Publications by authors named "Petros Kolovos"

36 Publications

Chromatin Conformation in Development and Disease.

Front Cell Dev Biol 2021 4;9:723859. Epub 2021 Aug 4.

Department of Molecular Biology and Genetics, Democritus University of Thrace, Alexandroupolis, Greece.

Chromatin domains and loops are important elements of chromatin structure and dynamics, but much remains to be learned about their exact biological role and nature. Topological associated domains and functional loops are key to gene expression and hold the answer to many questions regarding developmental decisions and diseases. Here, we discuss new findings, which have linked chromatin conformation with development, differentiation and diseases and hypothesized on various models while integrating all recent findings on how chromatin architecture affects gene expression during development, evolution and disease.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.3389/fcell.2021.723859DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8371409PMC
August 2021

Low Input Targeted Chromatin Capture (Low-T2C).

Methods Mol Biol 2021 ;2351:165-179

Department of Molecular Biology and Genetics, Democritus University of Thrace, University Campus Dragana, Alexandroupolis, Greece.

Targeted chromatin capture (T2C) is a 3C-based method and is used to study the 3D chromatin organization, interactomes and structural changes associated with gene regulation, progression through the cell cycle, and cell survival and development. Low input targeted chromatin capture (low-T2C) is an optimized version of the T2C protocol for low numbers of cells. Here, we describe the protocol for low-T2C, including all experimental steps and bioinformatics tools in detail.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1007/978-1-0716-1597-3_9DOI Listing
September 2021

The NUPHAC-EU Framework for Nurses' Role in Interprofessional Pharmaceutical Care: Cross-Sectional Evaluation in Europe.

Int J Environ Res Public Health 2021 07 25;18(15). Epub 2021 Jul 25.

Centre for Research and Innovation in Care (CRIC), Nurse and Pharmaceutical Care (NuPhaC), Department of Nursing and Midwifery Science, Faculty of Medicine and Health Sciences, University of Antwerp, 2610 Antwerp, Belgium.

Clear role descriptions promote the quality of interprofessional collaboration. Currently, it is unclear to what extent healthcare professionals consider pharmaceutical care (PC) activities to be nurses' responsibility in order to obtain best care quality. This study aimed to create and evaluate a framework describing potential nursing tasks in PC and to investigate nurses' level of responsibility. A framework of PC tasks and contextual factors was developed based on literature review and previous DeMoPhaC project results. Tasks and context were cross-sectionally evaluated using an online survey in 14 European countries. A total of 923 nurses, 240 physicians and 199 pharmacists responded. The majority would consider nurses responsible for tasks within: medication self-management (86-97%), patient education (85-96%), medication safety (83-95%), monitoring adherence (82-97%), care coordination (82-95%), and drug monitoring (78-96%). The most prevalent level of responsibility was 'with shared responsibility'. Prescription management tasks were considered to be nurses' responsibility by 48-81% of the professionals. All contextual factors were indicated as being relevant for nurses' role in PC by at least 74% of the participants. No task nor contextual factor was removed from the framework after evaluation. This framework can be used to enable healthcare professionals to openly discuss allocation of specific (shared) responsibilities and tasks.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.3390/ijerph18157862DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8345454PMC
July 2021

Developing a competence framework for nurses in pharmaceutical care: A Delphi study.

Nurse Educ Today 2021 Sep 24;104:104926. Epub 2021 Apr 24.

Research Group Care for the Chronically Ill, HU University of Applied Sciences Utrecht, Utrecht, the Netherlands. Electronic address:

Background: Nurses play an important role in pharmaceutical care. They are involved in: detecting clinical change; communicating/discussing pharmacotherapy with patients, their advocates, and other healthcare professionals; proposing and implementing medication-related interventions; and ensuring follow-up of patients and medication regimens. To date, a framework of nurses' competences on knowledge, skills, and attitudes as to interprofessional pharmaceutical care tasks is missing.

Objectives: To reach agreement with experts about nurses' competences for tasks in interprofessional pharmaceutical care.

Methods: A two-phase study starting with a scoping review followed by five Delphi rounds was performed. Competences extracted from the literature were assessed by an expert panel on relevance by using the RAND/UCLA method. The experts (n = 22) involved were healthcare professionals, nurse researchers, and educators from 14 European countries with a specific interest in nurses' roles in interprofessional pharmaceutical care. Descriptive statistics supported the data analysis.

Results: The expert panel reached consensus on the relevance of 60 competences for 22 nursing tasks. Forty-one competences were related to 15 generic nursing tasks and 33 competences were related to seven specific nursing tasks.

Conclusions: This study resulted in a competence framework for competency-based nurse education. Future research should focus on imbedding these competences in nurse education. A structured instrument should be developed to assess students' readiness to achieve competence in interprofessional pharmaceutical care in clinical practice.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.nedt.2021.104926DOI Listing
September 2021

Perspectives of nurses' role in interprofessional pharmaceutical care across 14 European countries: A qualitative study in pharmacists, physicians and nurses.

PLoS One 2021 27;16(5):e0251982. Epub 2021 May 27.

Faculty of Medicine and Health Sciences, University of Antwerp, Antwerp, Belgium.

Objectives: To understand healthcare professionals' experiences and perceptions of nurses' potential or ideal roles in pharmaceutical care (PC).

Design: Qualitative study conducted through semi-structured in-depth interviews.

Setting: Between December 2018 and October 2019, interviews were conducted with healthcare professionals of 14 European countries in four healthcare settings: hospitals, community care, mental health and long-term residential care.

Participants: In each country, pharmacists, physicians and nurses in each of the four settings were interviewed. Participants were selected on the basis that they were key informants with broad knowledge and experience of PC.

