Computer Science and Biomedical Informatics

v-ErbA is a mutated variant of thyroid hormone receptor (TRa/NR1A1) borne by the Avian Erythroblastosis virus causing erythroleukemia. TRa is known to activate transcription of speci®c genes in the presence of its cognate ligand, T3 hormone, while in its absence it represses it. v-ErbA is unable to bind ligand, and hence is thought to contribute to leukemogenesis by actively repressing erythroid-speci®c genes such as the carbonic anhydrase II gene (CA II). In the prevailing model, v-ErbA occludes liganded TR from binding to its cognate elements and constitutively interacts with the corepressors NCoR/ SMRT. We previously identi®ed a v-ErbA responsive element (VRE) within a DNase I hypersensitive region (HS2) located in the second intron of the CA II gene. We now show that HS2 ful®ls all the requirements for a genuine enhancer that functions independent of its orientation and position with a profound erythroid-speci®c activity in normal erythroid progenitors (T2ECs) and in leukemic erythroid cell lines. We ®nd that the HS2 enhancer activity is governed by two adjacent GATAfactor binding sites. v-ErbA as well as unliganded TR prevent HS2 activity by nullifying the positive function of factors bound to GATA-sites. However, v-ErbA, in contrast to TR, does not convey active repression to silence the transcriptional activity intrinsic to a heterologous tk promoter. We propose that depending on the sequence and context of the binding site, v-ErbA contributes to leukomogenesis by occluding liganded TR as well as unliganded TR thereby preventing activation or repression, respectively. Oncogene (2001) 20, 775 ± 787.

Hypoxia-inducible transcription factor 1 (HIF-1) mediates the cellular response to hypoxia. HIF-1 activity is controlled via the synthesis, degradation or intracellular localization of its a subunit. HIF-1a contains a C-terminal bipartite basic NLS that interacts with importins a. We have recently shown that HIF-1a also contains an atypical hydrophobic CRM1-and phosphorylation-dependent NES and can therefore shuttle in and out of the nucleus. We now report that C-terminal NLS mutants of HIF-1a can still enter the nucleus when CRM1-dependent nuclear export is inhibited, indicating that HIF-1a contains an additional functional nuclear import signal. Using an in vitro nuclear import assay, we further show that importins 4 and 7 accomplish nuclear import of HIF-1a more efficiently than the classical importin a/b NLS receptor. Binding assays confirmed the specific physical interaction between HIF-1a and importins 4 and 7. Moreover, the interaction of importin 7 with HIF-1a is mapped at its N-terminal part encompassing the bHLH-PAS A domain. By expressing functional HIF-1 in yeast, we show that Nmd5, the yeast orthologue of importin 7, is required for HIF-1a nuclear accumulation and activity. Taken together, our data show that shuttling of HIF-1a between cytoplasm and nucleus is a complex process involving several members of the nuclear transport receptor family.

Hypoxia inducible factor 1 (HIF-1), the master regulator of hypoxia-activated genes, is involved in many diseases and is a valid drug target. In order to develop a simple and genetically tractable in vivo system for HIF-1 analysis, we tested the inducible expression of both human HIF-1 subunits (HIF-1a and ARNT) in the yeast Saccharomyces cerevisiae and showed the formation of transcriptionally active HIF-1. The use of this system for the identification and characterization of HIF-1 effectors was first validated by showing that two chemical Hsp90 inhibitors, geldanamycin and radicicol, impaired the activity of HIF-1 in yeast. By applying this system in mutant yeast strains, we then identified Hsp90 co-chaperones, which were required for HIF-1 activity. Furthermore, using yeast strains co-expressing truncated forms of HIF-1a with ARNT or both HIF-1a and ARNT, we characterized fragments of HIF-1a that acted as dominant negative mutants and suppressed HIF-1 activity.

