1
|
Falckenhayn C, Bienkowska A, Söhle J, Wegner K, Raddatz G, Kristof B, Kuck D, Siegner R, Kaufmann R, Korn J, Baumann S, Lange D, Schepky A, Völzke H, Kaderali L, Winnefeld M, Lyko F, Grönniger E. Identification of dihydromyricetin as a natural DNA methylation inhibitor with rejuvenating activity in human skin. Front Aging 2024; 4:1258184. [PMID: 38500495 PMCID: PMC10944877 DOI: 10.3389/fragi.2023.1258184] [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] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/13/2023] [Accepted: 12/12/2023] [Indexed: 03/20/2024]
Abstract
Changes in DNA methylation patterning have been reported to be a key hallmark of aged human skin. The altered DNA methylation patterns are correlated with deregulated gene expression and impaired tissue functionality, leading to the well-known skin aging phenotype. Searching for small molecules, which correct the aged methylation pattern therefore represents a novel and attractive strategy for the identification of anti-aging compounds. DNMT1 maintains epigenetic information by copying methylation patterns from the parental (methylated) strand to the newly synthesized strand after DNA replication. We hypothesized that a modest inhibition of this process promotes the restoration of the ground-state epigenetic pattern, thereby inducing rejuvenating effects. In this study, we screened a library of 1800 natural substances and 640 FDA-approved drugs and identified the well-known antioxidant and anti-inflammatory molecule dihydromyricetin (DHM) as an inhibitor of the DNA methyltransferase DNMT1. DHM is the active ingredient of several plants with medicinal use and showed robust inhibition of DNMT1 in biochemical assays. We also analyzed the effect of DHM in cultivated keratinocytes by array-based methylation profiling and observed a moderate, but significant global hypomethylation effect upon treatment. To further characterize DHM-induced methylation changes, we used published DNA methylation clocks and newly established age predictors to demonstrate that the DHM-induced methylation change is associated with a reduction in the biological age of the cells. Further studies also revealed re-activation of age-dependently hypermethylated and silenced genes in vivo and a reduction in age-dependent epidermal thinning in a 3-dimensional skin model. Our findings thus establish DHM as an epigenetic inhibitor with rejuvenating effects for aged human skin.
Collapse
Affiliation(s)
| | - Agata Bienkowska
- Beiersdorf AG, Research and Development, Hamburg, Germany
- Institute for Bioinformatics, University Medicine Greifswald, Greifswald, Germany
| | - Jörn Söhle
- Beiersdorf AG, Research and Development, Hamburg, Germany
| | - Katrin Wegner
- Beiersdorf AG, Research and Development, Hamburg, Germany
| | - Guenter Raddatz
- Division of Epigenetics, DKFZ-ZMBH Alliance, German Cancer Research Center, Heidelberg, Germany
| | - Boris Kristof
- Beiersdorf AG, Research and Development, Hamburg, Germany
| | - Dirk Kuck
- Division of Epigenetics, DKFZ-ZMBH Alliance, German Cancer Research Center, Heidelberg, Germany
| | - Ralf Siegner
- Beiersdorf AG, Research and Development, Hamburg, Germany
| | - Ronny Kaufmann
- Beiersdorf AG, Research and Development, Hamburg, Germany
| | - Julia Korn
- Beiersdorf AG, Research and Development, Hamburg, Germany
| | - Sascha Baumann
- Beiersdorf AG, Research and Development, Hamburg, Germany
| | - Daniela Lange
- Beiersdorf AG, Research and Development, Hamburg, Germany
| | | | - Henry Völzke
- Institute for Community Medicine, University Medicine Greifswald, Greifswald, Germany
| | - Lars Kaderali
- Institute for Bioinformatics, University Medicine Greifswald, Greifswald, Germany
| | - Marc Winnefeld
- Beiersdorf AG, Research and Development, Hamburg, Germany
| | - Frank Lyko
- Division of Epigenetics, DKFZ-ZMBH Alliance, German Cancer Research Center, Heidelberg, Germany
| | - Elke Grönniger
- Beiersdorf AG, Research and Development, Hamburg, Germany
| |
Collapse
|
2
|
Matthaei A, Joecks S, Frauenstein A, Bruening J, Bankwitz D, Friesland M, Gerold G, Vieyres G, Kaderali L, Meissner F, Pietschmann T. Landscape of protein-protein interactions during hepatitis C virus assembly and release. Microbiol Spectr 2024; 12:e0256222. [PMID: 38230952 PMCID: PMC10846047 DOI: 10.1128/spectrum.02562-22] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2022] [Accepted: 10/11/2023] [Indexed: 01/18/2024] Open
Abstract
Assembly of infectious hepatitis C virus (HCV) particles requires multiple cellular proteins including for instance apolipoprotein E (ApoE). To describe these protein-protein interactions, we performed an affinity purification mass spectrometry screen of HCV-infected cells. We used functional viral constructs with epitope-tagged envelope protein 2 (E2), protein (p) 7, or nonstructural protein 4B (NS4B) as well as cells expressing a tagged variant of ApoE. We also evaluated assembly stage-dependent remodeling of protein complexes by using viral mutants carrying point mutations abrogating particle production at distinct steps of the HCV particle production cascade. Five ApoE binding proteins, 12 p7 binders, 7 primary E2 interactors, and 24 proteins interacting with NS4B were detected. Cell-derived PREB, STT3B, and SPCS2 as well as viral NS2 interacted with both p7 and E2. Only GTF3C3 interacted with E2 and NS4B, highlighting that HCV assembly and replication complexes exhibit largely distinct interactomes. An HCV core protein mutation, preventing core protein decoration of lipid droplets, profoundly altered the E2 interactome. In cells replicating this mutant, E2 interactions with HSPA5, STT3A/B, RAD23A/B, and ZNF860 were significantly enhanced, suggesting that E2 protein interactions partly depend on core protein functions. Bioinformatic and functional studies including STRING network analyses, RNA interference, and ectopic expression support a role of Rad23A and Rad23B in facilitating HCV infectious virus production. Both Rad23A and Rad23B are involved in the endoplasmic reticulum (ER)-associated protein degradation (ERAD). Collectively, our results provide a map of host proteins interacting with HCV assembly proteins, and they give evidence for the involvement of ER protein folding machineries and the ERAD pathway in the late stages of the HCV replication cycle.IMPORTANCEHepatitis C virus (HCV) establishes chronic infections in the majority of exposed individuals. This capacity likely depends on viral immune evasion strategies. One feature likely contributing to persistence is the formation of so-called lipo-viro particles. These peculiar virions consist of viral structural proteins and cellular lipids and lipoproteins, the latter of which aid in viral attachment and cell entry and likely antibody escape. To learn about how lipo-viro particles are coined, here, we provide a comprehensive overview of protein-protein interactions in virus-producing cells. We identify numerous novel and specific HCV E2, p7, and cellular apolipoprotein E-interacting proteins. Pathway analyses of these interactors show that proteins participating in processes such as endoplasmic reticulum (ER) protein folding, ER-associated protein degradation, and glycosylation are heavily engaged in virus production. Moreover, we find that the proteome of HCV replication sites is distinct from the assembly proteome, suggesting that transport process likely shuttles viral RNA to assembly sites.
Collapse
Affiliation(s)
- Alina Matthaei
- Institute of Experimental Virology, TWINCORE, Centre for Experimental and Clinical Infection Research, Hannover, Lower Saxony, Germany
| | - Sebastian Joecks
- Institute of Experimental Virology, TWINCORE, Centre for Experimental and Clinical Infection Research, Hannover, Lower Saxony, Germany
| | - Annika Frauenstein
- RG Experimental Systems Immunology, Max-Planck Institute for Biochemistry, Planegg, Bavaria, Germany
| | - Janina Bruening
- Institute of Experimental Virology, TWINCORE, Centre for Experimental and Clinical Infection Research, Hannover, Lower Saxony, Germany
| | - Dorothea Bankwitz
- Institute of Experimental Virology, TWINCORE, Centre for Experimental and Clinical Infection Research, Hannover, Lower Saxony, Germany
| | - Martina Friesland
- Institute of Experimental Virology, TWINCORE, Centre for Experimental and Clinical Infection Research, Hannover, Lower Saxony, Germany
| | - Gisa Gerold
- Institute of Experimental Virology, TWINCORE, Centre for Experimental and Clinical Infection Research, Hannover, Lower Saxony, Germany
- Department of Biochemistry & Research Center for Emerging Infections and Zoonoses (RIZ), University of Veterinary Medicine Hannover, Hannover, Lower Saxony, Germany
- Department of Clinical Microbiology, Virology, Umeå University, Umeå, Sweden
- Wallenberg Centre for Molecular Medicine (WCMM), Umeå University, Umeå, Sweden
| | - Gabrielle Vieyres
- Institute of Experimental Virology, TWINCORE, Centre for Experimental and Clinical Infection Research, Hannover, Lower Saxony, Germany
- Junior Research Group “Cell Biology of RNA Viruses,” Leibniz Institute of Experimental Virology, Hamburg, Germany
| | - Lars Kaderali
- Institute of Bioinformatics, University Medicine Greifswald, Greifswald, Germany
| | - Felix Meissner
- RG Experimental Systems Immunology, Max-Planck Institute for Biochemistry, Planegg, Bavaria, Germany
- Systems Immunology and Proteomics, Institute of Innate Immunity, Medical Faculty, University of Bonn, Bonn, Germany
| | - Thomas Pietschmann
- Institute of Experimental Virology, TWINCORE, Centre for Experimental and Clinical Infection Research, Hannover, Lower Saxony, Germany
| |
Collapse
|
3
|
Bienkowska A, Raddatz G, Söhle J, Kristof B, Völzke H, Gallinat S, Lyko F, Kaderali L, Winnefeld M, Grönniger E, Falckenhayn C. Development of an epigenetic clock to predict visual age progression of human skin. Front Aging 2024; 4:1258183. [PMID: 38274286 PMCID: PMC10809641 DOI: 10.3389/fragi.2023.1258183] [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] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/13/2023] [Accepted: 11/28/2023] [Indexed: 01/27/2024]
Abstract
Aging is a complex process characterized by the gradual decline of physiological functions, leading to increased vulnerability to age-related diseases and reduced quality of life. Alterations in DNA methylation (DNAm) patterns have emerged as a fundamental characteristic of aged human skin, closely linked to the development of the well-known skin aging phenotype. These changes have been correlated with dysregulated gene expression and impaired tissue functionality. In particular, the skin, with its visible manifestations of aging, provides a unique model to study the aging process. Despite the importance of epigenetic age clocks in estimating biological age based on the correlation between methylation patterns and chronological age, a second-generation epigenetic age clock, which correlates DNAm patterns with a particular phenotype, specifically tailored to skin tissue is still lacking. In light of this gap, we aimed to develop a novel second-generation epigenetic age clock explicitly designed for skin tissue to facilitate a deeper understanding of the factors contributing to individual variations in age progression. To achieve this, we used methylation patterns from more than 370 female volunteers and developed the first skin-specific second-generation epigenetic age clock that accurately predicts the skin aging phenotype represented by wrinkle grade, visual facial age, and visual age progression, respectively. We then validated the performance of our clocks on independent datasets and demonstrated their broad applicability. In addition, we integrated gene expression and methylation data from independent studies to identify potential pathways contributing to skin age progression. Our results demonstrate that our epigenetic age clock, VisAgeX, specifically predicting visual age progression, not only captures known biological pathways associated with skin aging, but also adds novel pathways associated with skin aging.
