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IRProfiler – a software toolbox for high throughput immune receptor profiling

Christos Maramis, Athanasios Gkoufas, Anna Vardi, Evangelia Stalika, Kostas Stamatopoulos, Anastasia Hatzidimitriou, Nicos Maglaveras, Ioanna Chouvarda
2018 BMC Bioinformatics  
The study of the huge diversity of immune receptors, often referred to as immune repertoire profiling, is a prerequisite for diagnosis, prognostication and monitoring of hematological disorders. In the era of high-throughput sequencing (HTS), the abundance of immunogenetic data has revealed unprecedented opportunities for the thorough profiling of T-cell receptors (TR) and B-cell receptors (BcR). However, the volume of the data to be analyzed mandates for efficient and ease-to-use immune
more » ... ire profiling software applications. Results: This work introduces Immune Repertoire Profiler (IRProfiler), a novel software pipeline that delivers a number of core receptor repertoire quantification and comparison functionalities on high-throughput TR and BcR sequencing data. Adopting 5 alternative clonotype definitions, IRProfiler implements a series of algorithms for 1) data filtering, 2) calculation of clonotype diversity and expression, 3) calculation of gene usage for the V and J subgroups, 4) detection of shared and exclusive clonotypes among multiple repertoires, and 5) comparison of gene usage for V and J subgroups among multiple repertoires. IRProfiler has been implemented as a toolbox of the Galaxy bioinformatics platform, comprising 6 tools. Theoretical and experimental evaluation has shown that the tools of IRProfiler are able to scale well with respect to the size of input dataset(s). IRProfiler has been utilized by a number of recently published studies concerning hematological disorders. Conclusion: IRProfiler is made freely available via 3 distribution channels, including the Galaxy Tool Shed. Despite being a new entry in a crowded ecosystem of immune repertoire profiling software, IRProfiler founds its added value on its support for alternative clonotype definitions in conjunction with a combination of properties stemming from its user-centric design, namely ease-of-use, ease-of-access, exploitability of the output data, and analysis flexibility.
doi:10.1186/s12859-018-2144-z pmid:29669518 pmcid:PMC5907363 fatcat:giqdpgrf7zbopmotimnvzp6rfe

The Potential Impact of Blood System on Dietary Habits and Smoking

Ioannis Tsamesidis, Evangelia Stalika, Chinedu O. Egwu, Agathi Pritsa, Maria Parpori, Argyrios Gkinoudis, Diana Samara, Evgenia Lymperaki
2022 Medicines  
The 'Blood-Type' diet advises individuals to eat according to their ABO blood group to improve their health and decrease the risk of chronic diseases. However, the food preferences of individuals with different blood groups have not been examined. The aim of our study was to investigate, in healthy regular blood donors (rBDs), the associations of smoke, alcohol, caffeine, vitamin and fat intake with their different blood groups and if ABO groups could be a potential predictor tool for disease
more » ... evention. A total of 329 volunteers were divided into four groups according to their ABO types: Group 1 (A) comprised 141 rBDs; Group 2 (B), 65 rBDs; Group 3 (O), 96 rBDs; and Group 4, 27 rBDs. Additionally, they were divided into two groups according to their rhesus types and their preferences for smoke, too. Dietary intake was assessed using 3-day food recall and the Food Processor computer program for nutrient analysis. Alcohol, caffeine, sugar and Vitamin D consumption were significantly (p < 0.05) higher in the O group. The A group presented statistically significantly (p < 0.05) greater preferences for cholesterol intake and a higher trend for smoking (25%) habits compared with all the other groups, whereas Group B preferred more fatty foods. The blood group AB appeared to be the most controlled food intake group. Regarding the rhesus comparisons, alcohol; caffeine; and Vitamin C, D, E and K consumptions were significantly (p < 0.05) higher in rhesus-positive individuals than their rhesus-negative counterparts. For the non-smoker group, compared with the smokers, a higher consumption of Vitamin D and fibers was found. In conclusion, in the present study, statistically significant correlations of the ABO and rhesus system with some dietary parameters were found, indicating a consequent influence of these preferences on the progression of different diseases.
doi:10.3390/medicines9010003 pmid:35049936 pmcid:PMC8780104 fatcat:bt6hbiym7ngd5mzpro2zennugu

