Publications by authors named "Elena De Domenico"

12 Publications

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Disease severity-specific neutrophil signatures in blood transcriptomes stratify COVID-19 patients.

Genome Med 2021 01 13;13(1). Epub 2021 Jan 13.

Systems Medicine, German Center for Neurodegenerative Diseases (DZNE), Bonn, Germany.

Background: The SARS-CoV-2 pandemic is currently leading to increasing numbers of COVID-19 patients all over the world. Clinical presentations range from asymptomatic, mild respiratory tract infection, to severe cases with acute respiratory distress syndrome, respiratory failure, and death. Reports on a dysregulated immune system in the severe cases call for a better characterization and understanding of the changes in the immune system.

Methods: In order to dissect COVID-19-driven immune host responses, we performed RNA-seq of whole blood cell transcriptomes and granulocyte preparations from mild and severe COVID-19 patients and analyzed the data using a combination of conventional and data-driven co-expression analysis. Additionally, publicly available data was used to show the distinction from COVID-19 to other diseases. Reverse drug target prediction was used to identify known or novel drug candidates based on finding from data-driven findings.

Results: Here, we profiled whole blood transcriptomes of 39 COVID-19 patients and 10 control donors enabling a data-driven stratification based on molecular phenotype. Neutrophil activation-associated signatures were prominently enriched in severe patient groups, which was corroborated in whole blood transcriptomes from an independent second cohort of 30 as well as in granulocyte samples from a third cohort of 16 COVID-19 patients (44 samples). Comparison of COVID-19 blood transcriptomes with those of a collection of over 3100 samples derived from 12 different viral infections, inflammatory diseases, and independent control samples revealed highly specific transcriptome signatures for COVID-19. Further, stratified transcriptomes predicted patient subgroup-specific drug candidates targeting the dysregulated systemic immune response of the host.

Conclusions: Our study provides novel insights in the distinct molecular subgroups or phenotypes that are not simply explained by clinical parameters. We show that whole blood transcriptomes are extremely informative for COVID-19 since they capture granulocytes which are major drivers of disease severity.
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http://dx.doi.org/10.1186/s13073-020-00823-5DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7805430PMC
January 2021

Optimized workflow for single-cell transcriptomics on infectious diseases including COVID-19.

STAR Protoc 2020 Dec 16;1(3):100233. Epub 2020 Dec 16.

German Center for Neurodegenerative Diseases (DZNE), PRECISE Platform for Genomics and Epigenomics at DZNE, and University of Bonn, Bonn, Germany.

In December 2019, a new coronavirus, SARS-CoV-2, which causes the respiratory illness that led to the COVID-19 pandemic, was reported. In the face of such a new pathogen, special precautions must be taken to examine potentially infectious materials due to the lack of knowledge on disease transmissibility, infectivity, and molecular pathogenicity. Here, we present a complete and safe workflow for performing scRNA-seq experiments on blood samples of infected patients from cell isolation to data analysis using the micro-well based BD Rhapsody platform. For complete information on the use and execution of this protocol, please refer to Schulte-Schrepping et al. (2020).
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http://dx.doi.org/10.1016/j.xpro.2020.100233DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7757730PMC
December 2020

Severe COVID-19 Is Marked by a Dysregulated Myeloid Cell Compartment.

Cell 2020 09 5;182(6):1419-1440.e23. Epub 2020 Aug 5.

Department of Infectious Diseases and Respiratory Medicine, Charité, Universitätsmedizin Berlin, Berlin, Germany; German Center for Lung Research (DZL).

Coronavirus disease 2019 (COVID-19) is a mild to moderate respiratory tract infection, however, a subset of patients progress to severe disease and respiratory failure. The mechanism of protective immunity in mild forms and the pathogenesis of severe COVID-19 associated with increased neutrophil counts and dysregulated immune responses remain unclear. In a dual-center, two-cohort study, we combined single-cell RNA-sequencing and single-cell proteomics of whole-blood and peripheral-blood mononuclear cells to determine changes in immune cell composition and activation in mild versus severe COVID-19 (242 samples from 109 individuals) over time. HLA-DRCD11c inflammatory monocytes with an interferon-stimulated gene signature were elevated in mild COVID-19. Severe COVID-19 was marked by occurrence of neutrophil precursors, as evidence of emergency myelopoiesis, dysfunctional mature neutrophils, and HLA-DR monocytes. Our study provides detailed insights into the systemic immune response to SARS-CoV-2 infection and reveals profound alterations in the myeloid cell compartment associated with severe COVID-19.
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http://dx.doi.org/10.1016/j.cell.2020.08.001DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7405822PMC
September 2020

An RNA-Seq Protocol for Differential Expression Analysis.

