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Kitanovski S, Horemheb-Rubio G, Adams O, Gärtner B, Lengauer T, Hoffmann D, Kaiser R. Rhinovirus prevalence as indicator for efficacy of measures against SARS-CoV-2. BMC Public Health 2021; 21:1178. [PMID: 34154549 PMCID: PMC8215636 DOI: 10.1186/s12889-021-11178-w] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2021] [Accepted: 05/27/2021] [Indexed: 12/17/2022] Open
Abstract
BACKGROUND Non-pharmaceutical measures to control the spread of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) should be carefully tuned as they can impose a heavy social and economic burden. To quantify and possibly tune the efficacy of these anti-SARS-CoV-2 measures, we have devised indicators based on the abundant historic and current prevalence data from other respiratory viruses. METHODS We obtained incidence data of 17 respiratory viruses from hospitalized patients and outpatients collected by 37 clinics and laboratories between 2010-2020 in Germany. With a probabilistic model for Bayes inference we quantified prevalence changes of the different viruses between months in the pre-pandemic period 2010-2019 and the corresponding months in 2020, the year of the pandemic with noninvasive measures of various degrees of stringency. RESULTS We discovered remarkable reductions δ in rhinovirus (RV) prevalence by about 25% (95% highest density interval (HDI) [-0.35,-0.15]) in the months after the measures against SARS-CoV-2 were introduced in Germany. In the months after the measures began to ease, RV prevalence increased to low pre-pandemic levels, e.g. in August 2020 δ=-0.14 (95% HDI [-0.28,0.12]). CONCLUSIONS RV prevalence is negatively correlated with the stringency of anti-SARS-CoV-2 measures with only a short time delay. This result suggests that RV prevalence could possibly be an indicator for the efficiency for these measures. As RV is ubiquitous at higher prevalence than SARS-CoV-2 or other emerging respiratory viruses, it could reflect the efficacy of noninvasive measures better than such emerging viruses themselves with their unevenly spreading clusters.
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Affiliation(s)
- Simo Kitanovski
- Bioinformatics and Computational Biophysics, Faculty of Biology and Centre for Medical Biotechnology (ZMB), University of Duisburg-Essen, Essen, 45141, Germany
| | - Gibran Horemheb-Rubio
- Institute of Virology, University of Cologne, Faculty of Medicine and University Hospital of Cologne, Cologne, 50935, Germany
- Department of Infectious Diseases, Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán, Mexico City, 14080, Mexico
| | - Ortwin Adams
- Institute of Virology, University Hospital Düsseldorf, Heinrich Heine University Düsseldorf, Düsseldorf, 40225, Germany
| | - Barbara Gärtner
- Institute of Medical Microbiology and Hygiene, Saarland University Medical Center, Homburg, 66421, Germany
| | - Thomas Lengauer
- Computational Biology, Max Planck Institute for Informatics, Saarland Informatics Campus, Saarbrücken, 66123, Germany
| | - Daniel Hoffmann
- Bioinformatics and Computational Biophysics, Faculty of Biology and Centre for Medical Biotechnology (ZMB), University of Duisburg-Essen, Essen, 45141, Germany.
| | - Rolf Kaiser
- Institute of Virology, University of Cologne, Faculty of Medicine and University Hospital of Cologne, Cologne, 50935, Germany
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Cao Y, Xu X, Kitanovski S, Song L, Wang J, Hao P, Hoffmann D. Comprehensive Comparison of RNA-Seq Data of SARS-CoV-2, SARS-CoV and MERS-CoV Infections: Alternative Entry Routes and Innate Immune Responses. Front Immunol 2021; 12:656433. [PMID: 34122413 PMCID: PMC8195239 DOI: 10.3389/fimmu.2021.656433] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2021] [Accepted: 04/06/2021] [Indexed: 12/27/2022] Open
Abstract
Background The pathogenesis of COVID-19 emerges as complex, with multiple factors leading to injury of different organs. Some of the studies on aspects of SARS-CoV-2 cell entry and innate immunity have produced seemingly contradictory claims. In this situation, a comprehensive comparative analysis of a large number of related datasets from several studies could bring more clarity, which is imperative for therapy development. Methods We therefore performed a comprehensive comparative study, analyzing RNA-Seq data of infections with SARS-CoV-2, SARS-CoV and MERS-CoV, including data from different types of cells as well as COVID-19 patients. Using these data, we investigated viral entry routes and innate immune responses. Results and Conclusion First, our analyses support the existence of cell entry mechanisms for SARS and SARS-CoV-2 other than the ACE2 route with evidence of inefficient infection of cells without expression of ACE2; expression of TMPRSS2/TPMRSS4 is unnecessary for efficient SARS-CoV-2 infection with evidence of efficient infection of A549 cells transduced with a vector expressing human ACE2. Second, we find that innate immune responses in terms of interferons and interferon simulated genes are strong in relevant cells, for example Calu3 cells, but vary markedly with cell type, virus dose, and virus type.