Background/Aims: Hepcidin is a liver-produced hormone that regulates systemic iron homeostasis. Hepcidin expression is stimulated upon iron overload or inflammation while iron deficiency, anemia and tissue hypoxia are negative regulators. We investigated the involvement of 2-oxoglutarate-dependent oxygenases, HIF-1 and other transcription factors in the hypoxic suppression of hepcidin. Methods: Northern blotting analysis and real time PCR were used to determine hepcidin mRNA levels in hepatoma cells and hepcidin promoter activity was measured using Huh7 cells transfected with suitable reporter constructs under various conditions. Results: Treatment of human cultured hepatoma cells with hypoxia or known inhibitors of 2-oxoglutarate-dependent oxygenases, such as the iron chelator desferrioxamine, cobalt or the 2-oxoglutarate analogue dimethyl-oxalylglycine significantly reduced hepcidin mRNA levels and down-regulated its gene promoter activity. This effect was not dependent on the HREs or other known putative response elements in the hepcidin promoter and was observed even under interleukin-6 treatment. Conclusions: 2-Oxoglutarate-dependent oxygenases are important to maintain high hepcidin mRNA expression in a HIF-1-independent manner. We suggest that modulation of oxygenase activity may be of therapeutic value in iron-related disorders.

Active promoters generally contain histone H3/H4 hyperacetylation and tri-methylation at H3 lysine 4, whereas repressed promoters are associated with DNA methylation. Here we show that the repressed erythroid-specific carbonic anhydrase II (CAII) promoter has active histone modifications localized around the transcription start, while high levels of CpG methylation are present directly upstream from these active marks. Despite the presence of active histone modifications, the repressed promoter requires hormone-induced activation for efficient preinitiation complex assembly. Transient and positional changes in histone H3/H4 acetylation and local changes in nucleosome density are evident during activation, but the bipartite epigenetic code is stably maintained. Our results suggest that active histone modifications may prevent spreading of CpG methylation towards the promoter and show that repressive DNA methylation immediately adjacent to a promoter does not necessarily repress transcription.

Renal failure has a complex phenotype resulting from an underlying kidney disease as well as environmental and genetic factors. In the present study we performed a systematic review and meta-analyses to evaluate the association of the A1166C polymorphism of Angiotensin II type 1 Receptor gene (AGTR1) with Chronic Kidney Disease (CKD), End Stage Renal Disease (ESRD), IgA Nephropathy (IgAN) and Vesicoureteral Reflux (VUR) as well as the association of A1332G polymorphism of Angiotensin II type 2 Receptor (AGTR2) gene with Vesicoureteral Reflux (VUR). We found that neither AGTR1 Α1166C, nor AGTR2 A1332G polymorphisms were significantly associated with any of the aforementioned renal diseases, suggesting that they cannot be used as predictive markers in either general or subgroup ethnic populations.

CD24 is a cell-surface protein mainly expressed in cells of the immune and central nervous system (CNS), cells that play a critical role in the development of multiple sclerosis (MS). In the current study, we investigated four polymorphisms of the CD24 gene regarding their associations with MS. To this end, univariate and multivariate meta-analysis were applied along with modifications to include data from family-trios so as to increase the robustness of the meta-analysis. We found that the polymorphism 226 C>T (Ala57Val) of the CD24 gene is associated with MS according to the recessive mode of inheritance (odds ratio = 1.75; 95% CI: 1.09, 2.81). Moreover, the 1527-1528 TG>del polymorphism is inversely associated with MS according to the dominant mode of inheritance (odds ratio = 0.57; 95% CI 0.39, 0.83). Conversely, the 1056 A>G and 1626 A>G polymorphisms were not found to be associated with MS. We conclude that the CD24 226 C>T polymorphism increases the risk of MS, while the 1527-1528 TG>del polymorphism seems to have a protective role against MS, suggesting that these two polymorphisms can be used as predictive biomarkers for MS development.

