract</p> <p>Background</p> <p>The Dachshund homolog 2 (<it>DACH2</it>) gene has been implicated in development of the female genital tract in mouse models and premature ovarian failure syndrome, but to date, its expression in human normal and cancerous tissue remains unexplored. Using the Human Protein Atlas as a tool for cancer biomarker discovery, DACH2 protein was found to be differentially expressed in epithelial ovarian cancer (EOC). Here, the expression and prognostic significance of DACH2 was further evaluated in ovarian cancer cell lines and human EOC samples.</p> <p>Methods</p> <p>Immunohistochemical expression of DACH2 was examined in tissue microarrays with 143 incident EOC cases from two prospective, population-based cohorts, including a subset of benign-appearing fallopian tubes (n = 32). A nuclear score (NS), i.e. multiplier of staining fraction and intensity, was calculated. For survival analyses, cases were dichotomized into low (NS < = 3) and high (NS > 3) using classification and regression tree analysis. Kaplan Meier analysis and Cox proportional hazards modelling were used to assess the impact of DACH2 expression on survival. DACH2 expression was analysed in the cisplatin sensitive ovarian cancer cell line A2780 and its cisplatin resistant derivative A2780-Cp70. The specificity of the DACH2 antibody was tested using siRNA-mediated silencing of DACH2 in A2780-Cp70 cells.</p> <p>Results</p> <p>DACH2 expression was considerably higher in the cisplatin resistant A2780-Cp70 cells compared to the cisplatin-sensitive A2780 cells. While present in all sampled fallopian tubes, DACH2 expression ranged from negative to strong in EOC. In EOC, DACH2 expression correlated with several proteins involved in DNA integrity and repair, and proliferation. DACH2 expression was significantly higher in carcinoma of the serous subtype compared to non-serous carcinoma. In the full cohort, high DACH2 expression was significantly associated with poor prognosis in univariable analysis, and in carcinoma of the serous subtype, DACH2 remained an independent factor of poor prognosis.</p> <p>Conclusions</p> <p>This study provides a first demonstration of DACH2 protein being expressed in human fallopian tubes and EOC, with the highest expression in serous carcinoma where DACH2 was found to be an independent biomarker of poor prognosis. Future research should expand on the role of DACH2 in ovarian carcinogenesis and chemotherapy resistance.</p

PET/CT with 18F-FDG and 68Ga-DOTATOC in pulmonary carcinoid imaging

Background: PET/CT, positron emission tomography combined with computed tomography, with 18F-FDG (2-deoxy-2-[18F]fluoro-D-glucose) is well established in oncological imaging. Pulmonary carcinoid tumours may have metabolic activity, making them available for PET/CT imaging with 18F-FDG. Positron-emitting isotope-labelled somatostatin analogues, such as DOTATOC (DOTA = 1,4,7,10-tetraazacyclo-dodecane-1,4,7,10-tetraacetic acid, TOC = D-Phe1-Tyr3-Octreotide), have during the last years become more widely available for imaging of abdominal neuroendocrine neoplasms by PET. 68Ga -DOTATOC PET is recommended by the latest version of the National Care Program for neuroendocrine abdominal tumours (2018) in Sweden, for the imaging work-up of patients with suspected or verified abdominal neuroendocrine tumour, https://www.cancercentrum.se/samverkan/cancerdiagnoser/neuroendokrina-buktumorer/vardprogram/gallande-vardprogram/, [cited 2019 aug 15]. Pulmonary carcinoid tumours exhibit somatostatin receptors (SSTRs). PET/CT with 68Ga-DOTATOC presents the possibility of a more accurate evaluation of respiratory tract neoplasms such as pulmonary carcinoids. Purpose: To differentiate pulmonary carcinoids from pulmonary hamartomas and typical from atypical pulmonary carcinoids by means of 18F-FDG PET and/or 18F-FDG PET and 68Ga -DOTATOC PET. Study I showed that 18F-FDG PET/CT can distinguish pulmonary carcinoids from pulmonary hamartomas with a negative predictive value (NPV) of 92% by applying a partial volume effect corrected for the maximum standardised uptake value (SUVmax ) of 1.5 as a cutoff. However, these 18F-FDG PET measurements do not allow for the distinction between atypical and typical pulmonary carcinoids. Study II evaluated 18F-FDG PET/CT and 68Ga-DOTATOC PET/CT scans in pulmonary carcinoids in correlation with SSTR expression profiles, tumour proliferation and pulmonary carcinoid subtype (typical / atypical). No correlation was found between 18F-FDG or 68Ga-DOTATOC tracer uptake in PET/CT and tumour subtype (typical pulmonary carcinoid / atypical pulmonary carcinoid). Correlation between 68Ga-DOTATOC and 18F-FDG uptake, using the tumour-to-normal-liver ratio, and immunohistochemistry in tumours, regarded as somatostatin receptor subtype 2 (or 2 and 5), was investigated. Between 68Ga-DOTATOC and 18F-FDG uptake, an inverse imaging phenotype was shown in relation to the SSTR expression profile with high 68Ga-DOTATOC accumulation and low 18F-FDG uptake in carcinoids positive for SSTR subtypes 2 (or 2 and 5) and conversely, low 68Ga-DOTATOC accumulation and high 18F-FDG uptake in carcinoids negative for SSTR subtypes 2 (or 2 and 5). 68Ga-DOTATOC uptake was significantly higher for tumours expressing SSTR subtypes 2 (or 2 and 5) as compared to the tumours not expressing SSTR subtypes 2 (or 2 and 5). 18F-FDG uptake and Ki-67 (a marker for cell proliferation) labelling index were significantly higher for tumours not expressing SSTR subtypes 2 (or 2 and 5) as compared to the other subgroups. 68Ga-DOTATOC and 18F-FDG uptake were found to reflect tumour grading (as formulated in the study), based on Ki-67 labelling index. Conclusions: It was possible to differentiate pulmonary carcinoids from hamartomas using PET measurements of the 18F-FDG-uptake in the tumours, corrected for partial volume effect. Clinically more aggressive, atypical pulmonary carcinoids could not be differentiated from typical pulmonary carcinoids by neither 18F-FDG PET/CT nor by 68Ga-DOTATOC PET/CT. In pulmonary carcinoid tumours, an increased 68Ga-DOTATOC uptake reflected somatostatin receptor subtype 2 and 5 expression. The genotypes in pulmonary carcinoids were reflected in the imaging phenotypes with inverse 68Ga-DOTATOC and 18F-FDG accumulation patterns related to the tumour somatostatin receptor profile and proliferative activity