Data Collection And Analysis: All interviews were conducted face to face. Each country conducted an initial thematic analysis. Consensus was reached through a face-to-face discussion of all 14 national leads.

Results: 340 interviews were completed. Several tasks were described within four potential nursing responsibilities, that came up as the analysis themes, being: 1) monitoring therapeutic/adverse effects of medicines, 2) monitoring medicines adherence, 3) decision making on medicines, including prescribing 4) providing patient education/information. Nurses' autonomy varied across Europe, from none to limited to a few tasks and emergencies to a broad range of tasks and responsibilities. Intended level of autonomy depended on medicine types and level of education. Some changes are needed before nursing roles can be optimised and implemented in practice. Lack of time, shortage of nurses, absence of legal frameworks and limited education and knowledge are main threats to European nurses actualising their ideal role in PC.

Conclusions: European nurses have an active role in PC. Respondents reported positive impacts on care quality and patient outcomes when nurses assumed PC responsibilities. Healthcare professionals expect nurses to report observations and assessments. This key patient information should be shared and addressed by the interprofessional team. The study evidences the need of a unique and consensus-based PC framework across Europe.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0251982PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8158867PMC
October 2021

Interplay between FLI-1 and the LDB1 complex in murine erythroleukemia cells and during megakaryopoiesis.

iScience 2021 Mar 20;24(3):102210. Epub 2021 Feb 20.

Department of Cell Biology, Erasmus Medical Centre, 3015CN Rotterdam, the Netherlands.

Transcription factors are key players in a broad range of cellular processes such as cell-fate decision. Understanding how they act to control these processes is of critical importance for therapy purposes. FLI-1 controls several hematopoietic lineage differentiation including megakaryopoiesis and erythropoiesis. Its aberrant expression is often observed in cancer and is associated with poor prognosis. We showed that FLI-1 interacts with the LDB1 complex, which also plays critical roles in erythropoiesis and megakaryopoiesis. In this study, we aimed to unravel how FLI-1 and the LDB1 complex act together in murine erythroleukemia cells and in megakaryocyte. Combining omics techniques, we show that FLI-1 enables the recruitment of the LDB1 complex to regulatory sequences of megakaryocytic genes and to enhancers. We show as well for the first time that FLI-1 is able to modulate the 3D chromatin organization by promoting chromatin looping between enhancers and promoters most likely through the LDB1 complex.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.isci.2021.102210DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7940982PMC
March 2021

PR-DUB maintains the expression of critical genes through FOXK1/2- and ASXL1/2/3-dependent recruitment to chromatin and H2AK119ub1 deubiquitination.

Genome Res 2020 08 3;30(8):1119-1130. Epub 2020 Aug 3.

Biotech Research and Innovation Centre (BRIC), University of Copenhagen, DK-2200 Copenhagen N, Denmark.

Polycomb group proteins are important for maintaining gene expression patterns and cell identity in metazoans. The mammalian Polycomb repressive deubiquitinase (PR-DUB) complexes catalyze removal of monoubiquitination on lysine 119 of histone H2A (H2AK119ub1) through a multiprotein core comprised of BAP1, HCFC1, FOXK1/2, and OGT in combination with either of ASXL1, 2, or 3. Mutations in PR-DUB components are frequent in cancer. However, mechanistic understanding of PR-DUB function in gene regulation is limited. Here, we show that BAP1 is dependent on the ASXL proteins and FOXK1/2 in facilitating gene activation across the genome. Although PR-DUB was previously shown to cooperate with PRC2, we observed minimal overlap and functional interaction between BAP1 and PRC2 in embryonic stem cells. Collectively, these results demonstrate that PR-DUB, by counteracting accumulation of H2AK119ub1, maintains chromatin in an optimal configuration ensuring expression of genes important for general functions such as cell metabolism and homeostasis.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1101/gr.261016.120DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7462075PMC
August 2020

Targeted chromatin conformation analysis identifies novel distal neural enhancers of ZEB2 in pluripotent stem cell differentiation.

Hum Mol Genet 2020 08;29(15):2535-2550

Department of Cell Biology, Erasmus University Medical Center, Rotterdam, CN 3015, The Netherlands.

The transcription factor zinc finger E-box binding protein 2 (ZEB2) controls embryonic and adult cell fate decisions and cellular maturation in many stem/progenitor cell types. Defects in these processes in specific cell types underlie several aspects of Mowat-Wilson syndrome (MOWS), which is caused by ZEB2 haplo-insufficiency. Human ZEB2, like mouse Zeb2, is located on chromosome 2 downstream of a ±3.5 Mb-long gene-desert, lacking any protein-coding gene. Using temporal targeted chromatin capture (T2C), we show major chromatin structural changes based on mapping in-cis proximities between the ZEB2 promoter and this gene desert during neural differentiation of human-induced pluripotent stem cells, including at early neuroprogenitor cell (NPC)/rosette state, where ZEB2 mRNA levels increase significantly. Combining T2C with histone-3 acetylation mapping, we identified three novel candidate enhancers about 500 kb upstream of the ZEB2 transcription start site. Functional luciferase-based assays in heterologous cells and NPCs reveal co-operation between these three enhancers. This study is the first to document in-cis Regulatory Elements located in ZEB2's gene desert. The results further show the usability of T2C for future studies of ZEB2 REs in differentiation and maturation of multiple cell types and the molecular characterization of newly identified MOWS patients that lack mutations in ZEB2 protein-coding exons.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1093/hmg/ddaa141DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7471508PMC
August 2020

EUPRON: nurses' practice in interprofessional pharmaceutical care in Europe. A cross-sectional survey in 17 countries.