Towards an integrated framework for clinico-biological data management and analysis: The case of Chronic Lymphocytic Leukemia

Evangelia Minga, Athanasios Gkoufas, Anna Vardi, Evangelia Stalika, Anastasia Hadzidimitriou, Kostas Stamatopoulos, Nicos Maglaveras, Ioanna Chouvarda
2013 13th IEEE International Conference on BioInformatics and BioEngineering  
Evangelia, Minga, Anna Vardi, Evangelia Stalika, Anastasia Hadzidimitriou, and Kostas Stamatopoulos are with the Institute of Applied Biosciences (INAB), Center for Research and Technology Hellas Athanasios  ...  Minga, Athanasios Gkoufas, Anna Vardi, Evangelia Stalika, Anastasia Hadzidimitriou, Kostas Stamatopoulos, Nicos Maglaveras, Sr Member, IEEE, and Ioanna Chouvarda, Member, IEEE I 978-1-4799-3163-7/13/$31.00  ... 
doi:10.1109/bibe.2013.6701690 dblp:conf/bibe/MingaGVSHSMC13 fatcat:ju2kixoqbneq5nly6sly3ih72a

The Effectiveness of an Online Positive Psychology Intervention among Healthcare Professionals with Depression, Anxiety or Stress Symptoms and Burnout

Evangelia Alexiou, Aikaterini Kotsoni, Anastasios Stalikas
2021 Psychology  
The scale has been validated in the Greek population by Kyriazos, Stalikas, Prassa, & Yotsidi (2018) .  ...  Satisfaction with Life Scale (SWLS) Diener's Satisfaction with Life Scale was provided in its Greek version (Diener, Emmons, Larsen, & Griffin, 1985; Stalikas & Lakioti, 2012) .  ... 
doi:10.4236/psych.2021.123025 fatcat:ay5e6365tfbkjolp3lz3tlhmxq

GLASS: assisted and standardized assessment of gene variations from Sanger sequence trace data [article]

Karol Pal, Vojtech Bystry, Tomas Reigl, Martin Demko, Adam Krejci, Tasoula Touloumenidou, Evangelia Stalika, Boris Tichy, Paolo Ghia, Kostas Stamatopoulos, Sarka Pospisilova, Jitka Malcikova (+1 others)
2016 bioRxiv   pre-print
Motivation: Sanger sequencing remains the reference method for sequence variant detection, especially in a clinical setting. However, chromatogram interpretation often requires manual inspection and in some cases considerable expertise. Additionally, variant reporting and nomenclature is typically left to the user, which can lead to inconsistencies. Results: We introduce GLASS, a tool built to assist with the assessment of gene variations in Sanger sequencing data. Critically, it provides a
more » ... dardized variant output as recommended by the Human Genome Variation Society. Availability: The program is freely available online at http://bat.infspire.org/genomepd/glass/.
doi:10.1101/088401 fatcat:emmntlnod5bpxkl3243gxp6cda

SBA-15 Mesoporous Silica as Delivery Vehicle for rhBMP-2 Bone Morphogenic Protein for Dental Applications

Dimitrios Gkiliopoulos, Ioannis Tsamesidis, Anna Theocharidou, Georgia Κ. Pouroutzidou, Evi Christodoulou, Evangelia Stalika, Konstantinos Xanthopoulos, Dimitrios Bikiaris, Konstantinos Triantafyllidis, Eleana Kontonasaki
2022 Nanomaterials  
(1) Background: A proposed approach to promote periodontal tissue regeneration in cases of peri-implantitis is the local administration of growth factors at the implant site. Recombinant human bone morphogenetic protein-2 (rh-BMP- 2) can effectively promote bone regeneration and osseointegration and the development of appropriate carriers for its delivery is of paramount importance. The aim of the present study was to develop SBA-15 mesoporous nanoparticles (MSNs) with varying porosity,
more » ... their biocompatibility with human Periodontal Ligament Cells (hPDLCs) and to investigate their effectiveness as carriers of rh-BMP-2. (2) Methods: SBA-15 type mesoporous silicas were synthesized via sol–gel reaction. The calcined SBA-15 samples were characterized by N2 porosimetry, Fourier transform–infrared spectrometry (FTIR), Scanning (SEM) and Transmission Electron Microscopy (TEM). Rh-BMP-2 loading and release kinetics were evaluated by UV spectroscopy. (3) Results: MSNs presented hexagonally arranged, tubular pores of varying length and diameter. Slightly higher loading capacity was achieved for SBA-15 with large pores that presented good hemocompatibility. MTT assay revealed no cytotoxic effects for all the tested materials, while SBA-15 with large pores induced a significant upregulation of cell viability at day 5. (4) Conclusions: SBA-15 MSNs may prove a valuable delivery platform towards the effective release of bone-inducing proteins.
doi:10.3390/nano12050822 pmid:35269309 pmcid:PMC8912683 fatcat:35cbhnttuzd6rdsfdyxq4utwza