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Affiliation(s)
- Yingying Cao
- Bioinformatics and Computational Biophysics, Faculty of Biology and Center for Medical Biotechnology (ZMB), University of Duisburg-Essen, Essen, Germany
| | - Xintian Xu
- Key Laboratory of Molecular Virology and Immunology, Institut Pasteur of Shanghai, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Shanghai, China
| | - Simo Kitanovski
- Bioinformatics and Computational Biophysics, Faculty of Biology and Center for Medical Biotechnology (ZMB), University of Duisburg-Essen, Essen, Germany
| | - Lina Song
- Department of Dermatology, University Hospital Essen, Essen, Germany
- Department of Translational Skin Cancer Research (TSCR), German Cancer Consortium (DKTK), Partner Site Essen, German Cancer Research Center, Heidelberg, Germany
| | - Jun Wang
- Bioinformatics and Computational Biophysics, Faculty of Biology and Center for Medical Biotechnology (ZMB), University of Duisburg-Essen, Essen, Germany
| | - Pei Hao
- Key Laboratory of Molecular Virology and Immunology, Institut Pasteur of Shanghai, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Shanghai, China
| | - Daniel Hoffmann
- Bioinformatics and Computational Biophysics, Faculty of Biology and Center for Medical Biotechnology (ZMB), University of Duisburg-Essen, Essen, Germany
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Wuelling M, Neu C, Thiesen AM, Kitanovski S, Cao Y, Lange A, Westendorf AM, Hoffmann D, Vortkamp A. Epigenetic Mechanisms Mediating Cell State Transitions in Chondrocytes. J Bone Miner Res 2021; 36:968-985. [PMID: 33534175 DOI: 10.1002/jbmr.4263] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/28/2020] [Revised: 01/21/2021] [Accepted: 01/26/2021] [Indexed: 01/06/2023]
Abstract
Epigenetic modifications play critical roles in regulating cell lineage differentiation, but the epigenetic mechanisms guiding specific differentiation steps within a cell lineage have rarely been investigated. To decipher such mechanisms, we used the defined transition from proliferating (PC) into hypertrophic chondrocytes (HC) during endochondral ossification as a model. We established a map of activating and repressive histone modifications for each cell type. ChromHMM state transition analysis and Pareto-based integration of differential levels of mRNA and epigenetic marks revealed that differentiation-associated gene repression is initiated by the addition of H3K27me3 to promoters still carrying substantial levels of activating marks. Moreover, the integrative analysis identified genes specifically expressed in cells undergoing the transition into hypertrophy. Investigation of enhancer profiles detected surprising differences in enhancer number, location, and transcription factor binding sites between the two closely related cell types. Furthermore, cell type-specific upregulation of gene expression was associated with increased numbers of H3K27ac peaks. Pathway analysis identified PC-specific enhancers associated with chondrogenic genes, whereas HC-specific enhancers mainly control metabolic pathways linking epigenetic signature to biological functions. Since HC-specific enhancers show a higher conservation in postnatal tissues, the switch to metabolic pathways seems to be a hallmark of differentiated tissues. Surprisingly, the analysis of H3K27ac levels at super-enhancers revealed a rapid adaption of H3K27ac occupancy to changes in gene expression, supporting the importance of enhancer modulation for acute alterations in gene expression. © 2021 The Authors. Journal of Bone and Mineral Research published by Wiley Periodicals LLC on behalf of American Society for Bone and Mineral Research (ASBMR).