BMJ Open 2020 06 3;10(6):e036269. Epub 2020 Jun 3.

Nursing and Midwifery, Faculty of Medicine and Health Sciences, University of Antwerp, Wilrijk, Belgium.

Objectives: Safe pharmaceutical care (PC) requires an interprofessional team approach, involving physicians, nurses and pharmacists. Nurses' roles however, are not always explicit and clear, complicating interprofessional collaboration. The aim of this study is to describe nurses' practice and interprofessional collaboration in PC, from the viewpoint of nurses, physicians and pharmacists.

Design: A cross-sectional survey.

Setting: The study was conducted in 17 European countries, each with their own health systems.

Participants: Pharmacists, physicians and nurses with an active role in PC were surveyed.

Main Outcome Measures: Nurses' involvement in PC, experiences of interprofessional collaboration and communication and views on nurses' competences.

Results: A total of 4888 nurses, 974 physicians and 857 pharmacists from 17 European countries responded. Providing patient education and information (PEI), monitoring medicines adherence (MMA), monitoring adverse/therapeutic effects (ME) and prescribing medicines were considered integral to nursing practice by 78%, 73%, 69% and 15% of nurses, respectively. Most respondents were convinced that quality of PC would be improved by increasing nurses' involvement in ME (95%), MMA (95%), PEI (91%) and prescribing (53%). Mean scores for the reported quality of collaboration between nurses and physicians, collaboration between nurses and pharmacists and interprofessional communication were respectively <7/10, ≤4/10, <6/10 for all four aspects of PC.

Conclusions: ME, MMA, PEI and prescribing are part of nurses' activities, and most healthcare professionals felt their involvement should be extended. Collaboration between nurses and physicians on PC is limited and between nurses and pharmacists even more.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1136/bmjopen-2019-036269DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7282395PMC
June 2020

The dynamic emergence of GATA1 complexes identified in embryonic stem cell differentiation and mouse fetal liver.

Haematologica 2020 07 3;105(7):1802-1812. Epub 2019 Oct 3.

Department of Cell Biology, ErasmusMC, Rotterdam, the Netherlands

GATA1 is an essential transcriptional regulator of myeloid hematopoietic differentiation towards red blood cells. During erythroid differentiation, GATA1 forms different complexes with other transcription factors such as LDB1, TAL1, E2A and LMO2 ("the LDB1 complex") or with FOG1. The functions of GATA1 complexes have been studied extensively in definitive erythroid differentiation; however, the temporal and spatial formation of these complexes during erythroid development is unknown. We applied proximity ligation assay (PLA) to detect, localize and quantify individual interactions during embryonic stem cell differentiation and in mouse fetal liver (FL) tissue. We show that GATA1/LDB1 interactions appear before the proerythroblast stage and increase in a subset of the CD71/TER119 cells to activate the terminal erythroid differentiation program in 12.5 day FL. Using and knockdown FL cells, we studied the functional contribution of the GATA1/LDB1 complex during differentiation. This shows that the active LDB1 complex appears quite late at the proerythroblast stage of differentiation and confirms the power of PLA in studying the dynamic interaction of proteins in cell differentiation at the single cell level. We provide dynamic insight into the temporal and spatial formation of the GATA1 and LDB1 transcription factor complexes during hematopoietic development and differentiation.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.3324/haematol.2019.216010DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7327653PMC
July 2020

Nursing staff and patients' length of stay.

Int J Health Care Qual Assur 2019 Jul;32(6):1004-1012

Department of Nursing, University of Peloponnese , Tripoli, Greece.

Purpose: The purpose of this paper is to investigate the effect of nurse staffing, nurse education and work experience on patients' length of stay (LOS) in the Greek public hospitals.

Design/methodology/approach: A cross-sectional study, with retrospective administrative data, was implemented. From all seven Regional Health Authorities of Greece, 25 general surgical units in 17 public hospitals participated in the study.

Findings: All over the hospitals were studied, 32,287 patients ⩾17 years old and 203 nursing staff, who were working in the study units, were included in the analysis. According to the multivariate linear regression model, increased years of experience as a nurse (= -0.04, 95% CI= -0.06 to -0.02, =0.001) and increased percentage of registered nurse to the total nursing staff (= -1.18, CI= -1.88 to -0.47, =0.03) were associated with decreased patient LOS.

Originality/value: This was the first extended study in Greece, which explored the relationship between nurse staffing, nurse education, work experience and the LOS. The role that nurse staffing play together with its characteristics in the provision toward the quality healthcare services has already been recognized worldwide. The findings revealed the great shortage of nursing staff and the significant correlation between the work experience and educational level to patients' LOS.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1108/IJHCQA-09-2018-0215DOI Listing
July 2019

Modeling the Pathological Long-Range Regulatory Effects of Human Structural Variation with Patient-Specific hiPSCs.

Cell Stem Cell 2019 05 11;24(5):736-752.e12. Epub 2019 Apr 11.

Center for Molecular Medicine Cologne (CMMC), University of Cologne, Cologne, Germany; Cluster of Excellence Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, Cologne, Germany; Institute of Biomedicine and Biotechnology of Cantabria (IBBTEC), University of Cantabria, Cantabria, Spain. Electronic address:

The pathological consequences of structural variants disrupting 3D genome organization can be difficult to elucidate in vivo due to differences in gene dosage sensitivity between mice and humans. This is illustrated by branchiooculofacial syndrome (BOFS), a rare congenital disorder caused by heterozygous mutations within TFAP2A, a neural crest regulator for which humans, but not mice, are haploinsufficient. Here, we present a BOFS patient carrying a heterozygous inversion with one breakpoint located within a topologically associating domain (TAD) containing enhancers essential for TFAP2A expression in human neural crest cells (hNCCs). Using patient-specific hiPSCs, we show that, although the inversion shuffles the TFAP2A hNCC enhancers with novel genes within the same TAD, this does not result in enhancer adoption. Instead, the inversion disconnects one TFAP2A allele from its cognate enhancers, leading to monoallelic and haploinsufficient TFAP2A expression in patient hNCCs. Our work illustrates the power of hiPSC differentiation to unveil long-range pathomechanisms.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.stem.2019.03.004DOI Listing
May 2019

Investigation of the spatial structure and interactions of the genome at sub-kilobase-pair resolution using T2C.