Collapse
Affiliation(s)
- Agata Bienkowska
- Beiersdorf AG, Research and Development, Hamburg, Germany
- Institute for Bioinformatics, University Medicine Greifswald, Greifswald, Germany
| | - Günter Raddatz
- Division of Epigenetics, DKFZ-ZMBH Alliance, German Cancer Research Center, Heidelberg, Germany
| | - Jörn Söhle
- Beiersdorf AG, Research and Development, Hamburg, Germany
| | - Boris Kristof
- Beiersdorf AG, Research and Development, Hamburg, Germany
| | - Henry Völzke
- Institute for Community Medicine, SHIP/KEF, University Medicine Greifswald, Greifswald, Germany
| | | | - Frank Lyko
- Division of Epigenetics, DKFZ-ZMBH Alliance, German Cancer Research Center, Heidelberg, Germany
| | - Lars Kaderali
- Institute for Bioinformatics, University Medicine Greifswald, Greifswald, Germany
| | - Marc Winnefeld
- Beiersdorf AG, Research and Development, Hamburg, Germany
| | - Elke Grönniger
- Beiersdorf AG, Research and Development, Hamburg, Germany
| | | |
Collapse
|
4
|
Kohler C, King J, Stacker L, Goller KV, Moritz J, Pohlmann A, Nath N, Tzvetkova A, Rieck M, Paraskevopoulou S, Beslic D, Hölzer M, Fuchs S, Ziemann J, Kaderali L, Beer M, Hübner NO, Becker K. Neighbourhood watch: genomic epidemiology of SARS-CoV-2 variants circulating in a German federal state, Mecklenburg-Western Pomerania, in 2020-2022. Emerg Microbes Infect 2023; 12:2245916. [PMID: 37585712 PMCID: PMC10446807 DOI: 10.1080/22221751.2023.2245916] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2023] [Revised: 07/03/2023] [Accepted: 08/03/2023] [Indexed: 08/18/2023]
Abstract
ABSTRACTGlobal and even national genome surveillance approaches do not provide the resolution necessary for rapid and accurate direct response by local public health authorities. Hence, a regional network of microbiological laboratories in collaboration with the health departments of all districts of the German federal state of Mecklenburg-Western Pomerania (M-V) was formed to investigate the regional molecular epidemiology of circulating SARS-CoV-2 lineages between 11/2020 and 03/2022. More than 4750 samples from all M-V counties were sequenced using Illumina and Nanopore technologies. Overall, 3493 (73.5%) sequences fulfilled quality criteria for time-resolved and/or spatially-resolved maximum likelihood phylogenic analyses and k-mean/ median clustering (KMC). We identified 116 different Pangolin virus lineages that can be assigned to 16 Nextstrain clades. The ten most frequently detected virus lineages belonged to B.1.1.7, AY.122, AY.43, BA.1, B.1.617.2, BA.1.1, AY.9.2, AY.4, P.1 and AY.126. Time-resolved phylogenetic analyses showed the occurrence of virus clades as determined worldwide, but with a substantial delay of one to two months. Further spatio-temporal phylogenetic analyses revealed a regional outbreak of a Gamma variant limited to western M-V counties. Finally, KMC elucidated a successive introduction of the various virus lineages into M-V, possibly triggered by vacation periods with increased (inter-) national travel activities. The COVID-19 pandemic in M-V was shaped by a combination of several SARS-CoV-2 introductions, lockdown measures, restrictive quarantine of patients and the lineage specific replication rate. Complementing global and national surveillance, regional surveillance adds value by providing a higher level of surveillance resolution tailored to local health authorities.
Collapse
Affiliation(s)
- Christian Kohler
- Friedrich-Loeffler-Institute of Medical Microbiology, University Medicine Greifswald, Greifswald, Germany
| | - Jacqueline King
- Institute of Diagnostic Virology, Friedrich-Loeffler-Institute—Federal Research Institute for Animal Health, Greifswald-Insel Riems, Germany
| | - Lina Stacker
- Institute of Diagnostic Virology, Friedrich-Loeffler-Institute—Federal Research Institute for Animal Health, Greifswald-Insel Riems, Germany
| | - Katja V. Goller
- Institute for Hygiene and Environmental Medicine and Central Unit for Infection Prevention and Control, University Medicine Greifswald, Greifswald, Germany
| | - Juliane Moritz
- Institute for Hygiene and Environmental Medicine and Central Unit for Infection Prevention and Control, University Medicine Greifswald, Greifswald, Germany
| | - Anne Pohlmann
- Institute of Diagnostic Virology, Friedrich-Loeffler-Institute—Federal Research Institute for Animal Health, Greifswald-Insel Riems, Germany
| | - Neetika Nath
- Institute of Bioinformatics, University Medicine Greifswald, Greifswald, Germany
| | - Ana Tzvetkova
- Institute of Bioinformatics, University Medicine Greifswald, Greifswald, Germany
- Human Molecular Genetics Group, Department of Functional Genomics, Interfaculty Institute for Genetics and Functional Genomics, University Medicine Greifswald, Greifswald, Germany
| | - Maximilian Rieck
- Institute for Hygiene and Environmental Medicine and Central Unit for Infection Prevention and Control, University Medicine Greifswald, Greifswald, Germany
| | | | - Denis Beslic
- Genome Competence Center (MF1), Robert Koch Institute, Berlin, Germany
| | - Martin Hölzer
- Genome Competence Center (MF1), Robert Koch Institute, Berlin, Germany
| | - Stephan Fuchs
- Genome Competence Center (MF1), Robert Koch Institute, Berlin, Germany
| | - Janine Ziemann
- Institute for Hygiene and Environmental Medicine and Central Unit for Infection Prevention and Control, University Medicine Greifswald, Greifswald, Germany
| | - Lars Kaderali
- Institute of Bioinformatics, University Medicine Greifswald, Greifswald, Germany
| | - Martin Beer
- Institute of Diagnostic Virology, Friedrich-Loeffler-Institute—Federal Research Institute for Animal Health, Greifswald-Insel Riems, Germany
| | - Nils-Olaf Hübner
- Institute for Hygiene and Environmental Medicine and Central Unit for Infection Prevention and Control, University Medicine Greifswald, Greifswald, Germany
| | - Karsten Becker
- Friedrich-Loeffler-Institute of Medical Microbiology, University Medicine Greifswald, Greifswald, Germany
| |
Collapse
|
5
|
Becker AK, Ittermann T, Dörr M, Felix SB, Nauck M, Teumer A, Völker U, Völzke H, Kaderali L, Nath N. Correction: Analysis of epidemiological association patterns of serum thyrotropin by combining random forests and Bayesian networks. PLoS One 2023; 18:e0294489. [PMID: 37948441 PMCID: PMC10637647 DOI: 10.1371/journal.pone.0294489] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2023] Open
Abstract
[This corrects the article DOI: 10.1371/journal.pone.0271610.].
Collapse
|
6
|
Burkart SS, Schweinoch D, Frankish J, Sparn C, Wüst S, Urban C, Merlo M, Magalhães VG, Piras A, Pichlmair A, Willemsen J, Kaderali L, Binder M. High-resolution kinetic characterization of the RIG-I-signaling pathway and the antiviral response. Life Sci Alliance 2023; 6:e202302059. [PMID: 37558422 PMCID: PMC10412806 DOI: 10.26508/lsa.202302059] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2023] [Revised: 07/24/2023] [Accepted: 07/27/2023] [Indexed: 08/11/2023] Open
Abstract
RIG-I recognizes viral dsRNA and activates a cell-autonomous antiviral response. Upon stimulation, it triggers a signaling cascade leading to the production of type I and III IFNs. IFNs are secreted and signal to elicit the expression of IFN-stimulated genes, establishing an antiviral state of the cell. The topology of this pathway has been studied intensively, however, its exact dynamics are less understood. Here, we employed electroporation to synchronously activate RIG-I, enabling us to characterize cell-intrinsic innate immune signaling at a high temporal resolution. Employing IFNAR1/IFNLR-deficient cells, we could differentiate primary RIG-I signaling from secondary signaling downstream of the IFN receptors. Based on these data, we developed a comprehensive mathematical model capable of simulating signaling downstream of dsRNA recognition by RIG-I and the feedback and signal amplification by IFN. We further investigated the impact of viral antagonists on signaling dynamics. Our work provides a comprehensive insight into the signaling events that occur early upon virus infection and opens new avenues to study and disentangle the complexity of the host-virus interface.
Collapse
Affiliation(s)
- Sandy S Burkart
- Research Group "Dynamics of Early Viral Infection and the Innate Antiviral Response", Division Virus-Associated Carcinogenesis (F170), German Cancer Research Center, Heidelberg, Germany
- Faculty of Biosciences, Heidelberg University, Heidelberg, Germany
| | - Darius Schweinoch
- Institute of Bioinformatics & Center for Functional Genomics of Microbes, University Medicine Greifswald, Greifswald, Germany
| | - Jamie Frankish
- Research Group "Dynamics of Early Viral Infection and the Innate Antiviral Response", Division Virus-Associated Carcinogenesis (F170), German Cancer Research Center, Heidelberg, Germany
- Faculty of Biosciences, Heidelberg University, Heidelberg, Germany
| | - Carola Sparn
- Research Group "Dynamics of Early Viral Infection and the Innate Antiviral Response", Division Virus-Associated Carcinogenesis (F170), German Cancer Research Center, Heidelberg, Germany
- Faculty of Biosciences, Heidelberg University, Heidelberg, Germany
| | - Sandra Wüst
- Research Group "Dynamics of Early Viral Infection and the Innate Antiviral Response", Division Virus-Associated Carcinogenesis (F170), German Cancer Research Center, Heidelberg, Germany
| | - Christian Urban
- Technical University of Munich, School of Medicine, Institute of Virology, Munich, Germany
| | - Marta Merlo
- Research Group "Dynamics of Early Viral Infection and the Innate Antiviral Response", Division Virus-Associated Carcinogenesis (F170), German Cancer Research Center, Heidelberg, Germany
- Faculty of Biosciences, Heidelberg University, Heidelberg, Germany
| | - Vladimir G Magalhães
- Research Group "Dynamics of Early Viral Infection and the Innate Antiviral Response", Division Virus-Associated Carcinogenesis (F170), German Cancer Research Center, Heidelberg, Germany
| | - Antonio Piras
- Technical University of Munich, School of Medicine, Institute of Virology, Munich, Germany
| | - Andreas Pichlmair
- Technical University of Munich, School of Medicine, Institute of Virology, Munich, Germany
- German Center for Infection Research (DZIF), Munich Partner Site, Munich, Germany
| | - Joschka Willemsen
- Research Group "Dynamics of Early Viral Infection and the Innate Antiviral Response", Division Virus-Associated Carcinogenesis (F170), German Cancer Research Center, Heidelberg, Germany
| | - Lars Kaderali
- Institute of Bioinformatics & Center for Functional Genomics of Microbes, University Medicine Greifswald, Greifswald, Germany
| | - Marco Binder
- Research Group "Dynamics of Early Viral Infection and the Innate Antiviral Response", Division Virus-Associated Carcinogenesis (F170), German Cancer Research Center, Heidelberg, Germany
| |
Collapse
|
7
|
Osterman A, Krenn F, Iglhaut M, Badell I, Lehner A, Späth PM, Stern M, Both H, Bender S, Muenchhoff M, Graf A, Krebs S, Blum H, Grimmer T, Durner J, Czibere L, Dächert C, Grzimek-Koschewa N, Protzer U, Kaderali L, Baldauf HM, Keppler OT. Automated antigen assays display a high heterogeneity for the detection of SARS-CoV-2 variants of concern, including several Omicron sublineages. Med Microbiol Immunol 2023; 212:307-322. [PMID: 37561226 PMCID: PMC10501957 DOI: 10.1007/s00430-023-00774-9] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2022] [Accepted: 07/11/2023] [Indexed: 08/11/2023]
Abstract
Diagnostic tests for direct pathogen detection have been instrumental to contain the severe acute respiratory syndrome coronavirus type 2 (SARS-CoV-2) pandemic. Automated, quantitative, laboratory-based nucleocapsid antigen (Ag) tests for SARS-CoV-2 have been launched alongside nucleic acid-based test systems and point-of-care (POC) lateral-flow Ag tests. Here, we evaluated four commercial Ag tests on automated platforms for the detection of different sublineages of the SARS-CoV-2 Omicron variant of concern (VoC) (B.1.1.529) in comparison with "non-Omicron" VoCs. A total of 203 Omicron PCR-positive respiratory swabs (53 BA.1, 48 BA.2, 23 BQ.1, 39 XBB.1.5 and 40 other subvariants) from the period February to March 2022 and from March 2023 were examined. In addition, tissue culture-expanded clinical isolates of Delta (B.1.617.2), Omicron-BA.1, -BF.7, -BN.1 and -BQ.1 were studied. These results were compared to previously reported data from 107 clinical "non-Omicron" samples from the end of the second pandemic wave (February to March 2021) as well as cell culture-derived samples of wildtype (wt) EU-1 (B.1.177), Alpha VoC (B.1.1.7) and Beta VoC (B.1.351)). All four commercial Ag tests were able to detect at least 90.9% of Omicron-containing samples with high viral loads (Ct < 25). The rates of true-positive test results for BA.1/BA.2-positive samples with intermediate viral loads (Ct 25-30) ranged between 6.7% and 100.0%, while they dropped to 0 to 15.4% for samples with low Ct values (> 30). This heterogeneity was reflected also by the tests' 50%-limit of detection (LoD50) values ranging from 44,444 to 1,866,900 Geq/ml. Respiratory samples containing Omicron-BQ.1/XBB.1.5 or other Omicron subvariants that emerged in 2023 were detected with enormous heterogeneity (0 to 100%) for the intermediate and low viral load ranges with LoD50 values between 23,019 and 1,152,048 Geq/ml. In contrast, detection of "non-Omicron" samples was more sensitive, scoring positive in 35 to 100% for the intermediate and 1.3 to 32.9% of cases for the low viral loads, respectively, corresponding to LoD50 values ranging from 6181 to 749,792 Geq/ml. All four assays detected cell culture-expanded VoCs Alpha, Beta, Delta and Omicron subvariants carrying up to six amino acid mutations in the nucleocapsid protein with sensitivities comparable to the non-VoC EU-1. Overall, automated quantitative SARS-CoV-2 Ag assays are not more sensitive than standard rapid antigen tests used in POC settings and show a high heterogeneity in performance for VoC recognition. The best of these automated Ag tests may have the potential to complement nucleic acid-based assays for SARS-CoV-2 diagnostics in settings not primarily focused on the protection of vulnerable groups. In light of the constant emergence of new Omicron subvariants and recombinants, most recently the XBB lineage, these tests' performance must be regularly re-evaluated, especially when new VoCs carry mutations in the nucleocapsid protein or immunological and clinical parameters change.