MOESM1 of Temporal Dynamics of Clonal Evolution in Chronic Lymphocytic Leukemia with Stereotyped IGHV4-34/IGKV2-30 Antigen Receptors: Longitudinal Immunogenetic Evidence

Lesley-Ann Sutton, Efterpi Kostareli, Evangelia Stalika, Athanasios Tsaftaris, Achilles Anagnostopoulos, Nikos Darzentas, Richard Rosenquist, Kostas Stamatopoulos
2018 Figshare  
Supplementary material, approximately 3.03 MB.
doi:10.6084/m9.figshare.7193825 fatcat:irsdxngwevbm7ppnwirfbaveje

The Clinical Utility of ABO and RHD Systems as Potential Indicators of Health Status, a Preliminary Study in Greek Population

Evgenia Lymperaki, Evangelia Stalika, George Tzavelas, Efthymia Tormpantoni, Diana Samara, Eleni Vagdatli, Ioannis Tsamesidis
2022 Clinics and Practice  
Objective: The objective of this study is to further highlight the differences between different ABO blood groups and Rhesus types with health biomarkers. Methods: In total 150 active healthy blood donors participated in our study comprising of 80 males from 19–61 years and 70 females aged from 21 to 64. Participants carrying blood group A were 55 individuals, blood group B 32, blood group O 51, and blood group AB 12, RHD+ 132, and RHD- 18. All the volunteer regular blood donors were selected
more » ... cognizing them as a healthy population excluding drug and supplements intake. Their blood samples were analyzed just before blood donation for biochemical, hematological, and antioxidant markers. Statistical computations were performed using the SPSS tool, specifically, the one-way ANOVA test, Chi-square statistics, and logistic regression were used as statistical models. Results: O blood donors presented better iron absorption and the worst lipid profile. Indeed, a significant trend of high atheromatic index values revealed an increased risk for hyperlipidemia, in contrast with blood group A presenting a better lipid profile with lower atheromatic index values. There was also a gender related association for blood group A compared with O that was further highlighted using binary logistic regression. Conclusion: In this study, a significant difference was observed among the ABO blood groups in several of the examined biochemical and hematological biomarkers. O blood group appeared different behavior in comparison to all the tested blood groups and furthermore the RHD-group presented a better lipid profile in comparison to the RHD+ group. In order to obtain a more comprehensive view of the correlation between the ABO blood group and biochemical markers, further studies are required.
doi:10.3390/clinpract12030045 pmid:35735664 pmcid:PMC9221977 fatcat:ugjje3ct5bf3vaervvkwx3jrgi

Temporal Dynamics of Clonal Evolution in Chronic Lymphocytic Leukemia with Stereotyped IGHV4-34/IGKV2-30 Antigen Receptors: Longitudinal Immunogenetic Evidence