Nat Protoc 2018 03 8;13(3):459-477. Epub 2018 Feb 8.

Department of Cell Biology, Erasmus Medical Centre, Rotterdam, the Netherlands.

Chromosome conformation capture (3C) and its derivatives (e.g., 4C, 5C and Hi-C) are used to analyze the 3D organization of genomes. We recently developed targeted chromatin capture (T2C), an inexpensive method for studying the 3D organization of genomes, interactomes and structural changes associated with gene regulation, the cell cycle, and cell survival and development. Here, we present the protocol for T2C based on capture, describing all experimental steps and bio-informatic tools in full detail. T2C offers high resolution, a large dynamic interaction frequency range and a high signal-to-noise ratio. Its resolution is determined by the resulting fragment size of the chosen restriction enzyme, which can lead to sub-kilobase-pair resolution. T2C's high coverage allows the identification of the interactome of each individual DNA fragment, which makes binning of reads (often used in other methods) basically unnecessary. Notably, T2C requires low sequencing efforts. T2C also allows multiplexing of samples for the direct comparison of multiple samples. It can be used to study topologically associating domains (TADs), determining their position, shape, boundaries, and intra- and inter-domain interactions, as well as the composition of aggregated loops, interactions between nucleosomes, individual transcription factor binding sites, and promoters and enhancers. T2C can be performed by any investigator with basic skills in molecular biology techniques in ∼7-8 d. Data analysis requires basic expertise in bioinformatics and in Linux and Python environments.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1038/nprot.2017.132DOI Listing
March 2018

The Effect of Nutrition and Sleep Habits on Predisposition for Metabolic Syndrome in Greek Children.

J Pediatr Nurs 2018 May - Jun;40:e2-e8. Epub 2018 May 7.

Department of Nursing, Faculty of Human Movement and Quality of Life Sciences, University of Peloponnese, Sparta, Greece. Electronic address:

Purpose: To investigate the effect of lifestyle habits in childhood Metabolic Syndrome (MTS).

Design And Methods: Descriptive correlation study with 480 participants (5-12 years old) using a specially designed questionnaire was conducted. Anthropometric and biochemical analyses were performed.

Results: Fifteen percent of children exhibited predisposition for MTS. Regarding sleep habits, logistic regression analysis (LRA) showed that hour of sleep -before 22:00- was associated with decreased waist circumference (WC%) (p = .026). Midday siesta was negatively correlated with systolic (SBP) (p = .001) and diastolic blood pressure (DBP) (p = .046). In children without MTS, lack of sleep and night time sleep was positively correlated with DBP (p = .044) and fasting blood glucose (FBG) (p = .005). Regarding nutrition habits, fast food consumption was positively correlated with SBP (p = .006) and meat consumption was positively correlated with both Body Mass Index% (BMI%) (p = .038) and WC% (p = .023). LRA showed that fruit (p = .001) and legume (p = .040) consumption was associated with decreased FBG; fish consumption with decreased Low Density Lipoprotein (LDL) cholesterol (p = .031), vegetable (p = .054) and cereal consumption (p = .012) with decreased DBP. In children with MTS, fruits were associated with increased FBG (p = .034). In children without MTS, meat consumption was associated with increased LDL (p = .024), cereal with increased WC% (p = .002) and olive products with increased High Density Lipoprotein (HDL) cholesterol and BMI% (p = .037).

Conclusions: The adoption of both balanced diet and sleep habits seemed to be crucial for the prevention of MTS.

Practice Implications: Clinical health nurses could develop and implement preventive intervention programs in order to avoid metabolic complications in adulthood.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.pedn.2018.01.012DOI Listing
October 2018

Regulation of the cohesin-loading factor NIPBL: Role of the lncRNA NIPBL-AS1 and identification of a distal enhancer element.

PLoS Genet 2017 12 20;13(12):e1007137. Epub 2017 Dec 20.

Department of Cell Biology, Erasmus MC, Rotterdam, The Netherlands.

Cohesin is crucial for genome stability, cell division, transcription and chromatin organization. Its functions critically depend on NIPBL, the cohesin-loader protein that is found to be mutated in >60% of the cases of Cornelia de Lange syndrome (CdLS). Other mutations are described in the cohesin subunits SMC1A, RAD21, SMC3 and the HDAC8 protein. In 25-30% of CdLS cases no mutation in the known CdLS genes is detected. Until now, functional elements in the noncoding genome were not characterized in the molecular etiology of CdLS and therefore are excluded from mutation screening, although the impact of such mutations has now been recognized for a wide range of diseases. We have identified different elements of the noncoding genome involved in regulation of the NIPBL gene. NIPBL-AS1 is a long non-coding RNA transcribed upstream and antisense to NIPBL. By knockdown and transcription blocking experiments, we could show that not the NIPBL-AS1 gene product, but its actual transcription is important to regulate NIPBL expression levels. This reveals a possibility to boost the transcriptional activity of the NIPBL gene by interfering with the NIPBL-AS1 lncRNA. Further, we have identified a novel distal enhancer regulating both NIPBL and NIPBL-AS1. Deletion of the enhancer using CRISPR genome editing in HEK293T cells reduces expression of NIPBL, NIPBL-AS1 as well as genes found to be dysregulated in CdLS.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1371/journal.pgen.1007137DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5754091PMC
December 2017

Whole transcriptome analysis of human erythropoietic cells during ontogenesis suggests a role of VEGFA gene as modulator of fetal hemoglobin and pharmacogenomic biomarker of treatment response to hydroxyurea in β-type hemoglobinopathy patients.