Collapse
Affiliation(s)
- Andreas Osterman
- Max von Pettenkofer Institute and Gene Center, Virology, National Reference Center for Retroviruses, LMU München, Munich, Germany
| | - Franziska Krenn
- Max von Pettenkofer Institute and Gene Center, Virology, National Reference Center for Retroviruses, LMU München, Munich, Germany
| | - Maximilian Iglhaut
- Max von Pettenkofer Institute and Gene Center, Virology, National Reference Center for Retroviruses, LMU München, Munich, Germany
| | - Irina Badell
- Max von Pettenkofer Institute and Gene Center, Virology, National Reference Center for Retroviruses, LMU München, Munich, Germany
| | - Andreas Lehner
- Max von Pettenkofer Institute and Gene Center, Virology, National Reference Center for Retroviruses, LMU München, Munich, Germany
| | - Patricia M Späth
- Max von Pettenkofer Institute and Gene Center, Virology, National Reference Center for Retroviruses, LMU München, Munich, Germany
| | - Marcel Stern
- Max von Pettenkofer Institute and Gene Center, Virology, National Reference Center for Retroviruses, LMU München, Munich, Germany
| | - Hanna Both
- Max von Pettenkofer Institute and Gene Center, Virology, National Reference Center for Retroviruses, LMU München, Munich, Germany
| | - Sabine Bender
- Max von Pettenkofer Institute and Gene Center, Virology, National Reference Center for Retroviruses, LMU München, Munich, Germany
| | - Maximilian Muenchhoff
- Max von Pettenkofer Institute and Gene Center, Virology, National Reference Center for Retroviruses, LMU München, Munich, Germany
- German Center for Infection Research (DZIF), Partner Site, Munich, Germany
- COVID‑19 Registry of the LMU Munich (CORKUM), University Hospital, LMU München, Munich, Germany
| | - Alexander Graf
- Laboratory for Functional Genome Analysis, Gene Center, LMU München, Munich, Germany
| | - Stefan Krebs
- Laboratory for Functional Genome Analysis, Gene Center, LMU München, Munich, Germany
| | - Helmut Blum
- Laboratory for Functional Genome Analysis, Gene Center, LMU München, Munich, Germany
| | - Timo Grimmer
- Department of Psychiatry and Psychotherapy, Klinikum Rechts der Isar, School of Medicine, Technical University of Munich, Munich, Germany
| | - Jürgen Durner
- Labor Becker MVZ GbR, Munich, Germany
- Department of Conservative Dentistry and Periodontology, University Hospital, LMU München, Munich, Germany
| | | | - Christopher Dächert
- Max von Pettenkofer Institute and Gene Center, Virology, National Reference Center for Retroviruses, LMU München, Munich, Germany
| | - Natascha Grzimek-Koschewa
- Max von Pettenkofer Institute and Gene Center, Virology, National Reference Center for Retroviruses, LMU München, Munich, Germany
- German Center for Infection Research (DZIF), Partner Site, Munich, Germany
| | - Ulrike Protzer
- German Center for Infection Research (DZIF), Partner Site, Munich, Germany
- Institute of Virology, Technical University of Munich/Helmholtz Zentrum München, Munich, Germany
| | - Lars Kaderali
- Institute of Bioinformatics, University Medicine Greifswald, Greifswald, Germany
| | - Hanna-Mari Baldauf
- Max von Pettenkofer Institute and Gene Center, Virology, National Reference Center for Retroviruses, LMU München, Munich, Germany.
| | - Oliver T Keppler
- Max von Pettenkofer Institute and Gene Center, Virology, National Reference Center for Retroviruses, LMU München, Munich, Germany.
- German Center for Infection Research (DZIF), Partner Site, Munich, Germany.
- COVID‑19 Registry of the LMU Munich (CORKUM), University Hospital, LMU München, Munich, Germany.
| |
Collapse
|
8
|
Krenn F, Dächert C, Badell I, Lupoli G, Öztan GN, Feng T, Schneider N, Huber M, Both H, Späth PM, Muenchhoff M, Graf A, Krebs S, Blum H, Durner J, Czibere L, Kaderali L, Keppler OT, Baldauf HM, Osterman A. Ten rapid antigen tests for SARS-CoV-2 widely differ in their ability to detect Omicron-BA.4 and -BA.5. Med Microbiol Immunol 2023; 212:323-337. [PMID: 37561225 PMCID: PMC10501931 DOI: 10.1007/s00430-023-00775-8] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2023] [Accepted: 07/11/2023] [Indexed: 08/11/2023]
Abstract
Since late 2021, the variant landscape of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has been dominated by the variant of concern (VoC) Omicron and its sublineages. We and others have shown that the detection of Omicron-BA.1 and -BA.2-positive respiratory specimens by rapid antigen tests (RATs) is impaired compared to Delta VoC-containing samples. Here, in a single-center retrospective laboratory study, we evaluated the performance of ten most commonly used RATs for the detection of Omicron-BA.4 and -BA.5 infections. We used 171 respiratory swab specimens from SARS-CoV-2 RNA-positive patients, of which 71 were classified as BA.4 and 100 as BA.5. All swabs were collected between July and September 2022. 50 SARS-CoV-2 PCR-negative samples from healthy individuals, collected in October 2022, showed high specificity in 9 out of 10 RATs. When assessing analytical sensitivity using clinical specimens, the 50% limit of detection (LoD50) ranged from 7.6 × 104 to 3.3 × 106 RNA copies subjected to the RATs for BA.4 compared to 6.8 × 104 to 3.0 × 106 for BA.5. Overall, intra-assay differences for the detection of these two Omicron subvariants were not significant for both respiratory swabs and tissue culture-expanded virus isolates. In contrast, marked heterogeneity was observed among the ten RATs: to be positive in these point-of-care tests, up to 443-fold (BA.4) and up to 56-fold (BA.5) higher viral loads were required for the worst performing RAT compared to the best performing RAT. True-positive rates for Omicron-BA.4- or -BA.5-containing specimens in the highest viral load category (Ct values < 25) ranged from 94.3 to 34.3%, dropping to 25.6 to 0% for samples with intermediate Ct values (25-30). We conclude that the high heterogeneity in the performance of commonly used RATs remains a challenge for the general public to obtain reliable results in the evolving Omicron subvariant-driven pandemic.
Collapse
Affiliation(s)
- Franziska Krenn
- Max von Pettenkofer Institute & Gene Center, Virology, National Reference Center for Retroviruses, LMU München, Munich, Germany
| | - Christopher Dächert
- Max von Pettenkofer Institute & Gene Center, Virology, National Reference Center for Retroviruses, LMU München, Munich, Germany
- German Center for Infection Research (DZIF), Partner Site, Munich, Germany
| | - Irina Badell
- Max von Pettenkofer Institute & Gene Center, Virology, National Reference Center for Retroviruses, LMU München, Munich, Germany
| | - Gaia Lupoli
- Max von Pettenkofer Institute & Gene Center, Virology, National Reference Center for Retroviruses, LMU München, Munich, Germany
| | - Gamze Naz Öztan
- Max von Pettenkofer Institute & Gene Center, Virology, National Reference Center for Retroviruses, LMU München, Munich, Germany
| | - Tianle Feng
- Max von Pettenkofer Institute & Gene Center, Virology, National Reference Center for Retroviruses, LMU München, Munich, Germany
| | - Nikolas Schneider
- Max von Pettenkofer Institute & Gene Center, Virology, National Reference Center for Retroviruses, LMU München, Munich, Germany
| | - Melanie Huber
- Max von Pettenkofer Institute & Gene Center, Virology, National Reference Center for Retroviruses, LMU München, Munich, Germany
| | - Hanna Both
- Max von Pettenkofer Institute & Gene Center, Virology, National Reference Center for Retroviruses, LMU München, Munich, Germany
| | - Patricia M. Späth
- Max von Pettenkofer Institute & Gene Center, Virology, National Reference Center for Retroviruses, LMU München, Munich, Germany
| | - Maximilian Muenchhoff
- Max von Pettenkofer Institute & Gene Center, Virology, National Reference Center for Retroviruses, LMU München, Munich, Germany
- German Center for Infection Research (DZIF), Partner Site, Munich, Germany
- COVID-19 Registry of the LMU Munich (CORKUM), University Hospital, LMU München, Munich, Germany
| | - Alexander Graf
- Laboratory for Functional Genome Analysis, Gene Center, LMU München, Munich, Germany
| | - Stefan Krebs
- Laboratory for Functional Genome Analysis, Gene Center, LMU München, Munich, Germany
| | - Helmut Blum
- Laboratory for Functional Genome Analysis, Gene Center, LMU München, Munich, Germany
| | | | | | - Lars Kaderali
- Institute of Bioinformatics, University Medicine Greifswald, Greifswald, Germany
| | - Oliver T. Keppler
- Max von Pettenkofer Institute & Gene Center, Virology, National Reference Center for Retroviruses, LMU München, Munich, Germany
- German Center for Infection Research (DZIF), Partner Site, Munich, Germany
- COVID-19 Registry of the LMU Munich (CORKUM), University Hospital, LMU München, Munich, Germany
| | - Hanna-Mari Baldauf
- Max von Pettenkofer Institute & Gene Center, Virology, National Reference Center for Retroviruses, LMU München, Munich, Germany
| | - Andreas Osterman
- Max von Pettenkofer Institute & Gene Center, Virology, National Reference Center for Retroviruses, LMU München, Munich, Germany
| |
Collapse
|
9
|
Schönborn L, Seck SE, Thiele T, Kaderali L, Hoffmann T, Hlinka A, Lindhoff-Last E, Völker U, Selleng K, Buoninfante A, Cavaleri M, Greinacher A. Long-term outcome in vaccine-induced immune thrombocytopenia and thrombosis. J Thromb Haemost 2023; 21:2519-2527. [PMID: 37394120 DOI: 10.1016/j.jtha.2023.06.027] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Revised: 06/13/2023] [Accepted: 06/17/2023] [Indexed: 07/04/2023]
Abstract
BACKGROUND Rapid diagnosis and treatment has improved outcome of patients with vaccine-induced immune thrombocytopenia and thrombosis (VITT). However, after the acute episode, many questions on long-term management of VITT remained unanswered. OBJECTIVES To analyze, in patients with VITT, the long-term course of anti-platelet factor 4 (PF4) antibodies; clinical outcomes, including risk of recurrent thrombosis and/or thrombocytopenia; and the effects of new vaccinations. METHODS 71 patients with serologically confirmed VITT in Germany were enrolled into a prospective longitudinal study and followed for a mean of 79 weeks from March 2021 to January 2023. The course of anti-PF4 antibodies was analyzed by consecutive anti-PF4/heparin immunoglobulin G enzyme-linked immunosorbent assay and PF4-enhanced platelet activation assay. RESULTS Platelet-activating anti-PF4 antibodies became undetectable in 62 of 71 patients (87.3%; 95% CI, 77.6%-93.2%). In 6 patients (8.5%), platelet-activating anti-PF4 antibodies persisted for >18 months. Five of 71 patients (7.0%) showed recurrent episodes of thrombocytopenia and/or thrombosis; in 4 of them (80.0%), alternative explanations beside VITT were present. After further COVID-19 vaccination with a messenger RNA vaccine, no reactivation of platelet-activating anti-PF4 antibodies or new thrombosis was observed. No adverse events occurred in our patients subsequently vaccinated against influenza, tick-borne encephalitis, varicella, tetanus, diphtheria, pertussis, and polio. No new thrombosis occurred in the 24 patients (33.8%) who developed symptomatic SARS-CoV-2 infection following recovery from acute VITT. CONCLUSION Once the acute episode of VITT has passed, patients appear to be at low risk for recurrent thrombosis and/or thrombocytopenia.