Lesley-Ann Sutton, Efterpi Kostareli, Evangelia Stalika, Athanasios Tsaftaris, Achilles Anagnostopoulos, Nikos Darzentas, Richard Rosenquist, Kostas Stamatopoulos
2013 Molecular Medicine  
Chronic lymphocytic leukemia (CLL) patients assigned to stereotyped subset 4 possess distinctive patterns of intraclonal diversification (ID) within their immunoglobulin (IG) genes. Although highly indicative of an ongoing response to antigen(s), the critical question concerning the precise timing of antigen involvement is unresolved. Hence, we conducted a large-scale longitudinal study of eight subset 4 cases totaling 511 and 398 subcloned IG heavy and kappa sequences. Importantly, we could
more » ... ablish a hierarchical pattern of subclonal evolution, thus revealing which somatic hypermutations were negatively or positively selected. In addition, distinct clusters of subcloned sequences with cluster-specific mutational profiles were observed initially; however, at later time points, the minor cluster had often disappeared and hence not been selected. Despite the high intensity of ID, it was remarkable that certain residues remained essentially unaltered. These novel findings strongly support a role for persistent antigen stimulation in the clonal evolution of CLL subset 4.
doi:10.2119/molmed.2013.00042 pmid:23922244 pmcid:PMC3769528 fatcat:hs4vxiay6fam5epxouubkgzynu

Serum Ceramides as Prognostic Biomarkers of Large Thrombus Burden in Patients with STEMI: A Micro-Computed Tomography Study

Efstratios Karagiannidis, Andreas S. Papazoglou, Nikolaos Stalikas, Olga Deda, Eleftherios Panteris, Olga Begou, Georgios Sofidis, Dimitrios V. Moysidis, Anastasios Kartas, Evangelia Chatzinikolaou, Kleoniki Keklikoglou, Andreana Bompoti (+3 others)
2021 Journal of Personalized Medicine  
ST-elevation myocardial infarction (STEMI) remains one of the leading causes of mortality worldwide. The identification of novel metabolic and imaging biomarkers could unveil key pathophysiological mechanisms at the molecular level and promote personalized care in patients with acute coronary syndromes. We studied 38 patients with STEMI who underwent primary percutaneous coronary intervention and thrombus aspiration. We sought to correlate serum ceramide levels with micro-CT quantified
more » ... thrombus volume and relevant angiographic outcomes, including modified TIMI thrombus grade and pre- or post-procedural TIMI flow. Higher ceramide C16:0 levels were significantly but weakly correlated with larger aspirated thrombus volume (Spearman r = 0.326, p = 0.046), larger intracoronary thrombus burden (TB; p = 0.030) and worse pre- and post-procedural TIMI flow (p = 0.049 and p = 0.039, respectively). Ceramides C24:0 and C24:1 were also significantly associated with larger intracoronary TB (p = 0.008 and p = 0.001, respectively). Receiver operating characteristic analysis demonstrated that ceramides C24:0 and C24:1 could significantly predict higher intracoronary TB (area under the curve: 0.788, 95% CI: 0.629–0.946 and 0.846, 95% CI: 0.706–0.985, respectively). In conclusion, serum ceramide levels were higher among patients with larger intracoronary and aspirated TB. This suggests that quantification of serum ceramides might improve risk-stratification of patients with STEMI and facilitate an individualized approach in clinical practice.
doi:10.3390/jpm11020089 pmid:33572568 fatcat:ale3fajcgbdzbdrl2wyh3d3gmu

The frequency ofTP53gene defects differs between chronic lymphocytic leukaemia subgroups harbouring distinct antigen receptors

Jitka Malcikova, Evangelia Stalika, Zadie Davis, Karla Plevova, Martin Trbusek, Larry Mansouri, Lydia Scarfò, Panagiotis Baliakas, Anne Gardiner, Lesley-Ann Sutton, Hana Skuhrova Francova, Andreas Agathangelidis (+11 others)
2014 British Journal of Haematology  
doi:10.1111/bjh.12893 pmid:24725250 fatcat:rzgxn7mcpzb2bh2grb5x3rsn6y

Micro-CT-Based Quantification of Extracted Thrombus Burden Characteristics and Association With Angiographic Outcomes in Patients With ST-Elevation Myocardial Infarction: The QUEST-STEMI Study

