ECCB 2018: The 17th European conference on computational biology

[No abstract available

Profibrotic role of miR-154 in pulmonary fibrosis.

In this study, we explored the regulation and the role of up-regulated microRNAs in idiopathic pulmonary fibrosis (IPF), a progressive interstitial lung disease of unknown origin. We analyzed the expression of microRNAs in IPF lungs and identified 43 significantly up-regulated microRNAs. Twenty-four of the 43 increased microRNAs were localized to the chromosome 14q32 microRNA cluster. We validated the increased expression of miR-154, miR-134, miR-299-5p, miR-410, miR-382, miR-409-3p, miR-487b, miR-31, and miR-127 by quantitative RT-PCR and determined that they were similarly expressed in embryonic lungs. We did not find evidence for differential methylation in this region, but analysis of transcription factor binding sites identified multiple SMAD3-binding elements in the 14q32 microRNA cluster. TGF-β1 stimulation of normal human lung fibroblasts (NHLF) caused up-regulation of microRNAs on chr14q32 that were also increased in IPF lungs. Chromatin immunoprecipitation confirmed binding of SMAD3 to the putative promoter of miR-154. Mir-154 was increased in IPF fibroblasts, and transfection of NHLF with miR-154 caused significant increases in cell proliferation and migration. The increase in proliferation induced by TGF-β was not observed when NHLF or IPF fibroblasts were transfected with a mir-154 inhibitor. Transfection with miR-154 caused activation of the WNT pathway in NHLF. ICG-001 and XAV939, inhibitors of the WNT/β-catenin pathway, reduced the proliferative effect of miR-154. The potential role of miR-154, one of multiple chr14q32 microRNA cluster members up-regulated in IPF and a regulator of fibroblast migration and proliferation, should be further explored in IPF

National survey of morbidity and risk factors (EMENO): Protocol for a health examination survey representative of the adult Greek population

Background: Main causes of death in Greece are cardiovascular diseases (CVDs), malignant neoplasms, respiratory diseases, and road traffic crashes. To assess the population health status, monitor health systems, and adjust policies, national population-based health surveys are recommended. The previous health surveys that were conducted in Greece were restricted to specific regions or high-risk groups. Objective: This paper presents the design and methods of the Greek Health Examination Survey EMENO (National Survey of Morbidity and Risk Factors). The primary objectives are to describe morbidity (focusing on CVD, respiratory diseases, and diabetes), related risk factors, as well as health care and preventive measures utility patterns in a random sample of adults living in Greece. Methods: The sample was selected by applying multistage stratified random sampling on 2011 Census. Trained interviewers and physicians made home visits. Standardized questionnaires were administered; physical examination, anthropometric and blood pressure measurements, and spirometry were performed. Blood samples were collected for lipid profile, glucose, glycated hemoglobin, and transaminases measurements. The survey was conducted from May 2013 until June 2016. Results: In total, 6006 individuals were recruited (response rate 72%). Of these, 4827 participated in at least one physical examination, 4446 had blood tests, and 3622 spirometry, whereas 3580 provided consent for using stored samples for future research (3528 including DNA studies). Statistical analysis has started, and first results are expected to be submitted for publication by the end of 2018. Conclusions: EMENO comprises a unique health data resource and a bio-resource in a Mediterranean population. Its results will provide valid estimates of morbidity and risk factors’ prevalence (overall and in specific subdomains) and health care and preventive measures usage in Greece, necessary for an evidence-based strategy planning of health policies and preventive activities. © Giota Touloumi, Anna Karakatsani, Argiro Karakosta, Eleni Sofianopoulou, Panagiotis Koustenis, Magda Gavana, Yannis Alamanos, Maria Kantzanou, George Konstantakopoulos, Xenia Chryssochoou, Alexis Benos, Apostolos Vantarakis, Christos Hadjichristodoulou, Gregory Chlouverakis, Gregory Trypsianis, Paraskevi V Voulgari, Konstantinos Makrilakis, Stavros Liatis, George Stergiou, EMENO Study Group

National survey of morbidity and risk factors (EMENO): Protocol for a health examination survey representative of the adult Greek population

Background: Main causes of death in Greece are cardiovascular diseases (CVDs), malignant neoplasms, respiratory diseases, and road traffic crashes. To assess the population health status, monitor health systems, and adjust policies, national population-based health surveys are recommended. The previous health surveys that were conducted in Greece were restricted to specific regions or high-risk groups. Objective: This paper presents the design and methods of the Greek Health Examination Survey EMENO (National Survey of Morbidity and Risk Factors). The primary objectives are to describe morbidity (focusing on CVD, respiratory diseases, and diabetes), related risk factors, as well as health care and preventive measures utility patterns in a random sample of adults living in Greece. Methods: The sample was selected by applying multistage stratified random sampling on 2011 Census. Trained interviewers and physicians made home visits. Standardized questionnaires were administered; physical examination, anthropometric and blood pressure measurements, and spirometry were performed. Blood samples were collected for lipid profile, glucose, glycated hemoglobin, and transaminases measurements. The survey was conducted from May 2013 until June 2016. Results: In total, 6006 individuals were recruited (response rate 72%). Of these, 4827 participated in at least one physical examination, 4446 had blood tests, and 3622 spirometry, whereas 3580 provided consent for using stored samples for future research (3528 including DNA studies). Statistical analysis has started, and first results are expected to be submitted for publication by the end of 2018. Conclusions: EMENO comprises a unique health data resource and a bio-resource in a Mediterranean population. Its results will provide valid estimates of morbidity and risk factors’ prevalence (overall and in specific subdomains) and health care and preventive measures usage in Greece, necessary for an evidence-based strategy planning of health policies and preventive activities. © Giota Touloumi, Anna Karakatsani, Argiro Karakosta, Eleni Sofianopoulou, Panagiotis Koustenis, Magda Gavana, Yannis Alamanos, Maria Kantzanou, George Konstantakopoulos, Xenia Chryssochoou, Alexis Benos, Apostolos Vantarakis, Christos Hadjichristodoulou, Gregory Chlouverakis, Gregory Trypsianis, Paraskevi V Voulgari, Konstantinos Makrilakis, Stavros Liatis, George Stergiou, EMENO Study Group

Practical Computational Methods for Regulatory Genomics: A cisGRN-Lexicon and cisGRN-Browser for Gene Regulatory Networks

The CYRENE Project focuses on the study of cis-regulatory genomics and gene regulatory networks (GRN) and has three components: a cisGRN-Lexicon, a cisGRN-Browser, and the Virtual Sea Urchin software system. The project has been done in collaboration with Eric Davidson and is deeply inspired by his experimental work in genomic regulatory systems and gene regulatory networks. The current CYRENE cisGRN-Lexicon contains the regulatory architecture of 200 transcription factors encoding genes and 100 other regulatory genes in eight species: human, mouse, fruit fly, sea urchin, nematode, rat, chicken, and zebrafish, with higher priority on the first five species. The only regulatory genes included in the cisGRN-Lexicon (CYRENE genes) are those whose regulatory architecture is validated by what we call the Davidson Criterion: they contain functionally authenticated sites by site-specific mutagenesis, conducted in vivo, and followed by gene transfer and functional test. This is recognized as the most stringent experimental validation criterion to date for such a genomic regulatory architecture. The CYRENE cisGRN-Browser is a full genome browser tailored for cis-regulatory annotation and investigation. It began as a branch of the Celera Genome Browser (available as open source a