A SARS-CoV-2 sequence submission tool for the European Nucleotide Archive

Abstract Summary Many aspects of the global response to the COVID-19 pandemic are enabled by the fast and open publication of SARS-CoV-2 genetic sequence data. The European Nucleotide Archive (ENA) is the European recommended open repository for genetic sequences. In this work, we present a tool for submitting raw sequencing reads of SARS-CoV-2 to ENA. The tool features a single-step submission process, a graphical user interface, tabular-formatted metadata and the possibility to remove human reads prior to submission. A Galaxy wrap of the tool allows users with little or no bioinformatic knowledge to do bulk sequencing read submissions. The tool is also packed in a Docker container to ease deployment. Availability CLI ENA upload tool is available at github.com/usegalaxy-eu/ena-upload-cli (DOI 10.5281/zenodo.4537621); Galaxy ENA upload tool at toolshed.g2.bx.psu.edu/view/iuc/ena_upload/382518f24d6d and https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload (development) and; ENA upload Galaxy container at github.com/ELIXIR-Belgium/ena-upload-container (DOI 10.5281/zenodo.4730785) </jats:sec

DNA methylation repels binding of hypoxia-inducible transcription factors to maintain tumor immunotolerance.

BACKGROUND: Hypoxia is pervasive in cancer and other diseases. Cells sense and adapt to hypoxia by activating hypoxia-inducible transcription factors (HIFs), but it is still an outstanding question why cell types differ in their transcriptional response to hypoxia. RESULTS: We report that HIFs fail to bind CpG dinucleotides that are methylated in their consensus binding sequence, both in in vitro biochemical binding assays and in vivo studies of differentially methylated isogenic cell lines. Based on in silico structural modeling, we show that 5-methylcytosine indeed causes steric hindrance in the HIF binding pocket. A model wherein cell-type-specific methylation landscapes, as laid down by the differential expression and binding of other transcription factors under normoxia, control cell-type-specific hypoxia responses is observed. We also discover ectopic HIF binding sites in repeat regions which are normally methylated. Genetic and pharmacological DNA demethylation, but also cancer-associated DNA hypomethylation, expose these binding sites, inducing HIF-dependent expression of cryptic transcripts. In line with such cryptic transcripts being more prone to cause double-stranded RNA and viral mimicry, we observe low DNA methylation and high cryptic transcript expression in tumors with high immune checkpoint expression, but not in tumors with low immune checkpoint expression, where they would compromise tumor immunotolerance. In a low-immunogenic tumor model, DNA demethylation upregulates cryptic transcript expression in a HIF-dependent manner, causing immune activation and reducing tumor growth. CONCLUSIONS: Our data elucidate the mechanism underlying cell-type-specific responses to hypoxia and suggest DNA methylation and hypoxia to underlie tumor immunotolerance

DataHub platform - FAIR metadata by-design as a service for life sciences experiments.

&lt;p&gt;Poster on DataHub platform presented at the ELIXIR Belgium Conference, 2023: "ELIXIR Belgium: Your data, Our services, European success".&lt;/p&gt

RDMkit - The research data management toolkit for life sciences.

&lt;p&gt;Poster on RDMkit presented at the ELIXIR Belgium Conference, 2023: "ELIXIR Belgium: Your data, Our services, European success".&lt;/p&gt

DNA Hypermethylation drives EMT-mediated resistance to various cancer therapies

Overcoming therapeutic resistance is one of the major hurdles in cancer care. The process wherein epithelial cells switch to a mesenchymal state (epithelial-to-mesenchymal transition or EMT) often underlies this acquired resistance to cancer therapy. The precise mechanisms driving EMT are however not fully elucidated. Here, we explore whether DNA methylation changes are possibly involved in EMT-mediated therapeutic resistance. We selected 10 pairs of cell lines consisting of a â parentalâ cell line and a treatment â resistantâ cell line obtained after low-dose chronic exposure of the parental line to a targeted therapy (n=7) or chemotherapy (n=3). Based on changes in gene expression and cellular morphology, we observed that 8 resistant lines had undergone EMT. When transfecting resistant cell lines with miRNA-200, a known inhibitor of EMT, expression of EMT markers was reversed and resistance to therapy disappeared, indicating that EMT is essentially underlying the resistance. Resistant cells accumulated a remarkably high number of DNA methylation changes, and significantly more CpGs than expected based on random chance underwent methylation changes in >1 cell line. Importantly, promoters of epithelial marker genes were consistently more hypermethylated, while promoters of mesenchymal marker genes were hypomethylated in resistant cells. Mechanistically, we observed the majority of these methylation changes to be mediated by the demethylating TET enzymes. To prove that methylation changes were causal to EMT-driven therapeutic resistance, we exposed resistant cells to a non-cytotoxic dose of the demethylating agent 5-aza-2'-deoxycytidine. Interestingly, upon DNA demethylation, as confirmed by LC-MS, resistant cell lines lost their mesenchymal phenotype and became sensitive again to the corresponding therapy. Finally, to show that methylation changes were also functional, we exposed cells to hypoxia, a condition stabilizing HIF transcription factors such that they bind their unmethylated consensus domains. Interestingly, by overlaying methylation and gene expression data we could show that EMT-induced methylation changes indeed affect the hypoxia-induced gene expression program, including expression of several epithelial or mesenchymal genes. Based on these findings, we propose DNA methylation as a novel mechanism underlying EMT-mediated therapeutic resistance of tumors./status: publishe