Cold Spring Harb Protoc 2019 06 3;2019(6). Epub 2019 Jun 3.

The Francis Crick Institute, NW1 1ST London, United Kingdom

Here we consider RNA-Seq, used to measure global gene expression through RNA fragmentation, capture, sequencing, and subsequent computational analysis. , with its large number of RNA-rich, synchronously developing, and accessible embryos, is an excellent model organism for exploiting the power of high-throughput sequencing to understand gene expression during development. Here we present a standard RNA-Seq protocol for performing two-state differential gene expression analysis (between groups of replicates of control and treated embryos) using Illumina sequencing. Samples contain multiple whole embryos, and polyadenylated mRNA is measured under relative normalization. The protocol is divided into two parts: wet-lab processes to prepare samples for sequencing and downstream computational analysis including quality control, quantification of gene expression, and differential expression.
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http://dx.doi.org/10.1101/pdb.prot098368DOI Listing
June 2019

Molecular asymmetry in the 8-cell stage Xenopus tropicalis embryo described by single blastomere transcript sequencing.

Dev Biol 2015 Dec 19;408(2):252-68. Epub 2015 Jun 19.

The Francis Crick Institute, Mill Hill Laboratory, The Ridgeway, Mill Hill, London NW7 1AA, UK. Electronic address:

Correct development of the vertebrate body plan requires the early definition of two asymmetric, perpendicular axes. The first axis is established during oocyte maturation, and the second is established by symmetry breaking shortly after fertilization. The physical processes generating the second asymmetric, or dorsal-ventral, axis are well understood, but the specific molecular determinants, presumed to be maternal gene products, are poorly characterized. Whilst enrichment of maternal mRNAs at the animal and vegetal poles in both the oocyte and the early embryo has been studied, little is known about the distribution of maternal mRNAs along either the dorsal-ventral or left-right axes during the early cleavage stages. Here we report an unbiased analysis of the distribution of maternal mRNA on all axes of the Xenopus tropicalis 8-cell stage embryo, based on sequencing of single blastomeres whose positions within the embryo are known. Analysis of pooled data from complete sets of blastomeres from four embryos has identified 908 mRNAs enriched in either the animal or vegetal blastomeres, of which 793 are not previously reported as enriched. In contrast, we find no evidence for asymmetric distribution along either the dorsal-ventral or left-right axes. We confirm that animal pole enrichment is on average distinctly lower than vegetal pole enrichment, and that considerable variation is found between reported enrichment levels in different studies. We use publicly available data to show that there is a significant association between genes with human disease annotation and enrichment at the animal pole. Mutations in the human ortholog of the most animally enriched novel gene, Slc35d1, are causative for Schneckenbecken dysplasia, and we show that a similar phenotype is produced by depletion of the orthologous protein in Xenopus embryos.
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http://dx.doi.org/10.1016/j.ydbio.2015.06.010DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4684228PMC
December 2015

High-resolution analysis of gene activity during the Xenopus mid-blastula transition.

Development 2014 May;141(9):1927-39

Division of Systems Biology, MRC National Institute for Medical Research, The Ridgeway, Mill Hill, London NW7 1AA, UK.

The Xenopus mid-blastula transition (MBT) marks the onset of large-scale zygotic transcription, as well as an increase in cell cycle length and a loss of synchronous cell divisions. Little is known about what triggers the activation of transcription or how newly expressed genes interact with each other. Here, we use high-resolution expression profiling to identify three waves of gene activity: a post-fertilisation wave involving polyadenylation of maternal transcripts; a broad wave of zygotic transcription detectable as early as the seventh cleavage and extending beyond the MBT at the twelfth cleavage; and a shorter post-MBT wave of transcription that becomes apparent as development proceeds. Our studies have also allowed us to define a set of maternal mRNAs that are deadenylated shortly after fertilisation, and are likely to be degraded thereafter. Experimental analysis indicates that the polyadenylation of maternal transcripts is necessary for the establishment of proper levels of zygotic transcription at the MBT, and that genes activated in the second wave of expression, including Brachyury and Mixer, contribute to the regulation of genes expressed in the third. Together, our high-resolution time series and experimental studies have yielded a deeper understanding of the temporal organisation of gene regulatory networks in the early Xenopus embryo.
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http://dx.doi.org/10.1242/dev.102012DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3994770PMC
May 2014

Influence of continuous light treatment on expression of stress biomarkers in Atlantic cod.