Objective The aim of this study was to investigate the potential association of FZD3 polymorphisms with schizophrenia. Methods A systematic review and a meta-analysis were carried out comprising of nine genetic association studies, with both a population-based and a family-based design, and three genome-wide association studies. A total of 1601 family trios, 39 922 schizophrenic patients, and 61 287 healthy individuals were involved in the analysis and six polymorphisms were examined: rs2241802, rs2323019, rs352203, rs3757888, rs880481, and rs960914. A summarybased method for pooling genetic association studies under both family-based and population-based designs was used. Odds ratios along with their 95% confidence intervals were computed to compare the contrast of alleles in patients and controls. The results indicate a potentially weaker effect of FZD3 polymorphisms on schizophrenia than that suggested originally and possibly limited to Chinese populations. No relationship was identified between all examined polymorphisms and schizophrenia, except for rs352203, which plays a protective role against schizophrenia. However, this effect was mainly attributed to studies including Chinese patients. In the Chinese population, evidence for an elevated risk for schizophrenia linked to the rs2323019 polymorphism was also identified. Given the different linkage disequilibrium patterns observed in Chinese populations, schizophrenia may be related to some other polymorphisms of gene FZD3 that are in stronger linkage disequilibrium to Chinese than to the other populations studied.

Some subjects are repeatedly exposed to human immunodeficiency virus (HIV), yet they remain uninfected. This suggests the existence of host-resistance mechanisms. The current study synthesizes the evidence regarding the association between interleukin (IL) gene polymorphisms and HIV susceptibility. Medline, Scopus and the Web of Science databases were systematically searched, and a meta-analysis of case-control studies was conducted. Univariate and bivariate methods were used. The literature search identified 42 eligible studies involving 15,727 subjects. Evidence was obtained on eight single-nucleotide polymorphisms (SNPs): IL1A -889 C>T (rs1800587), IL1B +3953/4 C>T (rs1143634), IL4 -589/90 C>T (rs2243250), IL6 -174 G>C (rs1800795), IL10 -592 C>A (rs1800872), IL10-1082 A>G (rs1800896), IL12B -1188 A>C (rs3212227) and IL28B C>T (rs12979860). The IL1B +3953/4 C>T variant appears to increase the risk of HIV acquisition, under the assumption of a recessive genetic model (odds ratio (OR): 4.47, 95% CI: 2.35-8.52). The AA homozygotes of the IL10 -592 C>A SNP had an increased, marginally nonsignificant, risk (OR: 1.39, 95% CI: 0.97-2.01). It reached, however, significance in subanalyses (OR: 1.49, 95% CI: 1.04-2.12). Finally, the well-studied hepatitis C virus (HCV) infection IL28B (rs12979860) CT/TT genotypes were associated with a 27% decrease in HIV infection risk, especially in populations infected with HCV (OR: 0.73, 95% CI: 0.57-0.95). Interleukin signalling is perhaps important in HIV infection and some interleukin genetic variants may affect the risk of HIV acquisition. Approaches targeting specific genes and genomewide association studies should be conducted to decipher the effect of these polymorphisms.

Leishmaniases are cutaneous, mucocutaneous, and visceral diseases affecting humans and domesticated animals mostly in the tropical and subtropical areas of the planet. Host genetics have been widely investigated for their role in developing various infectious diseases. The SLC11A1 gene has been reported to play a role in neutrophil function and is associated with susceptibility to infectious and inflammatory diseases such as tuberculosis or rheumatoid arthritis. In the present meta-analysis, we investigate the genetic association of SLC11A1 polymorphisms with susceptibility to leishmaniasis. Genotypes and other risk-related data were collected from 13 case-control and family-based studies (after literature search). Conventional random-effects meta-analysis was performed using STATA 13. To pool case-control and family-based data, the weighted Stouffer's method was also applied. Eight polymorphisms were investigated: rs2276631, rs3731865, rs3731864, rs17221959, rs201565523, rs2279015, rs17235409, and rs17235416. We found that rs17235409 (D543N) and rs17235416 (1729 + 55del4) are significantly associated with a risk for cutaneous leishmaniasis (CL), whereas rs17221959, rs2279015, and rs17235409 are associated with visceral leishmaniasis (VL). Our results suggest that polymorphisms in SLC11A1 affect susceptibility to CL and VL. These findings open new pathways in understanding macrophage response to Leishmania infection and the genetic factors predisposing to symptomatic CL or VL that can lead to the usage of predictive biomarkers in populations at risk.