Collapse
Affiliation(s)
- Linda Schönborn
- Institute of Transfusion Medicine, University Medicine Greifswald, Greifswald, Germany
| | - Sabrina E Seck
- Institute of Transfusion Medicine, University Medicine Greifswald, Greifswald, Germany
| | - Thomas Thiele
- Institute of Transfusion Medicine, University Medicine Rostock, Rostock, Germany
| | - Lars Kaderali
- Institute of Bioinformatics, University Medicine Greifswald, Greifswald, Germany
| | - Till Hoffmann
- Institute for Transplantation Diagnostics and Cell Therapeutics, University Hospital Duesseldorf, Medical Faculty, Duesseldorf, Germany
| | - Annalena Hlinka
- Institute for Transplantation Diagnostics and Cell Therapeutics, University Hospital Duesseldorf, Medical Faculty, Duesseldorf, Germany
| | - Edelgard Lindhoff-Last
- Cardioangiology Center Bethanien Hospital, CCB Coagulation Center and CCB Coagulation Research Center, Frankfurt, Hessen, Germany
| | - Uwe Völker
- Interfaculty Institute of Genetics and Functional Genomics, University Medicine Greifswald, Greifswald, Germany
| | - Kathleen Selleng
- Institute of Transfusion Medicine, University Medicine Greifswald, Greifswald, Germany
| | - Alessandra Buoninfante
- Health Threats and Vaccines Strategy, European Medicines Agency, Amsterdam, The Netherlands
| | - Marco Cavaleri
- Health Threats and Vaccines Strategy, European Medicines Agency, Amsterdam, The Netherlands
| | - Andreas Greinacher
- Institute of Transfusion Medicine, University Medicine Greifswald, Greifswald, Germany.
| |
Collapse
|
10
|
Krause E, Vollmer M, Wittfeld K, Weihs A, Frenzel S, Dörr M, Kaderali L, Felix SB, Stubbe B, Ewert R, Völzke H, Grabe HJ. Evaluating heart rate variability with 10 second multichannel electrocardiograms in a large population-based sample. Front Cardiovasc Med 2023; 10:1144191. [PMID: 37252117 PMCID: PMC10213655 DOI: 10.3389/fcvm.2023.1144191] [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] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2023] [Accepted: 03/27/2023] [Indexed: 05/31/2023] Open
Abstract
Introduction Heart rate variability (HRV), defined as the variability of consecutive heart beats, is an important biomarker for dysregulations of the autonomic nervous system (ANS) and is associated with the development, course, and outcome of a variety of mental and physical health problems. While guidelines recommend using 5 min electrocardiograms (ECG), recent studies showed that 10 s might be sufficient for deriving vagal-mediated HRV. However, the validity and applicability of this approach for risk prediction in epidemiological studies is currently unclear to be used. Methods This study evaluates vagal-mediated HRV with ultra-short HRV (usHRV) based on 10 s multichannel ECG recordings of N = 4,245 and N = 2,392 participants of the Study of Health in Pomerania (SHIP) from two waves of the SHIP-TREND cohort, additionally divided into a healthy and health-impaired subgroup. Association of usHRV with HRV derived from long-term ECG recordings (polysomnography: 5 min before falling asleep [N = 1,041]; orthostatic testing: 5 min of rest before probing an orthostatic reaction [N = 1,676]) and their validity with respect to demographic variables and depressive symptoms were investigated. Results High correlations (r = .52-.75) were revealed between usHRV and HRV. While controlling for covariates, usHRV was the strongest predictor for HRV. Furthermore, the associations of usHRV and HRV with age, sex, obesity, and depressive symptoms were similar. Conclusion This study provides evidence that usHRV derived from 10 s ECG might function as a proxy of vagal-mediated HRV with similar characteristics. This allows the investigation of ANS dysregulation with ECGs that are routinely performed in epidemiological studies to identify protective and risk factors for various mental and physical health problems.
Collapse
Affiliation(s)
- Elischa Krause
- Department of Psychiatry and Psychotherapy, University Medicine Greifswald, Greifswald, Germany
| | - Marcus Vollmer
- Institute of Bioinformatics, University Medicine Greifswald, Greifswald, Germany
- German Centre for Cardiovascular Research (DZHK), Partner Site Greifswald, Greifswald, Germany
| | - Katharina Wittfeld
- Department of Psychiatry and Psychotherapy, University Medicine Greifswald, Greifswald, Germany
- German Centre for Neurodegenerative Diseases (DZNE), Partner Site Rostock/Greifswald, Greifswald, Germany
| | - Antoine Weihs
- Department of Psychiatry and Psychotherapy, University Medicine Greifswald, Greifswald, Germany
| | - Stefan Frenzel
- Department of Psychiatry and Psychotherapy, University Medicine Greifswald, Greifswald, Germany
| | - Marcus Dörr
- German Centre for Cardiovascular Research (DZHK), Partner Site Greifswald, Greifswald, Germany
- Department of Internal Medicine B, University Medicine Greifswald, Greifswald, Germany
| | - Lars Kaderali
- Institute of Bioinformatics, University Medicine Greifswald, Greifswald, Germany
- German Centre for Cardiovascular Research (DZHK), Partner Site Greifswald, Greifswald, Germany
| | - Stephan B. Felix
- German Centre for Cardiovascular Research (DZHK), Partner Site Greifswald, Greifswald, Germany
- Department of Internal Medicine B, University Medicine Greifswald, Greifswald, Germany
| | - Beate Stubbe
- Department of Internal Medicine B, University Medicine Greifswald, Greifswald, Germany
| | - Ralf Ewert
- Department of Internal Medicine B, University Medicine Greifswald, Greifswald, Germany
| | - Henry Völzke
- Department of Internal Medicine B, University Medicine Greifswald, Greifswald, Germany
- Institute for Community Medicine, University Medicine Greifswald, Greifswald, Germany
| | - Hans J. Grabe
- Department of Psychiatry and Psychotherapy, University Medicine Greifswald, Greifswald, Germany
- German Centre for Neurodegenerative Diseases (DZNE), Partner Site Rostock/Greifswald, Greifswald, Germany
| |
Collapse
|
11
|
Gholizadeh M, Łapczuk-Romańska J, Post M, Komaniecka N, Mazlooman SR, Kaderali L, Droździk M. A Mixture Method for Robust Detection HCV Early Diagnosis Biomarker with ML Approach and Molecular Docking. Int J Mol Sci 2023; 24:ijms24087207. [PMID: 37108370 PMCID: PMC10138470 DOI: 10.3390/ijms24087207] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2023] [Revised: 03/30/2023] [Accepted: 04/11/2023] [Indexed: 04/29/2023] Open
Abstract
Given the substantial correlation between early diagnosis and prolonged patient survival in HCV patients, it is vital to identify a reliable and accessible biomarker. The purpose of this research was to identify accurate miRNA biomarkers to aid in the early diagnosis of HCV and to identify key target genes for anti-hepatic fibrosis therapeutics. The expression of 188 miRNAs in 42 HCV liver patients with different functional states and 23 normal livers were determined using RT-qPCR. After screening out differentially expressed miRNA (DEmiRNAs), the target genes were predicted. To validate target genes, an HCV microarray dataset was subjected to five machine learning algorithms (Random Forest, Adaboost, Bagging, Boosting, XGBoost) and then, based on the best model, importance features were selected. After identification of hub target genes, to evaluate the potency of compounds that might hit key hub target genes, molecular docking was performed. According to our data, eight DEmiRNAs are associated with early stage and eight DEmiRNAs are linked to a deterioration in liver function and an increase in HCV severity. In the validation phase of target genes, model evaluation revealed that XGBoost (AUC = 0.978) outperformed the other machine learning algorithms. The results of the maximal clique centrality algorithm determined that CDK1 is a hub target gene, which can be hinted at by hsa-miR-335, hsa-miR-140, hsa-miR-152, and hsa-miR-195. Because viral proteins boost CDK1 activation for cell mitosis, pharmacological inhibition may have anti-HCV therapeutic promise. The strong affinity binding of paeoniflorin (-6.32 kcal/mol) and diosmin (-6.01 kcal/mol) with CDK1 was demonstrated by molecular docking, which may result in attractive anti-HCV compounds. The findings of this study may provide significant evidence, in the context of the miRNA biomarkers, for early-stage HCV diagnosis. In addition, recognized hub target genes and small molecules with high binding affinity may constitute a novel set of therapeutic targets for HCV.
Collapse
Affiliation(s)
- Maryam Gholizadeh
- Institute for Bioinformatics, University Medicine Greifswald, 17475 Greifswald, Germany
| | - Joanna Łapczuk-Romańska
- Department of Experimental and Clinical Pharmacology, Pomeranian Medical University, 70-111 Szczecin, Poland
| | - Mariola Post
- Department of General and Transplantation Surgery, County Hospital, 71-455 Szczecin, Poland
| | - Nina Komaniecka
- Department of Experimental and Clinical Pharmacology, Pomeranian Medical University, 70-111 Szczecin, Poland
| | - Seyed Reza Mazlooman
- Department of Psychiatry and Psychotherapy, University Medicine Greifswald, 17475 Greifswald, Germany
| | - Lars Kaderali
- Institute for Bioinformatics, University Medicine Greifswald, 17475 Greifswald, Germany
| | - Marek Droździk
- Department of Experimental and Clinical Pharmacology, Pomeranian Medical University, 70-111 Szczecin, Poland
| |
Collapse
|
12
|
Zitzmann C, Dächert C, Schmid B, van der Schaar H, van Hemert M, Perelson AS, van Kuppeveld FJM, Bartenschlager R, Binder M, Kaderali L. Mathematical modeling of plus-strand RNA virus replication to identify broad-spectrum antiviral treatment strategies. PLoS Comput Biol 2023; 19:e1010423. [PMID: 37014904 PMCID: PMC10104377 DOI: 10.1371/journal.pcbi.1010423] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2022] [Revised: 04/14/2023] [Accepted: 03/09/2023] [Indexed: 04/05/2023] Open
Abstract
Plus-strand RNA viruses are the largest group of viruses. Many are human pathogens that inflict a socio-economic burden. Interestingly, plus-strand RNA viruses share remarkable similarities in their replication. A hallmark of plus-strand RNA viruses is the remodeling of intracellular membranes to establish replication organelles (so-called "replication factories"), which provide a protected environment for the replicase complex, consisting of the viral genome and proteins necessary for viral RNA synthesis. In the current study, we investigate pan-viral similarities and virus-specific differences in the life cycle of this highly relevant group of viruses. We first measured the kinetics of viral RNA, viral protein, and infectious virus particle production of hepatitis C virus (HCV), dengue virus (DENV), and coxsackievirus B3 (CVB3) in the immuno-compromised Huh7 cell line and thus without perturbations by an intrinsic immune response. Based on these measurements, we developed a detailed mathematical model of the replication of HCV, DENV, and CVB3 and showed that only small virus-specific changes in the model were necessary to describe the in vitro dynamics of the different viruses. Our model correctly predicted virus-specific mechanisms such as host cell translation shut off and different kinetics of replication organelles. Further, our model suggests that the ability to suppress or shut down host cell mRNA translation may be a key factor for in vitro replication efficiency, which may determine acute self-limited or chronic infection. We further analyzed potential broad-spectrum antiviral treatment options in silico and found that targeting viral RNA translation, such as polyprotein cleavage and viral RNA synthesis, may be the most promising drug targets for all plus-strand RNA viruses. Moreover, we found that targeting only the formation of replicase complexes did not stop the in vitro viral replication early in infection, while inhibiting intracellular trafficking processes may even lead to amplified viral growth.
Collapse
Affiliation(s)
- Carolin Zitzmann
- Institute of Bioinformatics, University Medicine Greifswald, Greifswald, Germany
- Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos, New Mexico, United States of America
| | - Christopher Dächert
- Research Group "Dynamics of Early Viral Infection and the Innate Antiviral Response", Division Virus-Associated Carcinogenesis (F170), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Bianca Schmid
- Dept of Infectious Diseases, Molecular Virology, Heidelberg University, Heidelberg, Germany
| | - Hilde van der Schaar
- Division of infectious Diseases and Immunology, Virology Section, Dept of Biomolecular Health Sciences, Utrecht University, Utrecht, The Netherlands
| | - Martijn van Hemert
- Department of Medical Microbiology, Leiden University Medical Center, Leiden, The Netherlands
| | - Alan S Perelson
- Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos, New Mexico, United States of America
| | - Frank J M van Kuppeveld
- Division of infectious Diseases and Immunology, Virology Section, Dept of Biomolecular Health Sciences, Utrecht University, Utrecht, The Netherlands
| | - Ralf Bartenschlager
- Division of infectious Diseases and Immunology, Virology Section, Dept of Biomolecular Health Sciences, Utrecht University, Utrecht, The Netherlands
- Division Virus-Associated Carcinogenesis (F170), German Cancer Research Center (DKFZ), Heidelberg, Germany
- German Center for Infection Research (DZIF), Heidelberg partner site, Heidelberg, Germany
| | - Marco Binder
- Research Group "Dynamics of Early Viral Infection and the Innate Antiviral Response", Division Virus-Associated Carcinogenesis (F170), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Lars Kaderali
- Institute of Bioinformatics, University Medicine Greifswald, Greifswald, Germany
| |
Collapse
|
13
|
Osterman A, Badell I, Dächert C, Schneider N, Kaufmann AY, Öztan GN, Huber M, Späth PM, Stern M, Autenrieth H, Muenchhoff M, Graf A, Krebs S, Blum H, Czibere L, Durner J, Kaderali L, Baldauf HM, Keppler OT. Variable detection of Omicron-BA.1 and -BA.2 by SARS-CoV-2 rapid antigen tests. Med Microbiol Immunol 2023; 212:13-23. [PMID: 36370197 PMCID: PMC9660148 DOI: 10.1007/s00430-022-00752-7] [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] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2022] [Accepted: 10/22/2022] [Indexed: 11/15/2022]
Abstract
During 2022, the COVID-19 pandemic has been dominated by the variant of concern (VoC) Omicron (B.1.1.529) and its rapidly emerging subvariants, including Omicron-BA.1 and -BA.2. Rapid antigen tests (RATs) are part of national testing strategies to identify SARS-CoV-2 infections on site in a community setting or to support layman's diagnostics at home. We and others have recently demonstrated an impaired RAT detection of infections caused by Omicron-BA.1 compared to Delta. Here, we evaluated the performance of five SARS-CoV-2 RATs in a single-centre laboratory study examining a total of 140 SARS-CoV-2 PCR-positive respiratory swab samples, 70 Omicron-BA.1 and 70 Omicron-BA.2, as well as 52 SARS-CoV-2 PCR-negative swabs collected from March 8th until April 10th, 2022. One test did not meet minimal criteria for specificity. In an assessment of the analytical sensitivity in clinical specimen, the 50% limit of detection (LoD50) ranged from 4.2 × 104 to 9.2 × 105 RNA copies subjected to the RAT for Omicron-BA.1 compared to 1.3 × 105 to 1.5 × 106 for Omicron-BA.2. Overall, intra-assay differences for the detection of Omicron-BA.1-containing and Omicron-BA.2-containing samples were non-significant, while a marked overall heterogeneity among the five RATs was observed. To score positive in these point-of-care tests, up to 22-fold (LoD50) or 68-fold (LoD95) higher viral loads were required for the worst performing compared to the best performing RAT. The rates of true-positive test results for these Omicron subvariant-containing samples in the highest viral load category (Ct values < 25) ranged between 44.7 and 91.1%, while they dropped to 8.7 to 22.7% for samples with intermediate Ct values (25-30). In light of recent reports on the emergence of two novel Omicron-BA.2 subvariants, Omicron-BA.2.75 and BJ.1, awareness must be increased for the overall reduced detection rate and marked differences in RAT performance for these Omicron subvariants.