Hum Genomics 2017 10 23;11(1):24. Epub 2017 Oct 23.

Department of Pharmacy, School of Health Sciences, University of Patras, University Campus, Rion, GR-265 04, Patras, Greece.

Background: Human erythropoiesis is characterized by distinct gene expression profiles at various developmental stages. Previous studies suggest that fetal-to-adult hemoglobin switch is regulated by a complex mechanism, in which many key players still remain unknown. Here, we report our findings from whole transcriptome analysis of erythroid cells, isolated from erythroid tissues at various developmental stages in an effort to identify distinct molecular signatures of each erythroid tissue.

Results: From our in-depth data analysis, pathway analysis, and text mining, we opted to focus on the VEGFA gene, given its gene expression characteristics. Selected VEGFA genomic variants, identified through linkage disequilibrium analysis, were explored further for their association with elevated fetal hemoglobin levels in β-type hemoglobinopathy patients. Our downstream analysis of non-transfusion-dependent β-thalassemia patients, β-thalassemia major patients, compound heterozygous sickle cell disease/β-thalassemia patients receiving hydroxyurea as fetal hemoglobin augmentation treatment, and non-thalassemic individuals indicated that VEGFA genomic variants were associated with disease severity in β-thalassemia patients and hydroxyurea treatment efficacy in SCD/β-thalassemia compound heterozygous patients.

Conclusions: Our findings suggest that VEGFA may act as a modifier gene of human globin gene expression and, at the same time, serve as a genomic biomarker in β-type hemoglobinopathy disease severity and hydroxyurea treatment efficacy.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1186/s40246-017-0120-8DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5654038PMC
October 2017

Correlations Between Nutrition Habits, Anxiety and Metabolic Parameters in Greek Healthy Adults.

Adv Exp Med Biol 2017 ;987:23-34

Faculty of Human Movement and Quality of Life Sciences, Department of Nursing, Efstathiou & Stamatikis Valioti and Plateon, University of Peloponnese, Sparti, 23100, Greece.

Background: Anxiety combined with nervousness and apprehension consist a focal response to different life conditions. Lifestyle habits, anxiety and biochemical markers are in a constant interaction.

Aim: To investigate the prevalence of anxiety in healthy adults and its possible association with biochemical factors-lipid profile, liver markers, thyroid hormones-and lifestyle habits.

Methods: Quantitative descriptive correlation study. A total of 100 healthy adults participated in the research. A specially designed questionnaire and Hamilton's scale were used. Anthropometric and biochemical analyses were performed.

Findings: Overall, 61% of the participants presented moderate to very serious anxiety. The average score on the Hamilton scale was 13.82 (±9.000), with men exhibiting less stress than women. For p ≤ 0.05: Stress was positively correlated with impaired thyroid and hepatic function. Hepatic function was affected by both sugar products and water melon, which were positively correlated with total bilirubin and AST/SGOT respectively. Tomato, peppers and legumes were negatively correlated with AST/SGOT. Deep fried food was positively correlated with GGT and triglycerides. Legumes and fish were negatively correlated with CPK. Regarding the lipid metabolism, it was found that food cooked with oil was positively associated with uric acid, but non-cooked olive oil was negatively correlated with the risk for CAD. Thyroid function was negatively correlated with non-homemade food and pasta consumption and positively correlated with consumption of whole grains and green tea. Participants with subclinical hypothyroidism seemed to consume less vitamin B12, folic acid and vegetables.

Conclusion: No direct correlation between lifestyle habits and anxiety was found. Nevertheless, eating habits influenced biochemical markers-especially the thyroid hormones-which may be indirectly responsible for anxiety and related moods.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1007/978-3-319-57379-3_3DOI Listing
April 2018

Sport Participation and Ageing: Evidence from Marathon Events.

Adv Exp Med Biol 2017;989:129-139

Faculty of Human Movement and Quality of Life Sciences, Department of Sports Organization and Management, University of Peloponnese, Sparti, Greece.

The purpose of this research is to study expectations regarding ageing (ERA) among individuals who participate in running events as well as to explore personality and demographic features as potential variables that influence ERA values. A quantitative questionnaire was selected as the predominant means of collecting the data and 196 successfully completed questionnaires were analyzed by means of the SPSS. Results indicate a positive correlation between ERA values and Change Seeker Index in our sample. Moreover gender and frequency of exercise found to have no significant effect on ERA score. Finally, ERA was examined among three generational cohorts and differences were noticed to physical subscale.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1007/978-3-319-57348-9_11DOI Listing
May 2019

PRC2 Facilitates the Regulatory Topology Required for Poised Enhancer Function during Pluripotent Stem Cell Differentiation.

Cell Stem Cell 2017 05 9;20(5):689-705.e9. Epub 2017 Mar 9.