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Affiliation(s)
- Manuela Wuelling
- Developmental Biology, Centre for Medical Biotechnology, University Duisburg-Essen, Essen, Germany
| | - Christoph Neu
- Developmental Biology, Centre for Medical Biotechnology, University Duisburg-Essen, Essen, Germany
| | - Andrea M Thiesen
- Developmental Biology, Centre for Medical Biotechnology, University Duisburg-Essen, Essen, Germany
| | - Simo Kitanovski
- Bioinformatics and Computational Biophysics, Centre for Medical Biotechnology, University Duisburg-Essen, Essen, Germany
| | - Yingying Cao
- Bioinformatics and Computational Biophysics, Centre for Medical Biotechnology, University Duisburg-Essen, Essen, Germany
| | - Anja Lange
- Bioinformatics and Computational Biophysics, Centre for Medical Biotechnology, University Duisburg-Essen, Essen, Germany
| | - Astrid M Westendorf
- Institute of Medical Microbiology, University Hospital Essen, University Duisburg-Essen, Essen, Germany
| | - Daniel Hoffmann
- Bioinformatics and Computational Biophysics, Centre for Medical Biotechnology, University Duisburg-Essen, Essen, Germany
| | - Andrea Vortkamp
- Developmental Biology, Centre for Medical Biotechnology, University Duisburg-Essen, Essen, Germany
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Cao Y, Kitanovski S, Küppers R, Hoffmann D. UMI or not UMI, that is the question for scRNA-seq zero-inflation. Nat Biotechnol 2021; 39:158-159. [PMID: 33526946 DOI: 10.1038/s41587-020-00810-6] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2020] [Accepted: 12/23/2020] [Indexed: 12/16/2022]
Affiliation(s)
- Yingying Cao
- Bioinformatics and Computational Biophysics, Faculty of Biology and Center for Medical Biotechnology, University of Duisburg-Essen, Essen, Germany
| | - Simo Kitanovski
- Bioinformatics and Computational Biophysics, Faculty of Biology and Center for Medical Biotechnology, University of Duisburg-Essen, Essen, Germany
| | - Ralf Küppers
- Institute of Cell Biology (Cancer Research), University Hospital Essen, Essen, Germany
| | - Daniel Hoffmann
- Bioinformatics and Computational Biophysics, Faculty of Biology and Center for Medical Biotechnology, University of Duisburg-Essen, Essen, Germany.
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Duhan V, Khairnar V, Kitanovski S, Hamdan TA, Klein AD, Lang J, Ali M, Adomati T, Bhat H, Friedrich SK, Li F, Krebs P, Futerman AH, Addo MM, Hardt C, Hoffmann D, Lang PA, Lang KS. Integrin Alpha E (CD103) Limits Virus-Induced IFN-I Production in Conventional Dendritic Cells. Front Immunol 2021; 11:607889. [PMID: 33584680 PMCID: PMC7873973 DOI: 10.3389/fimmu.2020.607889] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2020] [Accepted: 12/14/2020] [Indexed: 11/17/2022] Open
Abstract
Early and strong production of IFN-I by dendritic cells is important to control vesicular stomatitis virus (VSV), however mechanisms which explain this cell-type specific innate immune activation remain to be defined. Here, using a genome wide association study (GWAS), we identified Integrin alpha-E (Itgae, CD103) as a new regulator of antiviral IFN-I production in a mouse model of vesicular stomatitis virus (VSV) infection. CD103 was specifically expressed by splenic conventional dendritic cells (cDCs) and limited IFN-I production in these cells during VSV infection. Mechanistically, CD103 suppressed AKT phosphorylation and mTOR activation in DCs. Deficiency in CD103 accelerated early IFN-I in cDCs and prevented death in VSV infected animals. In conclusion, CD103 participates in regulation of cDC specific IFN-I induction and thereby influences immune activation after VSV infection.