Collapse
Affiliation(s)
- Andreas Osterman
- Max Von Pettenkofer Institute and Gene Center, Virology, National Reference Center for Retroviruses, LMU München, Munich, Germany
| | - Irina Badell
- Max Von Pettenkofer Institute and Gene Center, Virology, National Reference Center for Retroviruses, LMU München, Munich, Germany
| | - Christopher Dächert
- Max Von Pettenkofer Institute and Gene Center, Virology, National Reference Center for Retroviruses, LMU München, Munich, Germany
| | - Nikolas Schneider
- Max Von Pettenkofer Institute and Gene Center, Virology, National Reference Center for Retroviruses, LMU München, Munich, Germany
| | - Anna-Yasemin Kaufmann
- Max Von Pettenkofer Institute and Gene Center, Virology, National Reference Center for Retroviruses, LMU München, Munich, Germany
| | - Gamze Naz Öztan
- Max Von Pettenkofer Institute and Gene Center, Virology, National Reference Center for Retroviruses, LMU München, Munich, Germany
| | - Melanie Huber
- Max Von Pettenkofer Institute and Gene Center, Virology, National Reference Center for Retroviruses, LMU München, Munich, Germany
| | - Patricia M Späth
- Max Von Pettenkofer Institute and Gene Center, Virology, National Reference Center for Retroviruses, LMU München, Munich, Germany
| | - Marcel Stern
- Max Von Pettenkofer Institute and Gene Center, Virology, National Reference Center for Retroviruses, LMU München, Munich, Germany
| | - Hanna Autenrieth
- Max Von Pettenkofer Institute and Gene Center, Virology, National Reference Center for Retroviruses, LMU München, Munich, Germany
| | - Maximilian Muenchhoff
- Max Von Pettenkofer Institute and Gene Center, Virology, National Reference Center for Retroviruses, LMU München, Munich, Germany
- German Center for Infection Research (DZIF), Partner Site Munich, Munich, Germany
- COVID-19 Registry of the LMU Munich (CORKUM), University Hospital, LMU München, Munich, Germany
| | - Alexander Graf
- Laboratory for Functional Genome Analysis, Gene Center, LMU München, Munich, Germany
| | - Stefan Krebs
- Laboratory for Functional Genome Analysis, Gene Center, LMU München, Munich, Germany
| | - Helmut Blum
- Laboratory for Functional Genome Analysis, Gene Center, LMU München, Munich, Germany
| | | | - Jürgen Durner
- Labor Becker MVZ GbR, Munich, Germany
- Department of Conservative Dentistry and Periodontology, University Hospital, LMU München, Munich, Germany
| | - Lars Kaderali
- Institute of Bioinformatics, University Medicine Greifswald, Greifswald, Germany
| | - Hanna-Mari Baldauf
- Max Von Pettenkofer Institute and Gene Center, Virology, National Reference Center for Retroviruses, LMU München, Munich, Germany.
| | - Oliver T Keppler
- Max Von Pettenkofer Institute and Gene Center, Virology, National Reference Center for Retroviruses, LMU München, Munich, Germany.
- German Center for Infection Research (DZIF), Partner Site Munich, Munich, Germany.
- COVID-19 Registry of the LMU Munich (CORKUM), University Hospital, LMU München, Munich, Germany.
| |
Collapse
|
14
|
Wagenhäuser I, Knies K, Hofmann D, Rauschenberger V, Eisenmann M, Reusch J, Gabel A, Flemming S, Andres O, Petri N, Topp MS, Papsdorf M, McDonogh M, Verma-Führing R, Scherzad A, Zeller D, Böhm H, Gesierich A, Seitz AK, Kiderlen M, Gawlik M, Taurines R, Wurmb T, Ernestus RI, Forster J, Weismann D, Weißbrich B, Dölken L, Liese J, Kaderali L, Kurzai O, Vogel U, Krone M. Virus variant-specific clinical performance of SARS coronavirus two rapid antigen tests in point-of-care use, from November 2020 to January 2022. Clin Microbiol Infect 2023; 29:225-232. [PMID: 36028089 PMCID: PMC9398563 DOI: 10.1016/j.cmi.2022.08.006] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [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: 04/27/2022] [Revised: 08/08/2022] [Accepted: 08/09/2022] [Indexed: 02/07/2023]
Abstract
OBJECTIVES Antigen rapid diagnostic tests (RDTs) for SARS coronavirus 2 (SARS-CoV-2) are quick, widely available, and inexpensive. Consequently, RDTs have been established as an alternative and additional diagnostic strategy to quantitative reverse transcription polymerase chain reaction (RT-qPCR). However, reliable clinical and large-scale performance data specific to a SARS-CoV-2 virus variant of concern (VOC) are limited, especially for the Omicron VOC. The aim of this study was to compare RDT performance among different VOCs. METHODS This single-centre prospective performance assessment compared RDTs from three manufacturers (NADAL, Panbio, MEDsan) with RT-qPCR including deduced standardized viral load from oropharyngeal swabs for detection of SARS-CoV-2 in a clinical point-of-care setting from November 2020 to January 2022. RESULTS Among 35 479 RDT/RT-qPCR tandems taken from 26 940 individuals, 164 of the 426 SARS-CoV-2 positive samples tested true positive with an RDT corresponding to an RDT sensitivity of 38.50% (95% CI, 34.00-43.20%), with an overall specificity of 99.67% (95% CI, 99.60-99.72%). RDT sensitivity depended on viral load, with decreasing sensitivity accompanied by descending viral load. VOC-dependent sensitivity assessment showed a sensitivity of 42.86% (95% CI, 32.82-53.52%) for the wild-type SARS-CoV-2, 43.42% (95% CI, 32.86-54.61%) for the Alpha VOC, 37.67% (95% CI, 30.22-45.75%) for the Delta VOC, and 33.67% (95% CI, 25.09-43.49%) for the Omicron VOC. Sensitivity in samples with high viral loads of ≥106 SARS-CoV-2 RNA copies per mL was significantly lower in the Omicron VOC (50.00%; 95% CI, 36.12-63.88%) than in the wild-type SARS-CoV-2 (79.31%; 95% CI, 61.61-90.15%; p 0.015). DISCUSSION RDT sensitivity for detection of the Omicron VOC is reduced in individuals infected with a high viral load, which curtails the effectiveness of RDTs. This aspect furthert: limits the use of RDTs, although RDTs are still an irreplaceable diagnostic tool for rapid, economic point-of-care and extensive SARS-CoV-2 screening.
Collapse
Affiliation(s)
- Isabell Wagenhäuser
- Infection Control and Antimicrobial Stewardship Unit, University Hospital Wuerzburg, Wuerzburg, Germany
| | - Kerstin Knies
- Institute for Virology and Immunobiology, University of Wuerzburg, Wuerzburg, Germany
| | - Daniela Hofmann
- Institute for Virology and Immunobiology, University of Wuerzburg, Wuerzburg, Germany
| | - Vera Rauschenberger
- Infection Control and Antimicrobial Stewardship Unit, University Hospital Wuerzburg, Wuerzburg, Germany,Institute for Hygiene and Microbiology, University of Wuerzburg, Wuerzburg, Germany
| | - Michael Eisenmann
- Infection Control and Antimicrobial Stewardship Unit, University Hospital Wuerzburg, Wuerzburg, Germany
| | - Julia Reusch
- Infection Control and Antimicrobial Stewardship Unit, University Hospital Wuerzburg, Wuerzburg, Germany
| | - Alexander Gabel
- Infection Control and Antimicrobial Stewardship Unit, University Hospital Wuerzburg, Wuerzburg, Germany
| | - Sven Flemming
- Department of General, Visceral, Transplantation, Vascular and Paediatric Surgery, University Hospital Wuerzburg, Wuerzburg, Germany
| | - Oliver Andres
- Department of Paediatrics, University Hospital Wuerzburg, Wuerzburg, Germany
| | - Nils Petri
- Department of Internal Medicine I, University Hospital Wuerzburg, Wuerzburg, Germany
| | - Max S. Topp
- Department of Internal Medicine II, University Hospital Wuerzburg, Wuerzburg, Germany
| | - Michael Papsdorf
- Department of Obstetrics and Gynaecology, University Hospital Wuerzburg, Wuerzburg, Germany
| | - Miriam McDonogh
- Department of Orthopaedic Trauma, Hand, Plastic and Reconstructive Surgery, University Hospital Wuerzburg, Wuerzburg, Germany
| | - Raoul Verma-Führing
- Department of Ophthalmology, University Hospital Wuerzburg, Wuerzburg, Germany
| | - Agmal Scherzad
- Department of Otorhinolaryngology, Plastic, Aesthetic and Reconstructive Head and Neck Surgery, University Hospital Wuerzburg, Wuerzburg, Germany
| | - Daniel Zeller
- Department of Neurology, University Hospital Wuerzburg, Wuerzburg, Germany
| | - Hartmut Böhm
- Department of Oral and Maxillofacial Surgery, University Hospital Wuerzburg, Wuerzburg, Germany
| | - Anja Gesierich
- Department of Dermatology, Venerology and Allergology, University Hospital Wuerzburg, Wuerzburg, Germany
| | - Anna K. Seitz
- Department of Urology, University Hospital Wuerzburg, Wuerzburg, Germany
| | - Michael Kiderlen
- Department of Neurosurgery, University Hospital Wuerzburg, Wuerzburg, Germany
| | - Micha Gawlik
- Department of Psychiatry and Psychotherapy, University Hospital Wuerzburg, Wuerzburg, Germany
| | - Regina Taurines
- Department of Child and Adolescent Psychiatry, Psychosomatics and Psychotherapy, University Hospital Wuerzburg, Wuerzburg, Germany
| | - Thomas Wurmb
- Department of Anaesthesia and Critical Care, University Hospital Wuerzburg, Wuerzburg, Germany
| | - Ralf-Ingo Ernestus
- Department of Neurosurgery, University Hospital Wuerzburg, Wuerzburg, Germany
| | - Johannes Forster
- Institute for Hygiene and Microbiology, University of Wuerzburg, Wuerzburg, Germany
| | - Dirk Weismann
- Department of Internal Medicine I, University Hospital Wuerzburg, Wuerzburg, Germany
| | - Benedikt Weißbrich
- Institute for Virology and Immunobiology, University of Wuerzburg, Wuerzburg, Germany
| | - Lars Dölken
- Institute for Virology and Immunobiology, University of Wuerzburg, Wuerzburg, Germany
| | - Johannes Liese
- Department of Paediatrics, University Hospital Wuerzburg, Wuerzburg, Germany
| | - Lars Kaderali
- Institute of Bioinformatics, University Medicine Greifswald, Greifswald, Germany
| | - Oliver Kurzai
- Institute for Hygiene and Microbiology, University of Wuerzburg, Wuerzburg, Germany,Leibniz Institute for Natural Product Research and Infection Biology—Hans-Knoell-Institute, Jena, Germany
| | - Ulrich Vogel
- Infection Control and Antimicrobial Stewardship Unit, University Hospital Wuerzburg, Wuerzburg, Germany,Institute for Hygiene and Microbiology, University of Wuerzburg, Wuerzburg, Germany
| | - Manuel Krone
- Infection Control and Antimicrobial Stewardship Unit, University Hospital Wuerzburg, Wuerzburg, Germany; Institute for Hygiene and Microbiology, University of Wuerzburg, Wuerzburg, Germany; Department of Internal Medicine I, University Hospital Wuerzburg, Wuerzburg, Germany.
| |
Collapse
|
15
|
Veinalde R, Pidelaserra-Martí G, Moulin C, Tan CL, Schäfer TE, Kang N, Ball CR, Leichsenring J, Stenzinger A, Kaderali L, Jäger D, Ungerechts G, Engeland CE. Virotherapy combined with anti-PD-1 transiently reshapes the tumor immune environment and induces anti-tumor immunity in a preclinical PDAC model. Front Immunol 2023; 13:1096162. [PMID: 36726983 PMCID: PMC9886093 DOI: 10.3389/fimmu.2022.1096162] [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] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2022] [Accepted: 12/12/2022] [Indexed: 01/18/2023] Open
Abstract
Introduction Pancreatic ductal adenocarcinoma (PDAC) is largely refractory to cancer immunotherapy with PD-1 immune checkpoint blockade (ICB). Oncolytic virotherapy has been shown to synergize with ICB. In this work, we investigated the combination of anti-PD-1 and oncolytic measles vaccine in an immunocompetent transplantable PDAC mouse model. Methods We characterized tumor-infiltrating T cells by immunohistochemistry, flow cytometry and T cell receptor sequencing. Further, we performed gene expression profiling of tumor samples at baseline, after treatment, and when tumors progressed. Moreover, we analyzed systemic anti-tumor and anti-viral immunity. Results Combination treatment significantly prolonged survival compared to monotherapies. Tumor-infiltrating immune cells were increased after virotherapy. Gene expression profiling revealed a unique, but transient signature of immune activation after combination treatment. However, systemic anti-tumor immunity was induced by virotherapy and remained detectable even when tumors progressed. Anti-PD-1 treatment did not impact anti-viral immunity. Discussion Our results indicate that combined virotherapy and ICB induces anti-tumor immunity and reshapes the tumor immune environment. However, further refinement of this approach may be required to develop its full potential and achieve durable efficacy.