Identification of an N-hydroxyguanidine reducing activity of xanthine oxidase

A guanoxabenz [1-(2,6-dichlorobenzylideneamino)-3-hydroxyguanidine; an N-hydroxyguanidine] reducing enzymatic activity of rat spleen cytosol was investigated by means of protein purification and N-terminal amino acid sequencing, the reducing activity was shown to reside in xanthine oxidase. The action of the enzyme on guanoxabenz resulted in the formation of guanabenz [1-(2,6-dichlorobenzylideneamino) -3-guanidine]; the product formation could be monitored by HPLC and its identity was confirmed by NMR analysis. The reduction of guanoxabenz required xanthine or NADH as reducing substrates, while the process could be blocked by allopurinol, a selective inhibitor of xanthine oxidase. By using bovine milk xanthine oxidase, the guanoxabenz reducing activity of the enzyme was also verified. We conclude that guanoxabenz is a novel electron acceptor structure for xanthine oxidase.publishersversionPeer reviewe

Prediction of indirect interactions in proteins

BACKGROUND: Both direct and indirect interactions determine molecular recognition of ligands by proteins. Indirect interactions can be defined as effects on recognition controlled from distant sites in the proteins, e.g. by changes in protein conformation and mobility, whereas direct interactions occur in close proximity of the protein's amino acids and the ligand. Molecular recognition is traditionally studied using three-dimensional methods, but with such techniques it is difficult to predict the effects caused by mutational changes of amino acids located far away from the ligand-binding site. We recently developed an approach, proteochemometrics, to the study of molecular recognition that models the chemical effects involved in the recognition of ligands by proteins using statistical sampling and mathematical modelling. RESULTS: A proteochemometric model was built, based on a statistically designed protein library's (melanocortin receptors') interaction with three peptides and used to predict which amino acids and sequence fragments that are involved in direct and indirect ligand interactions. The model predictions were confirmed by directed mutagenesis. The predicted presumed direct interactions were in good agreement with previous three-dimensional studies of ligand recognition. However, in addition the model could also correctly predict the location of indirect effects on ligand recognition arising from distant sites in the receptors, something that three-dimensional modelling could not afford. CONCLUSION: We demonstrate experimentally that proteochemometric modelling can be used with high accuracy to predict the site of origin of direct and indirect effects on ligand recognitions by proteins

The mucosa-associated bacteria from the sigmoid colon of nine healthy 60 years old individuals, identified by bacterial 16S rDNA

The bacterial flora of the gastro intestinal (GI) tract may be involved in chronic inflammation and colon cancer and affected by antibiotics, cytotoxic drugs and radiotherapy, trauma and intensive care therapy. It is important to map the mucosa-associated flora in healthy individuals to clarify the pathogenic risk under stressed conditions. The aim was to achieve an overview of the mucosa-associated bacterial flora in the sigmoid colon by direct 16S rDNA identification by sampling nine 60-years old volunteers, without clinical symptoms or medication. The bacterial flora was estimated by sequence analysis of cloned 16S rDNA as enriched by PCR from biopsies. 26% of the clones had ≥99% similarity to known species (36% had ≥98% similarity). The largest number of identified clones was related to Escherichia coli, Bacteroides vulgatus and Ruminicoccus torques. Most frequently distributed between the volunteers were Bacteroides uniformis and Bacteroides vulgatus (7 individuals). Bacteroides caccae, Bacteroides distasonis, Bacteroides putredinis, Bacteroides thetaiotaomicron and Ruminicoccus torques were found in 5 persons. Opportunistic pathogens found in more than one individual were Bacteroides fragilis, Escherichia coli and Bilophila wadsworthia. Acinetobacter baumannii, Brachyspira aalborgi, Cardiobacterium hominis, Clostridium perfringens, Klebsiella pneumoniae and Veillonella parvula were found in single individuals. A majority of the individuals had a heterogeneous flora but in one person, 91% of the clones were related to E. coli. The GI-flora differs between healthy individuals in respect to both composition and diversity, and it can include several opportunistic pathogens