Dev Comp Immunol 2014 May 1;44(1):30-4. Epub 2013 Dec 1.

Department of Biological and Environmental Sciences, University of Messina, 98166 Messina, Italy.

Continuous light treatment during early juvenile stages in Gadus morhua is a common farming management practice but the effects of these unnatural light conditions on fish stress have received scant attention. In the present study we investigated how continuous illumination affects transcription levels of key stress-related and antimicrobial peptide genes in juvenile Atlantic cod. Gene expression quantification by real-time PCR revealed higher levels of transcripts coding for antioxidant enzymes, namely superoxide dismutase, catalase and glutathione reductase in liver of fish reared under continuous illumination, concomitantly with a 43% decrease in glutathione content. Transcription of antimicrobial peptides such as piscidins, hepcidin and cathelicidin was also affected by constant illumination. Overall, the significant changes in liver transcript levels of these biomarkers in response to continuous light may be an adaptation to light stress.
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http://dx.doi.org/10.1016/j.dci.2013.11.011DOI Listing
May 2014

Biological responses of juvenile European sea bass (Dicentrarchus labrax) exposed to contaminated sediments.

Ecotoxicol Environ Saf 2013 Nov 14;97:114-23. Epub 2013 Aug 14.

Department of Biological and Environmental Sciences, University of Messina, Viale F. Stagno d'Alcontres 31, 98166 Messina, Italy.

Multiple anthropogenic activities present along coastal environments may affect the health status of aquatic ecosystems. In this study, specimens of European sea bass (Dicentrarchus labrax) were exposed for 30 days to highly contaminated sediment collected from the industrial area between Augusta and Priolo (Syracuse, Italy), defined as the most mercury polluted site in the Mediterranean. The aim was to evaluate the responses of juvenile D. labrax to highly contaminated sediments, particularly enriched in Hg, in order to enhance the scarce knowledge on the potential compensatory mechanisms developed by organisms under severe stress conditions. Apoptotic and proliferative activities [cell turnover: Proliferating Cell Nuclear Antigen (PCNA) and FAS Ligand (FasL)], onset of hypoxic condition [hypoxia: Hypoxia Inducibile Factor-1α (HIF-1α)], and changes in the neuroendocrine control mechanisms [neurotransmission: Tyrosine Hydroxylase (TH), Choline Acetyltransferase (ChAT), Acetylcholinesterase (AChE), 5-Hydroxytryptamine (5-HT) and 5-Hydroxytryptamine receptor 3 (5-HT3)] were investigated in sea bass gill tissues. In the specimens exposed to the polluted sediment, the occurrence of altered cell turnover may result in impaired gas exchange that leads to a condition of "functional hypoxia". Changes in neurotransmission pathways were also observed, suggesting a remodeling process as an adaptive response to increase the O2-carrying capacity and restore the normal physiological conditions of the gills. Overall, these findings demonstrated that although chronic exposure to heavy metal polluted sediments alters the functioning of both the nervous and endocrine systems, as well as plasticity of the gill epithelium, fish are able to trigger a series of physiological adjustments or adaptations interfering with specific neuroendocrine control mechanisms that enable their long-term survival.
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http://dx.doi.org/10.1016/j.ecoenv.2013.07.015DOI Listing
November 2013

Metabolomic investigation of Mytilus galloprovincialis (Lamarck 1819) caged in aquatic environments.

Ecotoxicol Environ Saf 2012 Oct 20;84:139-46. Epub 2012 Jul 20.

Department of Animal Biology and Marine Ecology, University of Messina, Viale F. Stagno D'Alcontres 31, 98166 Messina, Italy.

Environmental metabolomics was applied to assess the metabolic responses in transplanted mussels to environmental pollution. Specimens of Mytilus galloprovincialis, sedentary filter-feeders, were caged in anthropogenic-impacted and reference sites along the Augusta coastline (Sicily, Italy). Chemical analysis revealed increased levels of PAHs in the digestive gland of mussels from the industrial area compared with control, and marked morphological changes were also observed. Digestive gland metabolic profiles, obtained by 1H NMR spectroscopy and analyzed by multivariate statistics, showed changes in metabolites involved in energy metabolism. Specifically, changes in lactate and acetoacetate could indicate increased anaerobic fermentation and alteration in lipid metabolism, respectively, suggesting that the mussels transplanted to the contaminated field site were suffering from adverse environmental condition. The NMR-based environmental metabolomics applied in this study results thus in it being a useful and effective tool for assessing environmental influences on the health status of aquatic organisms.
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http://dx.doi.org/10.1016/j.ecoenv.2012.07.001DOI Listing
October 2012

Effects of "in vivo" exposure to toxic sediments on juveniles of sea bass (Dicentrarchus labrax).