Collapse
Affiliation(s)
- Rūta Veinalde
- Clinical Cooperation Unit Virotherapy, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Gemma Pidelaserra-Martí
- Clinical Cooperation Unit Virotherapy, German Cancer Research Center (DKFZ), Heidelberg, Germany,Faculty of Health, School of Medicine, Center for Biomedical Research and Education (ZBAF), Institute of Virology and Microbiology, Witten/Herdecke University, Witten, Germany,Faculty of Biosciences, Heidelberg University, Heidelberg, Germany
| | - Coline Moulin
- Faculty of Health, School of Medicine, Center for Biomedical Research and Education (ZBAF), Institute of Virology and Microbiology, Witten/Herdecke University, Witten, Germany,Ecole Normale Supérieure de Lyon, Lyon, France
| | - Chin Leng Tan
- Faculty of Biosciences, Heidelberg University, Heidelberg, Germany,Clinical Cooperation Unit Neuroimmunology and Brain Tumor Immunology, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Theresa E. Schäfer
- Clinical Cooperation Unit Virotherapy, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Na Kang
- Department of Translational Medical Oncology, National Center for Tumor Diseases (NCT) and German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Claudia R. Ball
- Department of Translational Medical Oncology, National Center for Tumor Diseases Dresden (NCT) Heidelberg and German Cancer Research Center (DKFZ), Heidelberg, Germany,Center for Personalized Oncology, National Center for Tumor Diseases (NCT) Dresden and University Hospital Carl Gustav Carus, Faculty of Medicine and Technische Universität Dresden, Dresden, Germany
| | - Jonas Leichsenring
- Institute of Pathology, Heidelberg University Hospital, Heidelberg, Germany,Institut für Pathologie, Zytologie und molekulare Diagnostik, Regiomed Klinikum Coburg, Coburg, Germany
| | | | - Lars Kaderali
- Institute for Bioinformatics, University Medicine Greifswald, Greifswald, Germany
| | - Dirk Jäger
- Clinical Cooperation Unit Applied Tumor Immunity, German Cancer Research Center (DKFZ), Heidelberg, Germany,Department of Medical Oncology, University Hospital Heidelberg, Heidelberg, Germany and National Center for Tumor Diseases (NCT) Heidelberg, Heidelberg, Germany
| | - Guy Ungerechts
- Clinical Cooperation Unit Virotherapy, German Cancer Research Center (DKFZ), Heidelberg, Germany,Department of Medical Oncology, University Hospital Heidelberg, Heidelberg, Germany and National Center for Tumor Diseases (NCT) Heidelberg, Heidelberg, Germany
| | - Christine E. Engeland
- Clinical Cooperation Unit Virotherapy, German Cancer Research Center (DKFZ), Heidelberg, Germany,Faculty of Health, School of Medicine, Center for Biomedical Research and Education (ZBAF), Institute of Virology and Microbiology, Witten/Herdecke University, Witten, Germany,Department of Medical Oncology, University Hospital Heidelberg, Heidelberg, Germany and National Center for Tumor Diseases (NCT) Heidelberg, Heidelberg, Germany,*Correspondence: Christine E. Engeland, ;
| |
Collapse
|
16
|
Völzke H, Schössow J, Schmidt CO, Jürgens C, Richter A, Werner A, Werner N, Radke D, Teumer A, Ittermann T, Schauer B, Henck V, Friedrich N, Hannemann A, Winter T, Nauck M, Dörr M, Bahls M, Felix SB, Stubbe B, Ewert R, Frost F, Lerch MM, Grabe HJ, Bülow R, Otto M, Hosten N, Rathmann W, Schminke U, Großjohann R, Tost F, Homuth G, Völker U, Weiss S, Holtfreter S, Bröker BM, Zimmermann K, Kaderali L, Winnefeld M, Kristof B, Berger K, Samietz S, Schwahn C, Holtfreter B, Biffar R, Kindler S, Wittfeld K, Hoffmann W, Kocher T. Cohort Profile Update: The Study of Health in Pomerania (SHIP). Int J Epidemiol 2022; 51:e372-e383. [PMID: 35348705 DOI: 10.1093/ije/dyac034] [Citation(s) in RCA: 61] [Impact Index Per Article: 30.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2021] [Accepted: 02/25/2022] [Indexed: 12/16/2022] Open
Affiliation(s)
- Henry Völzke
- Institute for Community Medicine, University Medicine Greifswald, Greifswald, Germany.,German Centre for Cardiovascular Research (DZHK), Partner Site Greifswald, Greifswald, Germany
| | - Janka Schössow
- Institute for Community Medicine, University Medicine Greifswald, Greifswald, Germany
| | | | - Clemens Jürgens
- Institute for Community Medicine, University Medicine Greifswald, Greifswald, Germany
| | - Adrian Richter
- Institute for Community Medicine, University Medicine Greifswald, Greifswald, Germany
| | - André Werner
- Institute for Community Medicine, University Medicine Greifswald, Greifswald, Germany
| | - Nicole Werner
- Institute for Community Medicine, University Medicine Greifswald, Greifswald, Germany
| | - Dörte Radke
- Institute for Community Medicine, University Medicine Greifswald, Greifswald, Germany
| | - Alexander Teumer
- Institute for Community Medicine, University Medicine Greifswald, Greifswald, Germany.,German Centre for Cardiovascular Research (DZHK), Partner Site Greifswald, Greifswald, Germany
| | - Till Ittermann
- Institute for Community Medicine, University Medicine Greifswald, Greifswald, Germany
| | - Birgit Schauer
- Institute for Community Medicine, University Medicine Greifswald, Greifswald, Germany
| | - Vivien Henck
- Institute for Community Medicine, University Medicine Greifswald, Greifswald, Germany
| | - Nele Friedrich
- Institute of Clinical Chemistry and Laboratory Medicine, University Medicine Greifswald, Greifswald, Germany
| | - Anke Hannemann
- German Centre for Cardiovascular Research (DZHK), Partner Site Greifswald, Greifswald, Germany.,Institute of Clinical Chemistry and Laboratory Medicine, University Medicine Greifswald, Greifswald, Germany
| | - Theresa Winter
- Institute of Clinical Chemistry and Laboratory Medicine, University Medicine Greifswald, Greifswald, Germany
| | - Matthias Nauck
- German Centre for Cardiovascular Research (DZHK), Partner Site Greifswald, Greifswald, Germany.,Institute of Clinical Chemistry and Laboratory Medicine, University Medicine Greifswald, Greifswald, Germany
| | - Marcus Dörr
- German Centre for Cardiovascular Research (DZHK), Partner Site Greifswald, Greifswald, Germany.,Department of Internal Medicine B, University Medicine Greifswald, Greifswald, Germany
| | - Martin Bahls
- German Centre for Cardiovascular Research (DZHK), Partner Site Greifswald, Greifswald, Germany.,Department of Internal Medicine B, University Medicine Greifswald, Greifswald, Germany
| | - Stephan B Felix
- German Centre for Cardiovascular Research (DZHK), Partner Site Greifswald, Greifswald, Germany.,Department of Internal Medicine B, University Medicine Greifswald, Greifswald, Germany
| | - Beate Stubbe
- Department of Internal Medicine B, University Medicine Greifswald, Greifswald, Germany
| | - Ralf Ewert
- Department of Internal Medicine B, University Medicine Greifswald, Greifswald, Germany
| | - Fabian Frost
- Department of Medicine A, University Medicine Greifswald, Greifswald, Germany
| | - Markus M Lerch
- Department of Medicine A, University Medicine Greifswald, Greifswald, Germany
| | - Hans J Grabe
- Clinic of Psychiatry and Psychotherapy, University Medicine Greifswald, Greifswald, Germany.,German Centre for Neurodegenerative Diseases, Site Rostock/Greifswald, Greifswald, Greifswald, Germany
| | - Robin Bülow
- German Centre for Cardiovascular Research (DZHK), Partner Site Greifswald, Greifswald, Germany.,Institute of Diagnostic Radiology and Neuroradiology, University Medicine Greifswald, Greifswald, Germany
| | - Markus Otto
- Institute of Diagnostic Radiology and Neuroradiology, University Medicine Greifswald, Greifswald, Germany
| | - Norbert Hosten
- Institute of Diagnostic Radiology and Neuroradiology, University Medicine Greifswald, Greifswald, Germany
| | - Wolfgang Rathmann
- Institute of Biometrics and Epidemiology, German Diabetes Center, Leibniz Center for Diabetes Research at Heinrich Heine University, Greifswald, Germany
| | - Ulf Schminke
- Department of Neurology, University Medicine Greifswald, Greifswald, Germany
| | - Rico Großjohann
- Clinic of Ophthalmology, University Medicine Greifswald, Greifswald, Germany
| | - Frank Tost
- Clinic of Ophthalmology, University Medicine Greifswald, Greifswald, Germany
| | - Georg Homuth
- Interfaculty Institute of Genetics and Functional Genomics, University Medicine Greifswald, Greifswald, Germany
| | - Uwe Völker
- German Centre for Cardiovascular Research (DZHK), Partner Site Greifswald, Greifswald, Germany.,Interfaculty Institute of Genetics and Functional Genomics, University Medicine Greifswald, Greifswald, Germany
| | - Stefan Weiss
- German Centre for Cardiovascular Research (DZHK), Partner Site Greifswald, Greifswald, Germany.,Interfaculty Institute of Genetics and Functional Genomics, University Medicine Greifswald, Greifswald, Germany
| | - Silva Holtfreter
- Department of Immunology, University Medicine Greifswald, Greifswald, Germany
| | - Barbara M Bröker
- Department of Immunology, University Medicine Greifswald, Greifswald, Germany
| | - Kathrin Zimmermann
- Friedrich Loeffler Institute for Medical Microbiology, University Medicine Greifswald, Greifswald, Germany
| | - Lars Kaderali
- Institute for Bioinformatics, University Medicine Greifswald, Greifswald, Germany
| | | | | | - Klaus Berger
- Institute of Epidemiology and Social Medicine, University of Munster, Munster, Germany
| | - Stefanie Samietz
- Department of Prosthetic Dentistry, Gerodontology and Biomaterials, University Medicine Greifswald, Greifswald, Germany
| | - Christian Schwahn
- Department of Prosthetic Dentistry, Gerodontology and Biomaterials, University Medicine Greifswald, Greifswald, Germany
| | - Birte Holtfreter
- Department of Restorative Dentistry, Periodontology, Endodontology, and Preventive and Pediatric Dentistry, University Medicine Greifswald, Greifswald, Germany
| | - Reiner Biffar
- Department of Prosthetic Dentistry, Gerodontology and Biomaterials, University Medicine Greifswald, Greifswald, Germany
| | - Stefan Kindler
- Department of Oral and Maxillofacial Surgery/Plastic Surgery, University Medicine Greifswald, Greifswald, Germany
| | - Katharina Wittfeld
- Clinic of Psychiatry and Psychotherapy, University Medicine Greifswald, Greifswald, Germany.,German Centre for Neurodegenerative Diseases, Site Rostock/Greifswald, Greifswald, Greifswald, Germany
| | - Wolfgang Hoffmann
- Institute for Community Medicine, University Medicine Greifswald, Greifswald, Germany.,German Centre for Cardiovascular Research (DZHK), Partner Site Greifswald, Greifswald, Germany.,German Centre for Neurodegenerative Diseases, Site Rostock/Greifswald, Greifswald, Greifswald, Germany
| | - Thomas Kocher
- Department of Restorative Dentistry, Periodontology, Endodontology, and Preventive and Pediatric Dentistry, University Medicine Greifswald, Greifswald, Germany
| |
Collapse
|
17
|
Wratil PR, Kotter K, Bischof ML, Hollerbach S, Apak E, Kalteis AL, Nayeli-Pflantz T, Kaderali L, Adorjan K, Keppler OT. Vaccine-hesitant individuals accumulate additional COVID-19 risk due to divergent perception and behaviors related to SARS-CoV-2 testing: a population-based, cross-sectional study. Infection 2022:10.1007/s15010-022-01947-z. [PMID: 36355269 PMCID: PMC9647754 DOI: 10.1007/s15010-022-01947-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2022] [Accepted: 10/25/2022] [Indexed: 11/11/2022]
Abstract
Purpose To investigate the perception of SARS-CoV-2 detection methods, information sources, and opinions on appropriate behavior after receiving negative or positive test results. Methods In a questionnaire-based, cross-sectional study conducted between September 1 and November 17, 2021, epidemiological, behavioral, and COVID-19-related data were acquired from the public in Munich, Germany. Results Most of the 1388 participants obtained information from online media (82.8%) as well as state and federal authorities (80.3%). 93.4% believed in the accuracy of SARS-CoV-2 PCR testing and 41.2% in the accuracy of rapid antigen tests (RATs). However, RATs were preferred for testing (59.1%) over PCR (51.1%). 24.0% of all individuals were willing to ignore hygiene measures and 76.9% were less afraid of SARS-CoV-2 transmission after receiving a negative PCR test (5.9% and 48.8% in case of a negative RAT). 28.8% reported not to self-isolate after receiving a positive RAT. Multivariate analyses revealed that non-vaccinated individuals relied less on information from governmental authorities (p = 0.0004) and more on social media (p = 0.0216), disbelieved in the accuracy of the PCR test (p ≤ 0.0001) while displaying strong preference towards using RATs (p ≤ 0.0001), were more willing to abandon pandemic-related hygiene measures (p ≤ 0.0001), less afraid of transmitting SARS-CoV-2 after a negative RAT (p ≤ 0.0001), and less likely to isolate after a positive RAT (p ≤ 0.0001). Conclusion Insights into preferred information sources as well as perception, preferences, and behavior related to SARS-CoV-2 testing and hygiene measures are key to refining public health information and surveillance campaigns. Non-vaccinated individuals’ divergent believes and behaviors possibly increase their COVID-19 risk. Supplementary Information The online version contains supplementary material available at 10.1007/s15010-022-01947-z .