A SARS-CoV-2 sequence submission tool for the European Nucleotide Archive

Many aspects of the global response to the COVID-19 pandemic are enabled by the fast and open publication of SARS-CoV-2 genetic sequence data. The European Nucleotide Archive (ENA) is the European recommended open repository for genetic sequences. In this work, we present a tool for submitting raw sequencing reads of SARS-CoV-2 to ENA. The tool features a single-step submission process, a graphical user interface, tabular-formatted metadata and the possibility to remove human reads prior to submission. A Galaxy wrap of the tool allows users with little or no bioinformatic knowledge to do bulk sequencing read submissions. The tool is also packed in a Docker container to ease deployment

Vascular smooth muscle cell dysfunction in patients with migraine.

Background: Migraine is associated with increased risk of cardiovascular disease, but the mechanisms are unclear.Objective: To investigate the activity of endothelial and vascular smooth muscle cells (VSMCs) in patients with migraine.Methods: Case-control study of 12 patients with migraine without aura and 12 matched healthy control subjects. Endothelial and VSMC components of vascular reactivity were explored by plethysmography measurement of forearm blood flow (FBF) during infusions of vasoactive agents into the brachial artery. Forearm production of nitric oxide (NO) and cyclic guanosine monophosphate (cGMP) was also quantified.Results: In patients with migraine, the vasodilating effect of acetylcholine (ACh), an endothelium-ependent vasodilator, was markedly reduced (p < 0.001 by analysis of variance). In response to the highest dose of ACh, FBF rose to 8.6 +/- 2.2 in patients with migraine and to 22.7 +/- 3.0 mL x dL(-1) x min(-1) in controls (p = 0.001). The dose-response curve to nitroprusside, a vasodilator directly acting on VSMCs, was depressed in patients with migraine (p < 0.001 by analysis of variance). The maximal response of FBF to nitroprusside was 12.1 +/- 2.0 in patients with migraine and 24.1 +/- 1.8 mL x dl(-1) x min(-1) in controls (p < 0.001). During ACh infusion, NO release from the endothelium was similar in patients and controls. In contrast, there was a marked release of cGMP from VSMCs in controls, but not in patients with migraine (-1.9 +/- 2.2 in patients with migraine and -19.1 +/- 5.4 nmol x dL(-1) x min(-1) in controls; p = 0.03).Conclusions: Patients with migraine are characterized by a distinct vascular smooth muscle cell dysfunction, revealed by impaired cyclic guanosine monophosphate and hemodynamic response to nitric oxide

HIF-1α Promotes Glutamine-Mediated Redox Homeostasis and Glycogen-Dependent Bioenergetics to Support Postimplantation Bone Cell Survival

Cell-based therapy is a promising strategy in regenerative medicine, but the poor survival rate of the implanted cells remains a major challenge and limits clinical translation. We preconditioned periosteal cells to the hypoxic and ischemic environment of the bone defect site by deleting prolyl hydroxylase domain-containing protein 2 (PHD2), resulting in hypoxia-inducible factor 1 alpha (HIF-1α) stabilization. This strategy increased postimplantation cell survival and improved bone regeneration. The enhanced cell viability was angiogenesis independent but relied on combined changes in glutamine and glycogen metabolism. HIF-1α stabilization stimulated glutaminase-mediated glutathione synthesis, maintaining redox homeostasis at baseline and during oxidative or nutrient stress. Simultaneously, HIF-1α signaling increased glycogen storage, preventing an energy deficit during nutrient or oxygen deprivation. Pharmacological inhibition of PHD2 recapitulated the adaptations in glutamine and glycogen metabolism and, consequently, the beneficial effects on cell survival. Thus, targeting cellular metabolism is an appealing strategy for bone regeneration and cell-based therapy in general.publisher: Elsevier articletitle: HIF-1α Promotes Glutamine-Mediated Redox Homeostasis and Glycogen-Dependent Bioenergetics to Support Postimplantation Bone Cell Survival journaltitle: Cell Metabolism articlelink: http://dx.doi.org/10.1016/j.cmet.2016.01.002 content_type: article copyright: Copyright © 2016 Elsevier Inc. All rights reserved.status: publishe