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MESH Headings
- Animals
- Antigens, CD/genetics
- Antigens, CD/metabolism
- Cells, Cultured
- Dendritic Cells/immunology
- Dendritic Cells/metabolism
- Dendritic Cells/virology
- Disease Models, Animal
- Genome-Wide Association Study
- Host-Pathogen Interactions
- Immunity, Innate
- Integrin alpha Chains/genetics
- Integrin alpha Chains/metabolism
- Interferon Type I/metabolism
- Mice, 129 Strain
- Mice, Inbred AKR
- Mice, Inbred BALB C
- Mice, Inbred C3H
- Mice, Inbred C57BL
- Mice, Inbred DBA
- Mice, Inbred NOD
- Mice, Knockout
- Phosphorylation
- Proto-Oncogene Proteins c-akt/metabolism
- Receptor, Interferon alpha-beta/genetics
- Receptor, Interferon alpha-beta/metabolism
- Signal Transduction
- TOR Serine-Threonine Kinases/metabolism
- Vesicular Stomatitis/genetics
- Vesicular Stomatitis/immunology
- Vesicular Stomatitis/metabolism
- Vesicular Stomatitis/virology
- Vesiculovirus/growth & development
- Vesiculovirus/pathogenicity
- Virus Replication
- Mice
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Affiliation(s)
- Vikas Duhan
- Institute of Immunology, Medical Faculty, University of Duisburg-Essen, Essen, Germany
- Immunology in Cancer and Infection Laboratory, QIMR Berghofer Medical Research Institute, Herston, QLD, Australia
| | - Vishal Khairnar
- Institute of Immunology, Medical Faculty, University of Duisburg-Essen, Essen, Germany
- Dana-Farber Cancer Institute, Harvard University, Boston, MA, United States
| | - Simo Kitanovski
- Bioinformatics and Computational Biophysics, Faculty of Biology, University of Duisburg-Essen, Essen, Germany
| | - Thamer A. Hamdan
- Institute of Immunology, Medical Faculty, University of Duisburg-Essen, Essen, Germany
- Department of Medical Laboratories, Faculty of Health Sciences, American University of Madaba, Amman, Jordan
| | - Andrés D. Klein
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot, Israel
- Centro de Genética y Genómica, Universidad Del Desarrollo Clínica Alemana de Santiago, Santiago, Chile
| | - Judith Lang
- Institute of Immunology, Medical Faculty, University of Duisburg-Essen, Essen, Germany
| | - Murtaza Ali
- Institute of Immunology, Medical Faculty, University of Duisburg-Essen, Essen, Germany
| | - Tom Adomati
- Institute of Immunology, Medical Faculty, University of Duisburg-Essen, Essen, Germany
| | - Hilal Bhat
- Institute of Immunology, Medical Faculty, University of Duisburg-Essen, Essen, Germany
- Center for Molecular Medicine Cologne, University Hospital Cologne, University of Cologne, Cologne, Germany
| | - Sarah-Kim Friedrich
- Institute of Immunology, Medical Faculty, University of Duisburg-Essen, Essen, Germany
| | - Fanghui Li
- Institute of Immunology, Medical Faculty, University of Duisburg-Essen, Essen, Germany
| | - Philippe Krebs
- Institute of Pathology, University of Bern, Bern, Switzerland
| | - Anthony H. Futerman
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot, Israel
| | - Marylyn M. Addo
- University Medical Center Hamburg-Eppendorf, Division of Infectious Diseases, 1st Department of Medicine, Hamburg, Germany
- German Center for Infection Research, partner site Hamburg-Lübeck-Borstel-Riemse, Hamburg, Germany
- Department of Clinical Immunology of Infectious Diseases, Bernhard-Nocht-Institute for Tropical Medicine, Hamburg, Germany
| | - Cornelia Hardt
- Institute of Immunology, Medical Faculty, University of Duisburg-Essen, Essen, Germany
| | - Daniel Hoffmann
- Bioinformatics and Computational Biophysics, Faculty of Biology, University of Duisburg-Essen, Essen, Germany
| | - Philipp A. Lang
- Department of Molecular Medicine II, Medical Faculty, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Karl S. Lang
- Institute of Immunology, Medical Faculty, University of Duisburg-Essen, Essen, Germany