Efstratios Karagiannidis, Andreas S Papazoglou, Georgios Sofidis, Evangelia Chatzinikolaou, Kleoniki Keklikoglou, Eleftherios Panteris, Anastasios Kartas, Nikolaos Stalikas, Thomas Zegkos, Fotios Girtovitis, Dimitrios V. Moysidis, Leandros Stefanopoulos (+7 others)
2021 Frontiers in Cardiovascular Medicine  
Angiographic detection of thrombus in STEMI is associated with adverse outcomes. However, routine thrombus aspiration failed to demonstrate the anticipated benefit. Hence, management of high coronary thrombus burden remains challenging. We sought to assess for the first time extracted thrombotic material characteristics utilizing micro-computed tomography (micro-CT).Methods: One hundred thirteen STEMI patients undergoing thrombus aspiration were enrolled. Micro-CT was undertaken to quantify
more » ... ieved thrombus volume, surface, and density. Correlation of these indices with angiographic and electrocardiographic outcomes was performed.Results: Mean aspirated thrombus volume, surface, and density (±standard deviation) were 15.71 ± 20.10 mm3, 302.89 ± 692.54 mm2, and 3139.04 ± 901.88 Hounsfield units, respectively. Aspirated volume and surface were significantly higher (p &lt; 0.001) in patients with higher angiographic thrombus burden. After multivariable analysis, independent predictors for thrombus volume were reference vessel diameter (RVD) (p = 0.011), right coronary artery (RCA) (p = 0.039), and smoking (p = 0.027), whereas RVD (p = 0.018) and RCA (p = 0.019) were predictive for thrombus surface. Thrombus volume and surface were independently associated with distal embolization (p = 0.007 and p = 0.028, respectively), no-reflow phenomenon (p = 0.002 and p = 0.006, respectively), and angiographically evident residual thrombus (p = 0.007 and p = 0.002, respectively). Higher thrombus density was correlated with worse pre-procedural TIMI flow (p &lt; 0.001). Patients with higher aspirated volume and surface developed less ST resolution (p = 0.042 and p = 0.023, respectively).Conclusions: Angiographic outcomes linked with worse prognosis were more frequent among patients with larger extracted thrombus. Despite retrieving larger thrombus load in these patients, current thrombectomy devices fail to deal with thrombotic material adequately. Further studies of novel thrombus aspiration technologies are warranted to improve patient outcomes.Clinical Trial Registration: QUEST-STEMI trial ClinicalTrials.gov number: NCT03429608 Date of registration: February 12, 2018. The study was prospectively registered.
doi:10.3389/fcvm.2021.646064 pmid:33969012 pmcid:PMC8096895 fatcat:uic4m4inqba7ple5iwojgg55si

Karyotypic complexity rather than chromosome 8 abnormalities aggravates the outcome of chronic lymphocytic leukemia patients with TP53 aberrations

Gonzalo Blanco, Anna Puiggros, Panagiotis Baliakas, Anastasia Athanasiadou, MªDolores García-Malo, Rosa Collado, Aliki Xochelli, María Rodríguez-Rivera, Margarita Ortega, Mª José Calasanz, Elisa Luño, MªTeresa Vargas (+18 others)
2016 OncoTarget  
Patients with chronic lymphocytic leukemia (CLL) harboring TP53 aberrations (TP53abs; chromosome 17p deletion and/or TP53 mutation) exhibit an unfavorable clinical outcome. Chromosome 8 abnormalities, namely losses of 8p (8p−) and gains of 8q (8q+) have been suggested to aggravate the outcome of patients with TP53abs. Research Paper Oncotarget 80917 www.impactjournals.com/oncotarget However, the reported series were small, thus hindering definitive conclusions. To gain insight into this issue,
more » ... e assessed a series of 101 CLL patients harboring TP53 disruption. The frequency of 8p− and 8q+ was 14.7% and 17.8% respectively. Both were associated with a significantly (P < 0.05) higher incidence of a complex karyotype (CK, ≥3 abnormalities) detected by chromosome banding analysis (CBA) compared to cases with normal 8p (N-8p) and 8q (N-8q) , respectively. In univariate analysis for 10-year overall survival (OS), 8p− (P = 0.002), 8q+ (P = 0.012) and CK (P = 0.009) were associated with shorter OS. However, in multivariate analysis only CK (HR = 2.47, P = 0.027) maintained independent significance, being associated with a dismal outcome regardless of chromosome 8 abnormalities. In conclusion, our results highlight the association of chromosome 8 abnormalities with CK amongst CLL patients with TP53abs, while also revealing that CK can further aggravate the prognosis of this aggressive subgroup.
doi:10.18632/oncotarget.13106 pmid:27821812 pmcid:PMC5348364 fatcat:wszsyonmyjdfvh2iqgrf6d2xmm