Collapse
Affiliation(s)
- Paul R Wratil
- Max von Pettenkofer Institute and Gene Center, Virology, National Reference Center for Retroviruses, LMU München, Munich, Germany.
- German Center for Infection Research (DZIF), Partner Site Munich, Munich, Germany.
- Max von Pettenkofer Institute and Gene Center, Virology, LMU München, Feodor-Lynen-Str. 23, 81377, Munich, Germany.
| | - Katharina Kotter
- Max von Pettenkofer Institute and Gene Center, Virology, National Reference Center for Retroviruses, LMU München, Munich, Germany
| | - Marie L Bischof
- Max von Pettenkofer Institute and Gene Center, Virology, National Reference Center for Retroviruses, LMU München, Munich, Germany
| | - Sophie Hollerbach
- Max von Pettenkofer Institute and Gene Center, Virology, National Reference Center for Retroviruses, LMU München, Munich, Germany
| | - Elif Apak
- Max von Pettenkofer Institute and Gene Center, Virology, National Reference Center for Retroviruses, LMU München, Munich, Germany
| | - Anna-Lena Kalteis
- Max von Pettenkofer Institute and Gene Center, Virology, National Reference Center for Retroviruses, LMU München, Munich, Germany
| | - Tamara Nayeli-Pflantz
- Max von Pettenkofer Institute and Gene Center, Virology, National Reference Center for Retroviruses, LMU München, Munich, Germany
| | - Lars Kaderali
- Institute of Bioinformatics, University Medicine Greifswald, Greifswald, Germany
| | - Kristina Adorjan
- Department of Psychiatry and Psychotherapy, University Hospital, LMU München, Nußbaumstraße 7, 80336, Munich, Germany.
| | - Oliver T Keppler
- Max von Pettenkofer Institute and Gene Center, Virology, National Reference Center for Retroviruses, LMU München, Munich, Germany.
- German Center for Infection Research (DZIF), Partner Site Munich, Munich, Germany.
- Faculty of Medicine, Max von Pettenkofer Institute and Gene Center, Virology, LMU München, Pettenkoferstr. 9a, 80336, Munich, Germany.
| |
Collapse
|
18
|
Schönborn L, Thiele T, Esefeld M, El Debuch K, Wesche J, Seck SE, Kaderali L, Wolff M, Warkentin TE, Greinacher A. Quantitative interpretation of PF4/heparin-EIA optical densities in predicting platelet-activating VITT antibodies. J Thromb Haemost 2022; 20:2579-2586. [PMID: 36006172 DOI: 10.1111/jth.15862] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2022] [Revised: 08/18/2022] [Accepted: 08/22/2022] [Indexed: 11/27/2022]
Abstract
BACKGROUND Vaccine-induced immune thrombotic thrombocytopenia (VITT) is a prothrombotic, heparin-induced thrombocytopenia (HIT)-mimicking, adverse reaction caused by platelet-activating anti-platelet factor 4 (PF4) antibodies that occurs rarely after adenovirus vector-based COVID-19 vaccination. Strength of PF4-dependent enzyme immunoassay (EIA) reactivity-judged by optical density (OD) measurements-strongly predicts platelet-activating properties of HIT antibodies in a functional test. Whether a similar relationship holds for VITT antibodies is unknown. OBJECTIVES To evaluate probability for positive platelet activation testing for VITT antibodies based upon EIA OD reactivity; and to investigate simple approaches to minimize false-negative platelet activation testing for VITT. METHODS All samples referred for VITT testing were systematically evaluated by semiquantitative in-house PF4/heparin-EIA (OD readings) and PF4-induced platelet activation (PIPA) testing within a cohort study. EIA-positive sera testing PIPA-negative were retested following 1/4 to 1/10 dilution. Logistic regression was performed to predict the probability of a positive PIPA per magnitude of EIA reactivity. RESULTS Greater EIA ODs in sera from patients with suspected VITT correlated strongly with greater likelihood of PIPA reactivity. Of 61 sera (with OD values >1.0) testing negative in the PIPA, a high proportion (27/61, 44.3%) became PIPA positive when tested at 1/4 to 1/10 dilution. CONCLUSIONS VITT serology resembles HIT in that greater EIA OD reactivity predicts higher probability of positive testing for platelet-activating antibodies. Unlike the situation with HIT antibodies, however, diluting putative VITT serum increases probability of a positive platelet activation assay, suggesting that optimal complex formation depends on the stoichiometric ratio of PF4 and anti-PF4 VITT antibodies.
Collapse
Affiliation(s)
- Linda Schönborn
- Institut für Transfusionsmedizin, Universitätsmedizin Greifswald, Greifswald, Germany
| | - Thomas Thiele
- Institut für Transfusionsmedizin, Universitätsmedizin Greifswald, Greifswald, Germany
| | - Max Esefeld
- Institut für Transfusionsmedizin, Universitätsmedizin Greifswald, Greifswald, Germany
| | - Khalil El Debuch
- Institut für Transfusionsmedizin, Universitätsmedizin Greifswald, Greifswald, Germany
| | - Jan Wesche
- Institut für Transfusionsmedizin, Universitätsmedizin Greifswald, Greifswald, Germany
| | - Sabrina E Seck
- Institut für Transfusionsmedizin, Universitätsmedizin Greifswald, Greifswald, Germany
| | - Lars Kaderali
- Institute of Bioinformatics, Universitätsmedizin Greifswald, Greifswald, Germany
| | - Martina Wolff
- Institut für Transfusionsmedizin, Universitätsmedizin Greifswald, Greifswald, Germany
| | - Theodore E Warkentin
- Department of Pathology and Molecular Medicine, and Department of Medicine, McMaster University, Hamilton, Ontario, Canada
| | - Andreas Greinacher
- Institut für Transfusionsmedizin, Universitätsmedizin Greifswald, Greifswald, Germany
| |
Collapse
|
19
|
Bhar A, Gierse LC, Meene A, Wang H, Karte C, Schwaiger T, Schröder C, Mettenleiter TC, Urich T, Riedel K, Kaderali L. Application of a maximal-clique based community detection algorithm to gut microbiome data reveals driver microbes during influenza A virus infection. Front Microbiol 2022; 13:979320. [PMID: 36338082 PMCID: PMC9630851 DOI: 10.3389/fmicb.2022.979320] [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] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2022] [Accepted: 09/21/2022] [Indexed: 11/20/2022] Open
Abstract
Influenza A Virus (IAV) infection followed by bacterial pneumonia often leads to hospitalization and death in individuals from high risk groups. Following infection, IAV triggers the process of viral RNA replication which in turn disrupts healthy gut microbial community, while the gut microbiota plays an instrumental role in protecting the host by evolving colonization resistance. Although the underlying mechanisms of IAV infection have been unraveled, the underlying complex mechanisms evolved by gut microbiota in order to induce host immune response following IAV infection remain evasive. In this work, we developed a novel Maximal-Clique based Community Detection algorithm for Weighted undirected Networks (MCCD-WN) and compared its performance with other existing algorithms using three sets of benchmark networks. Moreover, we applied our algorithm to gut microbiome data derived from fecal samples of both healthy and IAV-infected pigs over a sequence of time-points. The results we obtained from the real-life IAV dataset unveil the role of the microbial families Ruminococcaceae, Lachnospiraceae, Spirochaetaceae and Prevotellaceae in the gut microbiome of the IAV-infected cohort. Furthermore, the additional integration of metaproteomic data enabled not only the identification of microbial biomarkers, but also the elucidation of their functional roles in protecting the host following IAV infection. Our network analysis reveals a fast recovery of the infected cohort after the second IAV infection and provides insights into crucial roles of Desulfovibrionaceae and Lactobacillaceae families in combating Influenza A Virus infection. Source code of the community detection algorithm can be downloaded from https://github.com/AniBhar84/MCCD-WN.
Collapse
Affiliation(s)
- Anirban Bhar
- Institute of Bioinformatics, University Medicine Greifswald, Greifswald, Germany
| | | | - Alexander Meene
- Institute of Microbiology, University of Greifswald, Greifswald, Germany
| | - Haitao Wang
- Institute of Microbiology, University of Greifswald, Greifswald, Germany
| | - Claudia Karte
- Friedrich-Loeffler-Institut, Greifswald-Insel Riems, Greifswald, Germany
| | - Theresa Schwaiger
- Friedrich-Loeffler-Institut, Greifswald-Insel Riems, Greifswald, Germany
| | - Charlotte Schröder
- Friedrich-Loeffler-Institut, Greifswald-Insel Riems, Greifswald, Germany
| | | | - Tim Urich
- Institute of Microbiology, University of Greifswald, Greifswald, Germany
| | - Katharina Riedel
- Institute of Microbiology, University of Greifswald, Greifswald, Germany
| | - Lars Kaderali
- Institute of Bioinformatics, University Medicine Greifswald, Greifswald, Germany
| |
Collapse
|
20
|
Zitzmann C, Dächert C, Schmid B, van der Schaar H, van Hemert M, Perelson AS, van Kuppeveld FJ, Bartenschlager R, Binder M, Kaderali L. Mathematical modeling of plus-strand RNA virus replication to identify broad-spectrum antiviral treatment strategies. bioRxiv 2022:2022.07.25.501353. [PMID: 35923314 PMCID: PMC9347285 DOI: 10.1101/2022.07.25.501353] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Plus-strand RNA viruses are the largest group of viruses. Many are human pathogens that inflict a socio-economic burden. Interestingly, plus-strand RNA viruses share remarkable similarities in their replication. A hallmark of plus-strand RNA viruses is the remodeling of intracellular membranes to establish replication organelles (so-called "replication factories"), which provide a protected environment for the replicase complex, consisting of the viral genome and proteins necessary for viral RNA synthesis. In the current study, we investigate pan-viral similarities and virus-specific differences in the life cycle of this highly relevant group of viruses. We first measured the kinetics of viral RNA, viral protein, and infectious virus particle production of hepatitis C virus (HCV), dengue virus (DENV), and coxsackievirus B3 (CVB3) in the immuno-compromised Huh7 cell line and thus without perturbations by an intrinsic immune response. Based on these measurements, we developed a detailed mathematical model of the replication of HCV, DENV, and CVB3 and show that only small virus-specific changes in the model were necessary to describe the in vitro dynamics of the different viruses. Our model correctly predicted virus-specific mechanisms such as host cell translation shut off and different kinetics of replication organelles. Further, our model suggests that the ability to suppress or shut down host cell mRNA translation may be a key factor for in vitro replication efficiency which may determine acute self-limited or chronic infection. We further analyzed potential broad-spectrum antiviral treatment options in silico and found that targeting viral RNA translation, especially polyprotein cleavage, and viral RNA synthesis may be the most promising drug targets for all plus-strand RNA viruses. Moreover, we found that targeting only the formation of replicase complexes did not stop the viral replication in vitro early in infection, while inhibiting intracellular trafficking processes may even lead to amplified viral growth. Author summary Plus-strand RNA viruses comprise a large group of related and medically relevant viruses. The current global pandemic of COVID-19 caused by the SARS-coronavirus-2 as well as the constant spread of diseases such as dengue and chikungunya fever show the necessity of a comprehensive and precise analysis of plus-strand RNA virus infections. Plus-strand RNA viruses share similarities in their life cycle. To understand their within-host replication strategies, we developed a mathematical model that studies pan-viral similarities and virus-specific differences of three plus-strand RNA viruses, namely hepatitis C, dengue, and coxsackievirus. By fitting our model to in vitro data, we found that only small virus-specific variations in the model were required to describe the dynamics of all three viruses. Furthermore, our model predicted that ribosomes involved in viral RNA translation seem to be a key player in plus-strand RNA replication efficiency, which may determine acute or chronic infection outcome. Furthermore, our in-silico drug treatment analysis suggests that targeting viral proteases involved in polyprotein cleavage, in combination with viral RNA replication, may represent promising drug targets with broad-spectrum antiviral activity.