SummaryBackgroundWith the emergence of SARS-CoV-2 and the associated Coronavirus disease 2019 (COVID-19), there is an imperative need for diagnostic tests that can identify the infection. Although Nucleic Acid Test (NAT) is considered to be the gold standard, serological tests based on antibodies could be very helpful. However, individual studies measuring the accuracy of the various tests are usually underpowered and inconsistent, thus, a comparison of different tests is needed.MethodsWe performed a systematic review and meta-analysis following the PRISMA guidelines. We conducted the literature search in PubMed, medRxiv and bioRxiv. For the statistical analysis we used the bivariate method for meta-analysis of diagnostic tests pooling sensitivities and specificities. We evaluated IgM and IgG tests based on Enzyme-linked immunosorbent assay (ELISA), Chemiluminescence Enzyme Immunoassays (CLIA), Fluorescence Immunoassays (FIA) and the point-of-care (POC) Lateral Flow Immunoassays (LF...

Η θυρεοειδής ορμόνη (Τ3) παίζει πολλαπλό και σημαντικό ρόλο στην ομοιόσταση, στην ανάπτυξη, στην μεταμόρφωση των αμφίβιων, στη διαφοροποίηση και στη νεοπλασία. Η δράση της Τ3 διενεργείται μέσω της σύνδεσής της με τον υποδοχέα θυρεοειδούς ορμόνης (TR), ο οποίος με τη σειρά του συνδέεται σε ειδικές αλληλουχίες DNA που ονομάζονται στοιχεία απόκρισης στη θυρεοειδή ορμόνη (TREs). Ο TR παρουσία Τ3 ενεργοποιεί τη μεταγραφή ενώ χωρίς ορμόνη ο TR την καταστέλλει χρησιμοποιώντας πληθώρα μηχανισμών. Η v-ErbΑ ογκοπρωτεϊνη είναι μια ιική μεταλλαγμένη παραλλαγή του TRα που κωδικοποιείται από τον ιό της ερυθροβλάστωσης των πτηνών (AEV). Η συνεργασία του v-erbA με το v-erbB, το δεύτερο ογκογονίδιο του AEV με δραστικότητα κινάσης τυροσίνης, οδηγεί σε ερυθρολευχαιμία ως αποτέλεσμα του ανεξέλεγκτου πολλαπλασιασμού και της παύσης της διαφοροποίησης. Λόγω μεταλλάξεων, το ν-erbΑ δεν μπορεί να δεσμεύσει Τ3 και έτσι δεν μπορεί να ενεργοποιήσει τη μεταγραφή, όπως το κυτταρικό ομόλογό του, ο TR. Η υπόθεση ότ...

Coronavirus disease 2019 (COVID-19) initiated global health care challenges such as the necessity for new diagnostic tests. Diagnosis by real-time PCR remains the gold-standard method, yet economical and technical issues prohibit its use in points of care (POC) or for repetitive tests in populations. A lot of effort has been exerted in developing, using, and validating antigen-based tests (ATs). Since individual studies focus on few methodological aspects of ATs, a comparison of different tests is needed. Herein, we perform a systematic review and meta-analysis of data from articles in PubMed, medRxiv and bioRxiv. The bivariate method for meta-analysis of diagnostic tests pooling sensitivities and specificities was used. Most of the AT types for SARS-CoV-2 were lateral flow immunoassays (LFIA), fluorescence immunoassays (FIA), and chemiluminescence enzyme immunoassays (CLEIA). We identified 235 articles containing data from 220,049 individuals. All ATs using nasopharyngeal samples s...