Center for Molecular Medicine Cologne (CMMC), University of Cologne, Robert-Koch-Strasse 21, 50931 Cologne, Germany; Cologne Excellence Cluster for Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, Joseph-Stelzmann-Strasse 26, 50931 Cologne, Germany. Electronic address:

Poised enhancers marked by H3K27me3 in pluripotent stem cells have been implicated in the establishment of somatic expression programs during embryonic stem cell (ESC) differentiation. However, the functional relevance and mechanism of action of poised enhancers remain unknown. Using CRISPR/Cas9 technology to engineer precise genetic deletions, we demonstrate that poised enhancers are necessary for the induction of major anterior neural regulators. Interestingly, circularized chromosome conformation capture sequencing (4C-seq) shows that poised enhancers already establish physical interactions with their target genes in ESCs in a polycomb repressive complex 2 (PRC2)-dependent manner. Loss of PRC2 does not activate poised enhancers or induce their putative target genes in undifferentiated ESCs; however, loss of PRC2 in differentiating ESCs severely and specifically compromises the induction of major anterior neural genes representing poised enhancer targets. Overall, our work illuminates an unexpected function for polycomb proteins in facilitating neural induction by endowing major anterior neural loci with a permissive regulatory topology.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.stem.2017.02.004DOI Listing
May 2017

The detailed 3D multi-loop aggregate/rosette chromatin architecture and functional dynamic organization of the human and mouse genomes.

Epigenetics Chromatin 2016 24;9:58. Epub 2016 Dec 24.

Cell Biology, Department Cell Biology and Genetics, Erasmus MC, Dr. Molewaterplein 50, 3015 GE, Rotterdam, The Netherlands.

Background: The dynamic three-dimensional chromatin architecture of genomes and its co-evolutionary connection to its function-the storage, expression, and replication of genetic information-is still one of the central issues in biology. Here, we describe the much debated 3D architecture of the human and mouse genomes from the nucleosomal to the megabase pair level by a novel approach combining selective high-throughput high-resolution chromosomal interaction capture (), polymer simulations, and scaling analysis of the 3D architecture and the DNA sequence.

Results: The genome is compacted into a chromatin quasi-fibre with ~5 ± 1 nucleosomes/11 nm, folded into stable ~30-100 kbp loops forming stable loop aggregates/rosettes connected by similar sized linkers. Minor but significant variations in the architecture are seen between cell types and functional states. The architecture and the DNA sequence show very similar fine-structured multi-scaling behaviour confirming their co-evolution and the above.

Conclusions: This architecture, its dynamics, and accessibility, balance stability and flexibility ensuring genome integrity and variation enabling gene expression/regulation by self-organization of (in)active units already in proximity. Our results agree with the heuristics of the field and allow "architectural sequencing" at a genome mechanics level to understand the inseparable systems genomic properties.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1186/s13072-016-0089-xDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5192698PMC
December 2016

Exploiting native forces to capture chromosome conformation in mammalian cell nuclei.

Mol Syst Biol 2016 Dec 9;12(12):891. Epub 2016 Dec 9.

Center for Molecular Medicine, University of Cologne, Cologne, Germany

Mammalian interphase chromosomes fold into a multitude of loops to fit the confines of cell nuclei, and looping is tightly linked to regulated function. Chromosome conformation capture (3C) technology has significantly advanced our understanding of this structure-to-function relationship. However, all 3C-based methods rely on chemical cross-linking to stabilize spatial interactions. This step remains a "black box" as regards the biases it may introduce, and some discrepancies between microscopy and 3C studies have now been reported. To address these concerns, we developed "i3C", a novel approach for capturing spatial interactions without a need for cross-linking. We apply i3C to intact nuclei of living cells and exploit native forces that stabilize chromatin folding. Using different cell types and loci, computational modeling, and a methylation-based orthogonal validation method, "TALE-iD", we show that native interactions resemble cross-linked ones, but display improved signal-to-noise ratios and are more focal on regulatory elements and CTCF sites, while strictly abiding to topologically associating domain restrictions.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5199122PMC
http://dx.doi.org/10.15252/msb.20167311DOI Listing
December 2016

Binding of nuclear factor κB to noncanonical consensus sites reveals its multimodal role during the early inflammatory response.

Genome Res 2016 11 15;26(11):1478-1489. Epub 2016 Sep 15.

Center for Molecular Medicine, University of Cologne, 50931 Cologne, Germany.

Mammalian cells have developed intricate mechanisms to interpret, integrate, and respond to extracellular stimuli. For example, tumor necrosis factor (TNF) rapidly activates proinflammatory genes, but our understanding of how this occurs against the ongoing transcriptional program of the cell is far from complete. Here, we monitor the early phase of this cascade at high spatiotemporal resolution in TNF-stimulated human endothelial cells. NF-κB, the transcription factor complex driving the response, interferes with the regulatory machinery by binding active enhancers already in interaction with gene promoters. Notably, >50% of these enhancers do not encode canonical NF-κB binding motifs. Using a combination of genomics tools, we find that binding site selection plays a key role in NF-κΒ-mediated transcriptional activation and repression. We demonstrate the latter by describing the synergy between NF-κΒ and the corepressor JDP2. Finally, detailed analysis of a 2.8-Mbp locus using sub-kbp-resolution targeted chromatin conformation capture and genome editing uncovers how NF-κΒ that has just entered the nucleus exploits pre-existing chromatin looping to exert its multimodal role. This work highlights the involvement of topology in cis-regulatory element function during acute transcriptional responses, where primary DNA sequence and its higher-order structure constitute a regulatory context leading to either gene activation or repression.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1101/gr.210005.116DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5088591PMC
November 2016

Control of developmentally primed erythroid genes by combinatorial co-repressor actions.

Nat Commun 2015 Nov 23;6:8893. Epub 2015 Nov 23.

Department of Cell Biology, Erasmus Medical Center, 3015CN Rotterdam, The Netherlands.