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Cao Y, Kitanovski S, Hoffmann D. intePareto: an R package for integrative analyses of RNA-Seq and ChIP-Seq data. BMC Genomics 2020; 21:802. [PMID: 33372591 PMCID: PMC7771091 DOI: 10.1186/s12864-020-07205-6] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2020] [Accepted: 10/29/2020] [Indexed: 01/09/2023] Open
Abstract
BACKGROUND RNA-Seq, the high-throughput sequencing (HT-Seq) of mRNAs, has become an essential tool for characterizing gene expression differences between different cell types and conditions. Gene expression is regulated by several mechanisms, including epigenetically by post-translational histone modifications which can be assessed by ChIP-Seq (Chromatin Immuno-Precipitation Sequencing). As more and more biological samples are analyzed by the combination of ChIP-Seq and RNA-Seq, the integrated analysis of the corresponding data sets becomes, theoretically, a unique option to study gene regulation. However, technically such analyses are still in their infancy. RESULTS Here we introduce intePareto, a computational tool for the integrative analysis of RNA-Seq and ChIP-Seq data. With intePareto we match RNA-Seq and ChIP-Seq data at the level of genes, perform differential expression analysis between biological conditions, and prioritize genes with consistent changes in RNA-Seq and ChIP-Seq data using Pareto optimization. CONCLUSION intePareto facilitates comprehensive understanding of high dimensional transcriptomic and epigenomic data. Its superiority to a naive differential gene expression analysis with RNA-Seq and available integrative approach is demonstrated by analyzing a public dataset.
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Affiliation(s)
- Yingying Cao
- Bioinformatics and Computational Biophysics, Faculty of Biology and Center for Medical Biotechnology (ZMB), University of Duisburg-Essen, Universitätsstr.2, Essen, 45141, Germany.
| | - Simo Kitanovski
- Bioinformatics and Computational Biophysics, Faculty of Biology and Center for Medical Biotechnology (ZMB), University of Duisburg-Essen, Universitätsstr.2, Essen, 45141, Germany
| | - Daniel Hoffmann
- Bioinformatics and Computational Biophysics, Faculty of Biology and Center for Medical Biotechnology (ZMB), University of Duisburg-Essen, Universitätsstr.2, Essen, 45141, Germany
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Kitanovski S, Hoffmann D. IgGeneUsage: differential gene usage in immune repertoires. Bioinformatics 2020; 36:3590-3591. [PMID: 32163125 DOI: 10.1093/bioinformatics/btaa174] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2019] [Revised: 11/30/2019] [Accepted: 03/09/2020] [Indexed: 11/13/2022] Open
Abstract
SUMMARY Decoding the properties of immune repertoires is key to understanding the adaptive immune response to challenges such as viral infection. One important quantitative property is differential usage of Ig genes between biological conditions. Yet, most analyses for differential Ig gene usage are performed qualitatively or with inadequate statistical methods. Here we introduce IgGeneUsage, a computational tool for the analysis of differential Ig gene usage. IgGeneUsage employs Bayesian inference with hierarchical models to analyze complex gene usage data from high-throughput sequencing experiments of immune repertoires. It quantifies differential Ig gene usage probabilistically and avoids some common problems related to the current practice of null-hypothesis significance testing. AVAILABILITY AND IMPLEMENTATION IgGeneUsage is an R-package freely available as part of Bioconductor at: https://bioconductor.org/packages/IgGeneUsage/. CONTACT simo.kitanovski@uni-due.de. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Simo Kitanovski
- Bioinformatics and Computational Biophysics, Faculty of Biology and Centre for Medical Biotechnology (ZMB), University of Duisburg-Essen, Essen 45141, Germany
| | - Daniel Hoffmann
- Bioinformatics and Computational Biophysics, Faculty of Biology and Centre for Medical Biotechnology (ZMB), University of Duisburg-Essen, Essen 45141, Germany
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