Available drugs have been used as an urgent attempt through clinical trials to minimize severe cases of hospitalizations with Coronavirus disease (COVID-19), however, there are limited data on common pharmacogenomics affecting concomitant medications response in patients with comorbidities. To identify the genomic determinants that influence COVID-19 susceptibility, we use a computational, statistical, and network biology approach to analyze relationships of ineffective concomitant medication with an adverse effect on patients. We statistically construct a pharmacogenetic/biomarker network with significant drug-gene interactions originating from gene-disease associations. Investigation of the predicted pharmacogenes encompassing the genedisease-gene pharmacogenomics (PGx) network suggests that these genes could play a significant role in COVID-19 clinical manifestation due to their association with autoimmune, metabolic, neurological, cardiovascular, and degenerative disorders, some of which have been reported to be crucial comorbidities in a COVID-19 patient.

Leishmaniasis is a neglected tropical disease affecting humans and domesticated animals with high mortality in endemic countries. The pleiotropy of symptoms and the complicated gold-standard methods make the need for non-invasive, highly sensitive diagnostic tests imperative. Individual studies on molecular-based Leishmania diagnosis in urine show high discrepancy; thus, a data-evidenced comparison of various techniques is necessary. We performed a systematic review and meta-analysis using the bivariate method of diagnostic methods to pool sensitivities and specificities. We investigated the impact of DNA-extraction method, PCR type, amplified locus, host species, leishmaniasis form, and geographical region. The pooled sensitivity was 69.2%. Tests performed with the kit-based DNA extraction method and qPCR outweighed in sensitivity the phenol-chloroform-based and PCR methods, while their combination showed a sensitivity of 79.3%. Amplified locus, human or canine as host and cutaneou...

Kinetoplastea are free living and parasitic protists with unique features among Eukaryota. Pathogenic Kinetoplastea parasites (i.e., Trypanosoma and Leishmania spp.) undergo several developmental transitions essential for survival in their hosts. These transitions require membrane and cytoskeleton reorganizations that involve phosphoinositides (PIs). Phospholipids like PIs are key regulators of vital functions in all eukaryotes including signal transduction, protein transport and sorting, membrane trafficking, and cytoskeleton and membrane remodeling. A large repertoire of PI-metabolizing enzymes and PI-binding proteins/effectors carrying distinct PI-binding modules like the PX (phox homology) module could play significant roles in the life and virulence of pathogenic Kinetoplastea. The aim of this study was to retrieve the entire spectrum of Kinetoplastea protein sequences containing the PX module (PX-proteins), predict their structures, and identify in them evolutionary conserved ...

Stevia (Stevia rebaudiana Bertoni) is an aromatic plant known for its high sweetening power ascribed to its glycosides. Stevia also contains several bioactive compounds showing antioxidant, antiproliferative, antimicrobial, and anti-inflammatory activities. Since inflammation and oxidative stress play critical roles in the pathogenesis of many diseases, stevia emerges as a promising natural product that could support human health. In this study we set out to investigate the way stevia affects oxidative stress markers (e.g., SOD, CAT, GPx, GSH, MDA) in diseased rats administered stevia leaf extracts or glycosides. To this end, we performed an inclusive literature search, following PRISMA guidelines, and recruited multivariate meta-analysis and meta-regression to synthesize all available data on experimental animal models encountering (a) healthy, (b) diseased, and (c) stevia-treated diseased rats. From the 184 articles initially retrieved, 24 satisfied the eligibility criteria, conta...