How transcription factors (TFs) cooperate within large protein complexes to allow rapid modulation of gene expression during development is still largely unknown. Here we show that the key haematopoietic LIM-domain-binding protein-1 (LDB1) TF complex contains several activator and repressor components that together maintain an erythroid-specific gene expression programme primed for rapid activation until differentiation is induced. A combination of proteomics, functional genomics and in vivo studies presented here identifies known and novel co-repressors, most notably the ETO2 and IRF2BP2 proteins, involved in maintaining this primed state. The ETO2-IRF2BP2 axis, interacting with the NCOR1/SMRT co-repressor complex, suppresses the expression of the vast majority of archetypical erythroid genes and pathways until its decommissioning at the onset of terminal erythroid differentiation. Our experiments demonstrate that multimeric regulatory complexes feature a dynamic interplay between activating and repressing components that determines lineage-specific gene expression and cellular differentiation.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1038/ncomms9893DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4673834PMC
November 2015

TRIM33 switches off Ifnb1 gene transcription during the late phase of macrophage activation.

Nat Commun 2015 Nov 23;6:8900. Epub 2015 Nov 23.

CEA/DSV/iRCM/LRTS, 18 route du Panorama, Fontenay-aux-Roses 92265, France.

Despite its importance during viral or bacterial infections, transcriptional regulation of the interferon-β gene (Ifnb1) in activated macrophages is only partially understood. Here we report that TRIM33 deficiency results in high, sustained expression of Ifnb1 at late stages of toll-like receptor-mediated activation in macrophages but not in fibroblasts. In macrophages, TRIM33 is recruited by PU.1 to a conserved region, the Ifnb1 Control Element (ICE), located 15 kb upstream of the Ifnb1 transcription start site. ICE constitutively interacts with Ifnb1 through a TRIM33-independent chromatin loop. At late phases of lipopolysaccharide activation of macrophages, TRIM33 is bound to ICE, regulates Ifnb1 enhanceosome loading, controls Ifnb1 chromatin structure and represses Ifnb1 gene transcription by preventing recruitment of CBP/p300. These results characterize a previously unknown mechanism of macrophage-specific regulation of Ifnb1 transcription whereby TRIM33 is critical for Ifnb1 gene transcription shutdown.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1038/ncomms9900DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4673826PMC
November 2015

The Isl1/Ldb1 Complex Orchestrates Genome-wide Chromatin Organization to Instruct Differentiation of Multipotent Cardiac Progenitors.

Cell Stem Cell 2015 Sep 27;17(3):287-99. Epub 2015 Aug 27.

Max Planck Institute for Heart and Lung Research, 61231 Bad Nauheim, Germany; Medical Faculty, University of Frankfurt, 60590 Frankfurt am Main, Germany. Electronic address:

Cardiac stem/progenitor cells hold great potential for regenerative therapies; however, the mechanisms regulating their expansion and differentiation remain insufficiently defined. Here we show that Ldb1 is a central regulator of genome organization in cardiac progenitor cells, which is crucial for cardiac lineage differentiation and heart development. We demonstrate that Ldb1 binds to the key regulator of cardiac progenitors, Isl1, and protects it from degradation. Furthermore, the Isl1/Ldb1 complex promotes long-range enhancer-promoter interactions at the loci of the core cardiac transcription factors Mef2c and Hand2. Chromosome conformation capture followed by sequencing identified specific Ldb1-mediated interactions of the Isl1/Ldb1 responsive Mef2c anterior heart field enhancer with genes that play key roles in cardiac progenitor cell function and cardiovascular development. Importantly, the expression of these genes was downregulated upon Ldb1 depletion and Isl1/Ldb1 haplodeficiency. In conclusion, the Isl1/Ldb1 complex orchestrates a network for heart-specific transcriptional regulation and coordination in three-dimensional space during cardiogenesis.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.stem.2015.08.007DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5870759PMC
September 2015

The core spliceosome as target and effector of non-canonical ATM signalling.

Nature 2015 Jul 24;523(7558):53-8. Epub 2015 Jun 24.

Department of Genetics, Cancer Genomics Netherlands, Erasmus University Medical Center, Rotterdam, 3015 CN, The Netherlands.

In response to DNA damage, tissue homoeostasis is ensured by protein networks promoting DNA repair, cell cycle arrest or apoptosis. DNA damage response signalling pathways coordinate these processes, partly by propagating gene-expression-modulating signals. DNA damage influences not only the abundance of messenger RNAs, but also their coding information through alternative splicing. Here we show that transcription-blocking DNA lesions promote chromatin displacement of late-stage spliceosomes and initiate a positive feedback loop centred on the signalling kinase ATM. We propose that initial spliceosome displacement and subsequent R-loop formation is triggered by pausing of RNA polymerase at DNA lesions. In turn, R-loops activate ATM, which signals to impede spliceosome organization further and augment ultraviolet-irradiation-triggered alternative splicing at the genome-wide level. Our findings define R-loop-dependent ATM activation by transcription-blocking lesions as an important event in the DNA damage response of non-replicating cells, and highlight a key role for spliceosome displacement in this process.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1038/nature14512DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4501432PMC
July 2015

TNFα signalling primes chromatin for NF-κB binding and induces rapid and widespread nucleosome repositioning.

Genome Biol 2014 Dec 3;15(12):536. Epub 2014 Dec 3.

Background: The rearrangement of nucleosomes along the DNA fiber profoundly affects gene expression, but little is known about how signalling reshapes the chromatin landscape, in three-dimensional space and over time, to allow establishment of new transcriptional programs.