Aquat Toxicol 2011 Oct 21;105(3-4):688-97. Epub 2011 Sep 21.

Department Animal Biology and Marine Ecology, University of Messina, Viale Stagno D'Alcontres 31, 98166 Messina, Italy.

Aquatic ecosystems are affected by all the impacts generated by a variety of anthropogenic activities present along coastal environments. The sediment compartment is the final receptor of water-insoluble pollutants, acting both as a sink and as a source of pollutants to the water column, and affecting both nektonic and benthic organisms. The aim of this study is to assess the impact of metals in the sediments collected from two sites in the petrochemical area between Augusta and Priolo (SR, Sicily, Italy) on gills of Dicentrarchus labrax. This was done to enhance the scarce knowledge on the bioavailability of metals bound to sediment and their capacity to interact with the bioindicator species. Various sublethal endpoints were assessed such as histopathological lesions, metallothioneins (MTs) and molecules involved in the homeostasis pathways by immunolocalization and RT-PCR. In the specimens exposed to sediments, the data suggested a reduction of gill cell membrane permeability, which could result in altered osmotic balance and gas exchange. Further, an increase of MT expression was detected, consisted the involvement of this protein in detoxification of toxic non-essential metals. The findings of this study demonstrate that a subchronic test, conducted by using sensitive and sub-lethal endpoints, in combination with chemical analyses, is a powerful tool for early identification of environmental hazards associated with contaminated sediments.
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http://dx.doi.org/10.1016/j.aquatox.2011.08.026DOI Listing
October 2011

A multibiomarker approach in Coris julis living in a natural environment.

Ecotoxicol Environ Saf 2010 Oct 4;73(7):1565-73. Epub 2010 Feb 4.

Dipartimento di Biologia animale ed Ecologia marina, Università di Messina, Salita Sperone 31, 98166S. Agata, Messina, Italy.

To monitor the health of aquatic organisms, biomarkers have been used as effective tools in assessing environmental risk. In this study was examined the teleost Coris julis, sampled in two marine sites in Messina (Italy) at different pollution degree, Milazzo, characterized by a strong anthropogenic impact, and Marinello, the natural reserve. C. julis is a species particularly suitable to biomonitoring because its feeding habits favor bio-accumulation of xenobiotics. The following biomarkers were used to estimate the impact of highly persistent pollutants: cellular localization of cytochrome P4501A (CYP1A) and glutathione-S-transferase (GST) in the liver, their hepatic expression at the mRNA level, the enzymatic activity (EROD and BPMO), the micronucleus and comet assays in the blood, esterases (AChE in the brain and BChE in the blood) activity and evaluation of PAH metabolites in the bile. The present findings provide evidence of statistically significant differences in parameters between individuals collected in two sites.
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http://dx.doi.org/10.1016/j.ecoenv.2010.01.008DOI Listing
October 2010

Ultrastructural and immunohistochemical investigation on the gills of the teleost, Thalassoma pavo L., exposed to cadmium.

Acta Histochem 2011 Feb;113(2):201-13

Abele Saita Electron Microscopy Laboratories, Department of Ecology, University of Calabria, Via P. Bucci, Rende (Cosenza), Italy.

An investigation was conducted to determine the effects of the heavy metal, cadmium (Cd), on the gills of the teleost fish, Thalassoma pavo Linnaeus, 1758. The fishes were exposed to several sublethal concentrations of cadmium (10, 40, 60 and 120 μM (mg/L)) for a period of 48, 96 and 192 h. The value of the LC50 after 96 h of cadmium exposure, determined using the System of Finney, was equal to 128.3 μM. The gills of the fishes were examined by light and electron microscopy. Toxic, apoptotic and cadmium effects were analyzed using some neuropeptides, metallothioneins (MT), caspase 3, PCNA and calmodulin, as bioindicators, respectively. The results showed that the alterations in the gills were proportional to the exposure periods and concentrations of the metal, which were found to be both dose and time dependent. The biological responses in the gills of the tested animals are discussed in relation to results obtained by analysis of the biomarkers. These data may be used for the planning of a model to determine biological risk in the marine environment and may be particularly useful to investigate organisms exposed to cadmium.
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http://dx.doi.org/10.1016/j.acthis.2009.10.002DOI Listing
February 2011