Tailored approaches grounded on immunogenetic features for refined prognostication in chronic lymphocytic leukemia

Panagiotis Baliakas, Theodoros Moysiadis, Anastasia Hadzidimitriou, Aliki Xochelli, Sabine Jeromin, Andreas Agathangelidis, Mattias Mattsson, Lesley-Ann Sutton, Eva Minga, Lydia Scarfò, Davide Rossi, Zadie Davis (+27 others)
2018 Haematologica  
Chronic lymphocytic leukemia (CLL) patients with differential somatic hypermutation status of the immunoglobulin heavy variable genes, namely mutated or unmutated, display fundamental clinico-biological differences. Considering this, we assessed prognosis separately within mutated (M-CLL) and unmutated (U-CLL) CLL in 3015 patients, hypothesizing that the relative significance of relevant indicators may differ between these two categories. Within Binet A M-CLL patients, besides TP53
more » ... , trisomy 12 and stereotyped subset #2 membership were equivalently associated with the shortest time-to-first-treatment and a treatment probability at five and ten years after diagnosis of 40% and 55%, respectively; the remaining cases exhibited 5-year and 10-year treatment probability of 12% and 25%, respectively. Within Binet A U-CLL patients, besides TP53 abnormalities, del(11q) and/or SF3B1 mutations were associated with the shortest time-to-first-treatment (5- and 10-year treatment probability: 78% and 98%, respectively); in the remaining cases, males had a significantly worse prognosis than females. In conclusion, the relative weight of indicators that can accurately risk stratify early-stage CLL patients differs depending on the somatic hypermutation status of the immunoglobulin heavy variable genes of each patient. This finding highlights the fact that compartmentalized approaches based on immunogenetic features are necessary to refine and tailor prognostication in CLL.
doi:10.3324/haematol.2018.195032 pmid:30262567 pmcid:PMC6355487 fatcat:wb3lfbipx5e23ccoq366c2xgcq

Disease-biased and shared characteristics of the immunoglobulin gene repertoires in marginal zone B cell lymphoproliferations

Aliki Xochelli, Vasilis Bikos, Eleftheria Polychronidou, Chrysi Galigalidou, Andreas Agathangelidis, Frédéric Charlotte, Panagiotis Moschonas, Zadie Davis, Monica Colombo, Maria Roumelioti, Lesley-Ann Sutton, Patricia Groenen (+33 others)
2019 Journal of Pathology  
The B cell receptor immunoglobulin (Ig) gene repertoires of marginal zone (MZ) lymphoproliferations were analyzed in order to obtain insight into their ontogenetic relationships. Our cohort included cases with MZ lymphomas (n = 488), i.e. splenic (SMZL), nodal (NMZL) and extranodal (ENMZL), as well as provisional entities (n = 76), according to the WHO classification. The most striking Ig gene repertoire skewing was observed in SMZL. However, restrictions were also identified in all other MZ
more » ... phomas studied, particularly ENMZL, with significantly different Ig gene distributions depending on the primary site of involvement. Cross-entity comparisons of the MZ Ig sequence dataset with a large dataset of Ig sequences (MZ-related or not; n = 65 837) revealed four major clusters of cases sharing homologous ('public') heavy variable complementarity-determining region 3. These clusters included rearrangements from SMZL, ENMZL (gastric, salivary gland, ocular adnexa), chronic lymphocytic leukemia, but also rheumatoid factors and non-malignant splenic MZ cells. In conclusion, different MZ lymphomas display biased immunogenetic signatures indicating distinct antigen exposure histories. The existence of rare public stereotypes raises the intriguing possibility that common, pathogen-triggered, immune-mediated mechanisms may result in diverse B lymphoproliferations due to targeting versatile progenitor B cells and/or operating in particular microenvironments. Copyright © 2018 Pathological Society of Great Britain and Ireland. Published by John Wiley & Sons, Ltd.
doi:10.1002/path.5209 pmid:30484876 fatcat:vx3kcdllynh4lhplalgtguhvjq
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