Plastome-genome incompatibility (PGI) is prevalent in several plants including the Zantedeschia species, a worldwide commercial flower crop native to South Africa. Generally, hybrids suffering from PGI appear less vigorous and more susceptible than normal plants. Previous reports revealed that the PGI level in interspecific hybrids is correlated with the relatedness of the parental species in the genus Zantedeschia. To provide a basis for utilizing and improving resources in breeding programs, a total of 117 accessions of colored calla lily (Zantedeschia hybrid), collected from New Zealand, the Netherlands and the United States, were genotyped using 31 transferable expressed sequence tags-simple sequence repeats (EST-SSR) markers from the white calla lily (Zantedeschia aethiopica). A moderately high level of genetic diversity was observed, with 111 alleles in total, an observed/expected heterozygosity (Ho/He) of 0.453/0.478, and polymorphism information content (PIC) of 0.26. Geneti...

v-ErbA, a mutated thyroid hormone receptor alpha (TRα), is thought to contribute to avian erythroblastosis virus (AEV)-induced leukemic transformation by constitutively repressing transcription of target genes. However, the binding of v-ErbA or any unliganded nuclear receptor to a chromatin-embedded response element as well as the role of the N-CoR-SMRT-HDAC co-repressor complex in mediating repression remain hypothetical. Here we identify a v-ErbA-response element, VRE, in an intronic DNase I hypersensitive site (HS2) of the chicken erythroid carbonic anhydrase II (CAII) gene. In vivo footprinting shows that v-ErbA is constitutively bound to this HS2-VRE in transformed, undifferentiated erythroblasts along with other transcription factors like GATA-1. Transfection assays show that the repressed HS2 region can be turned into a potent enhancer in v-ErbAexpressing cells by mutation of the VRE. Differentiation of transformed cells alleviates v-ErbA binding concomitant with activation of CAII transcription. Co-expression of a gag-TRα fusion protein in AEV-transformed cells and addition of ligand derepresses CAII transcription. Treatment of transformed cells with the histone deacetylase inhibitor, trichostatin A, derepresses the endogenous, chromatin-embedded CAII gene, while a transfected HS2-enhancer construct remains repressed. Taken together, our data suggest that v-ErbA prevents CAII activation by 'neutralizing' in cis the activity of erythroid transcription factors.

Background: Myocardial infarction (MI) is a multifactorial disease with complex pathogenesis, mainly the result of the interplay of genetic and environmental risk factors. The regulation of thrombosis, inflammation and cholesterol and lipid metabolism are the main factors that have been proposed thus far to be involved in the pathogenesis of MI. Traditional risk-estimation tools depend largely on conventional risk factors but there is a need for identification of novel biochemical and genetic markers. The aim of the study is to identify differentially expressed genes that are consistently associated with the incidence myocardial infarction (MI), which could be potentially incorporated into the traditional cardiovascular diseases risk factors models. Methods: The biomedical literature and gene expression databases, PubMed and GEO, respectively, were searched following the PRISMA guidelines. The key inclusion criteria were gene expression data derived from case-control studies on MI patients from blood samples. Gene expression datasets regarding the effect of medicinal drugs on MI were excluded. The t-test was applied to gene expression data from case-control studies in MI patients. Results: A total of 162 articles and 174 gene expression datasets were retrieved. Of those a total of 4 gene expression datasets met the inclusion criteria, which contained data on 31,180 loci in 93 MI patients and 89 healthy individuals. Collectively, 626 differentially expressed genes were detected in MI patients as compared to nonaffected individuals at an FDR q-value = 0.01. Of those, 88 genes/gene products were interconnected in an interaction network. Totally, 15 genes were identified as hubs of the network. Conclusions: Functional enrichment analyses revealed that the DEGs and that they are mainly involved in inflammatory/wound healing, RNA processing/transport mechanisms and a yet not fully characterized pathway implicated in RNA transport and nuclear pore proteins. The overlap between the DEGs identified in this study and the genes identified through genetic-association studies is minimal. These data could be useful in future studies on the molecular mechanisms of MI as well as diagnostic and prognostic markers.