Results: Using micrococcal nuclease treatment and high-throughput sequencing, we map genome-wide changes in nucleosome positioning in primary human endothelial cells stimulated with tumour necrosis factor alpha (TNFα) - a proinflammatory cytokine that signals through nuclear factor kappa-B (NF-κB). Within 10 min, nucleosomes reposition at regions both proximal and distal to NF-κB binding sites, before the transcription factor quantitatively binds thereon. Similarly, in long TNFα-responsive genes, repositioning precedes transcription by pioneering elongating polymerases and appears to nucleate from intragenic enhancer clusters resembling super-enhancers. By 30 min, widespread repositioning throughout megabase pair-long chromosomal segments, with consequential effects on three-dimensional structure (detected using chromosome conformation capture), is seen.

Conclusions: Whilst nucleosome repositioning is viewed as a local phenomenon, our results point to effects occurring over multiple scales. Here, we present data in support of a TNFα-induced priming mechanism, mostly independent of NF-κB binding and/or elongating RNA polymerases, leading to a plastic network of interactions that affects DNA accessibility over large domains.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1186/s13059-014-0536-6DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4268828PMC
December 2014

Targeted Chromatin Capture (T2C): a novel high resolution high throughput method to detect genomic interactions and regulatory elements.

Epigenetics Chromatin 2014 16;7:10. Epub 2014 Jun 16.

Department of Cell Biology, Erasmus MC, Dr. Molewaterplein 50, 3015GE Rotterdam, The Netherlands.

Background: Significant efforts have recently been put into the investigation of the spatial organization and the chromatin-interaction networks of genomes. Chromosome conformation capture (3C) technology and its derivatives are important tools used in this effort. However, many of these have limitations, such as being limited to one viewpoint, expensive with moderate to low resolution, and/or requiring a large sequencing effort. Techniques like Hi-C provide a genome-wide analysis. However, it requires massive sequencing effort with considerable costs. Here we describe a new technique termed Targeted Chromatin Capture (T2C), to interrogate large selected regions of the genome. T2C provides an unbiased view of the spatial organization of selected loci at superior resolution (single restriction fragment resolution, from 2 to 6 kbp) at much lower costs than Hi-C due to the lower sequencing effort.

Results: We applied T2C on well-known model regions, the mouse β-globin locus and the human H19/IGF2 locus. In both cases we identified all known chromatin interactions. Furthermore, we compared the human H19/IGF2 locus data obtained from different chromatin conformation capturing methods with T2C data. We observed the same compartmentalization of the locus, but at a much higher resolution (single restriction fragments vs. the common 40 kbp bins) and higher coverage. Moreover, we compared the β-globin locus in two different biological samples (mouse primary erythroid cells and mouse fetal brain), where it is either actively transcribed or not, to identify possible transcriptional dependent interactions. We identified the known interactions in the β-globin locus and the same topological domains in both mouse primary erythroid cells and in mouse fetal brain with the latter having fewer interactions probably due to the inactivity of the locus. Furthermore, we show that interactions due to the important chromatin proteins, Ldb1 and Ctcf, in both tissues can be analyzed easily to reveal their role on transcriptional interactions and genome folding.

Conclusions: T2C is an efficient, easy, and affordable with high (restriction fragment) resolution tool to address both genome compartmentalization and chromatin-interaction networks for specific genomic regions at high resolution for both clinical and non-clinical research.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1186/1756-8935-7-10DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4100494PMC
July 2014

Patient participation in hospital care: Nursing staffs' point of view.

Int J Nurs Pract 2015 Jun 26;21(3):258-68. Epub 2014 Mar 26.

Faculty of Nursing, National and Kapodistrian University of Athens, Athens, Greece.

The aim was to investigate nursing staff's perceptions related to patient participation and the parameters affecting it during nursing care. A cross-sectional study with both a quantitative and qualitative orientation was conducted. The sample consisted of all nursing staff working in medical and surgical wards in three Greek hospitals. A questionnaire was developed and the data were analysed with exploratory factor analysis, whereas content analysis was used for qualitative data. Nursing staff perceived participation as the process of information giving to patients, communication of symptoms by patients and compliance with the staff's orders. 'Information providing' and 'ability to influence and responsibility' were significant aspects of the content of participation, whereas the parameters affecting participation were related to patients, nursing staff and the care context. These results support patient engagement in dialogue and shared decision-making, while highlighting the need to implement participation systematically and stimulate changes in nursing care organization.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1111/ijn.12242DOI Listing
June 2015

Patient Participation in Decision Making During Nursing Care in Greece--A Comparative Study.

Nurs Forum 2015 Jul-Sep;50(3):147-57. Epub 2014 Mar 13.

Faculty of Nursing, National and Kapodistrian University of Athens, Athens, Greece.

Aim: To describe patient participation in decision making during nursing care from patients' and nursing staff' perspectives.

Methods: The sample consisted of medical and surgical patients (n = 300) and the nursing staff (n = 118) working in the respective wards in three general hospitals. A questionnaire was used for the study; data were collected from April 2009 to September 2010. Data were analyzed by an exploratory factor analysis.

Results: Patient participation was recorded at a medium level during nursing care, although it was rated as important from both patients and nursing staff. Exploratory factor analysis revealed the factor structure for the planning and implementation of the nursing care. Providers and receivers of nursing care perceived participation in a similar way. Interpersonal interaction was supported from older and less educated patients, as well as from university-educated nurses. Patient participation was greater in practical aspects of care and limited in technical medical issues and supportive services.

Conclusions: Patient participation, although moderate, was evident during nursing care in hospital settings. Paternalism in the decision-making process was the dominant trend, whereas interpersonal interaction between the parties was recognized as a prerequisite for planning nursing care.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1111/nuf.12089DOI Listing
January 2017
-->