Collapse
Affiliation(s)
- Carolin Zitzmann
- Institute of Bioinformatics, University Medicine Greifswald, Greifswald, Germany
- Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos, New Mexico, United States of America
| | - Christopher Dächert
- Research Group “Dynamics of Early Viral Infection and the Innate Antiviral Response”, Division Virus-Associated Carcinogenesis (F170), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Bianca Schmid
- Dept of Infectious Diseases, Molecular Virology, Heidelberg University, Heidelberg, Germany
| | - Hilde van der Schaar
- Division of infectious Diseases and Immunology, Virology Section, Dept of Biomolecular Health Sciences, Utrecht University, Utrecht, The Netherlands
| | - Martijn van Hemert
- Department of Medical Microbiology, Leiden University Medical Center, Leiden, The Netherlands
| | - Alan S. Perelson
- Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos, New Mexico, United States of America
| | - Frank J.M. van Kuppeveld
- Division of infectious Diseases and Immunology, Virology Section, Dept of Biomolecular Health Sciences, Utrecht University, Utrecht, The Netherlands
| | - Ralf Bartenschlager
- Division Virus-Associated Carcinogenesis (F170), German Cancer Research Center (DKFZ), Heidelberg, Germany
- Dept of Infectious Diseases, Molecular Virology, Heidelberg University, Heidelberg, Germany
- German Center for Infection Research (DZIF), Heidelberg partner site, Heidelberg, Germany
| | - Marco Binder
- Research Group “Dynamics of Early Viral Infection and the Innate Antiviral Response”, Division Virus-Associated Carcinogenesis (F170), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Lars Kaderali
- Institute of Bioinformatics, University Medicine Greifswald, Greifswald, Germany
| |
Collapse
|
21
|
Becker AK, Ittermann T, Dörr M, Felix SB, Nauck M, Teumer A, Völker U, Völzke H, Kaderali L, Nath N. Analysis of epidemiological association patterns of serum thyrotropin by combining random forests and Bayesian networks. PLoS One 2022; 17:e0271610. [PMID: 35862421 PMCID: PMC9302835 DOI: 10.1371/journal.pone.0271610] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2022] [Accepted: 07/04/2022] [Indexed: 11/25/2022] Open
Abstract
BACKGROUND Approaching epidemiological data with flexible machine learning algorithms is of great value for understanding disease-specific association patterns. However, it can be difficult to correctly extract and understand those patterns due to the lack of model interpretability. METHOD We here propose a machine learning workflow that combines random forests with Bayesian network surrogate models to allow for a deeper level of interpretation of complex association patterns. We first evaluate the proposed workflow on synthetic data. We then apply it to data from the large population-based Study of Health in Pomerania (SHIP). Based on this combination, we discover and interpret broad patterns of individual serum TSH concentrations, an important marker of thyroid functionality. RESULTS Evaluations using simulated data show that feature associations can be correctly recovered by combining random forests and Bayesian networks. The presented model achieves predictive accuracy that is similar to state-of-the-art models (root mean square error of 0.66, mean absolute error of 0.55, coefficient of determination of R2 = 0.15). We identify 62 relevant features from the final random forest model, ranging from general health variables over dietary and genetic factors to physiological, hematological and hemostasis parameters. The Bayesian network model is used to put these features into context and make the black-box random forest model more understandable. CONCLUSION We demonstrate that the combination of random forest and Bayesian network analysis is helpful to reveal and interpret broad association patterns of individual TSH concentrations. The discovered patterns are in line with state-of-the-art literature. They may be useful for future thyroid research and improved dosing of therapeutics.
Collapse
Affiliation(s)
- Ann-Kristin Becker
- Institute of Bioinformatics, University Medicine Greifswald, Greifswald, Germany
- DZHK (German Centre for Cardiovascular Research), Partner Site Greifswald, Greifswald, Germany
| | - Till Ittermann
- Institute for Community Medicine, SHIP/Clinical-Epidemiological Research, University Medicine Greifswald, Greifswald, Germany
| | - Markus Dörr
- DZHK (German Centre for Cardiovascular Research), Partner Site Greifswald, Greifswald, Germany
- Department of Internal Medicine B, University Medicine Greifswald, Greifswald, Germany
| | - Stephan B. Felix
- DZHK (German Centre for Cardiovascular Research), Partner Site Greifswald, Greifswald, Germany
- Department of Internal Medicine B, University Medicine Greifswald, Greifswald, Germany
| | - Matthias Nauck
- DZHK (German Centre for Cardiovascular Research), Partner Site Greifswald, Greifswald, Germany
- Institute of Clinical Chemistry and Laboratory Medicine, University Medicine Greifswald, Greifswald, Germany
| | - Alexander Teumer
- Institute for Community Medicine, SHIP/Clinical-Epidemiological Research, University Medicine Greifswald, Greifswald, Germany
| | - Uwe Völker
- DZHK (German Centre for Cardiovascular Research), Partner Site Greifswald, Greifswald, Germany
- Interfaculty Institute of Genetics and Functional Genomics, Department of Functional Genomics, University Medicine Greifswald, Greifswald, Germany
| | - Henry Völzke
- DZHK (German Centre for Cardiovascular Research), Partner Site Greifswald, Greifswald, Germany
- Institute for Community Medicine, SHIP/Clinical-Epidemiological Research, University Medicine Greifswald, Greifswald, Germany
| | - Lars Kaderali
- Institute of Bioinformatics, University Medicine Greifswald, Greifswald, Germany
- DZHK (German Centre for Cardiovascular Research), Partner Site Greifswald, Greifswald, Germany
| | - Neetika Nath
- Institute of Bioinformatics, University Medicine Greifswald, Greifswald, Germany
- DZHK (German Centre for Cardiovascular Research), Partner Site Greifswald, Greifswald, Germany
| |
Collapse
|
22
|
Benkner A, Rüdebusch J, Nath N, Hammer E, Grube K, Gross S, Dhople VM, Eckstein G, Meitinger T, Kaderali L, Völker U, Fielitz J, Felix SB. Riociguat attenuates left ventricular proteome and microRNA profile changes after experimental aortic stenosis in mice. Br J Pharmacol 2022; 179:4575-4592. [PMID: 35751875 DOI: 10.1111/bph.15910] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2021] [Revised: 04/15/2022] [Accepted: 06/10/2022] [Indexed: 11/28/2022] Open
Abstract
BACKGROUND AND PURPOSE Development and progression of heart failure (HF) involve endothelial and myocardial dysfunction as well as a dysregulation of the nitric oxide - soluble guanylyl cyclase - cyclic guanosine monophosphate (NO-sGC-cGMP) signalling pathway. Recently, we reported that the sGC stimulator riociguat (RIO) has beneficial effects on cardiac remodelling and progression of HF in response to chronic pressure overload. Here, we examined if these favourable RIO effects are also reflected in alterations of the myocardial proteome and microRNA profiles. EXPERIMENTAL APPROACH Male C57BL/6N mice underwent transverse aortic constriction (TAC) and sham operated mice served as controls. TAC and sham animals were randomised and treated with either RIO or vehicle for five weeks, starting three weeks post-surgery when cardiac hypertrophy was established. Afterwards we performed mass spectrometric proteome analyses and microRNA sequencing of proteins and RNAs, respectively, isolated from left ventricles (LV). KEY RESULTS TAC-induced changes of the LV proteome were significantly reduced by RIO treatment. Bioinformatics analyses revealed that RIO improved TAC-induced cardiovascular disease related pathways, metabolism and energy production, e.g. reversed alterations in the levels of myosin heavy chain 7 (MYH7), cardiac phospholamban (PLN), and ankyrin repeat domain-containing protein 1 (ANKRD1). RIO also attenuated TAC-induced changes of microRNA levels in the LV. CONCLUSION AND IMPLICATIONS The sGC stimulator RIO has beneficial effects on cardiac structure and function during pressure overload, which is accompanied by a reversal of TAC-induced changes of the cardiac proteome and microRNA profile. Our data support the potential of RIO as a novel HF therapeutic.
Collapse
Affiliation(s)
- Alexander Benkner
- German Centre for Cardiovascular Research (DZHK), Greifswald, Germany.,Department of Internal Medicine B, Cardiology, University Medicine Greifswald, Greifswald, Germany
| | - Julia Rüdebusch
- German Centre for Cardiovascular Research (DZHK), Greifswald, Germany.,Department of Internal Medicine B, Cardiology, University Medicine Greifswald, Greifswald, Germany
| | - Neetika Nath
- Institute of Bioinformatics, University Medicine Greifswald, Greifswald, Germany
| | - Elke Hammer
- German Centre for Cardiovascular Research (DZHK), Greifswald, Germany.,Interfaculty Institute for Genetics and Functional Genomics, University Medicine Greifswald, Greifswald, Germany
| | - Karina Grube
- German Centre for Cardiovascular Research (DZHK), Greifswald, Germany.,Department of Internal Medicine B, Cardiology, University Medicine Greifswald, Greifswald, Germany
| | - Stefan Gross
- German Centre for Cardiovascular Research (DZHK), Greifswald, Germany.,Department of Internal Medicine B, Cardiology, University Medicine Greifswald, Greifswald, Germany
| | - Vishnu M Dhople
- German Centre for Cardiovascular Research (DZHK), Greifswald, Germany.,Interfaculty Institute for Genetics and Functional Genomics, University Medicine Greifswald, Greifswald, Germany
| | - Gertrud Eckstein
- Institute of Human Genetics, Helmholtz Centre Munich, Neuherberg, Germany
| | - Thomas Meitinger
- Institute of Human Genetics, Helmholtz Centre Munich, Neuherberg, Germany.,German Centre for Cardiovascular Research (DZHK), partner site Munich Heart Alliance, Munich, Germany
| | - Lars Kaderali
- German Centre for Cardiovascular Research (DZHK), Greifswald, Germany.,Institute of Bioinformatics, University Medicine Greifswald, Greifswald, Germany
| | - Uwe Völker
- German Centre for Cardiovascular Research (DZHK), Greifswald, Germany.,Interfaculty Institute for Genetics and Functional Genomics, University Medicine Greifswald, Greifswald, Germany
| | - Jens Fielitz
- German Centre for Cardiovascular Research (DZHK), Greifswald, Germany.,Department of Internal Medicine B, Cardiology, University Medicine Greifswald, Greifswald, Germany
| | - Stephan B Felix
- German Centre for Cardiovascular Research (DZHK), Greifswald, Germany.,Department of Internal Medicine B, Cardiology, University Medicine Greifswald, Greifswald, Germany
| |
Collapse
|
23
|
Osterman A, Badell I, Basara E, Stern M, Kriesel F, Eletreby M, Öztan GN, Huber M, Autenrieth H, Knabe R, Späth PM, Muenchhoff M, Graf A, Krebs S, Blum H, Durner J, Czibere L, Dächert C, Kaderali L, Baldauf HM, Keppler OT. Impaired detection of omicron by SARS-CoV-2 rapid antigen tests. Med Microbiol Immunol 2022; 211:105-117. [PMID: 35187580 PMCID: PMC8858605 DOI: 10.1007/s00430-022-00730-z] [Citation(s) in RCA: 69] [Impact Index Per Article: 34.5] [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: 02/09/2022] [Accepted: 02/12/2022] [Indexed: 01/25/2023]
Abstract
Since autumn 2020, rapid antigen tests (RATs) have been implemented in several countries as an important pillar of the national testing strategy to rapidly screen for infections on site during the SARS-CoV-2 pandemic. The current surge in infection rates around the globe is driven by the variant of concern (VoC) omicron (B.1.1.529). Here, we evaluated the performance of nine SARS-CoV-2 RATs in a single-centre laboratory study. We examined a total of 115 SARS-CoV-2 PCR-negative and 166 SARS-CoV-2 PCR-positive respiratory swab samples (101 omicron, 65 delta (B.1.617.2)) collected from October 2021 until January 2022 as well as cell culture-expanded clinical isolates of both VoCs. In an assessment of the analytical sensitivity in clinical specimen, the 50% limit of detection (LoD50) ranged from 1.77 × 106 to 7.03 × 107 RNA copies subjected to the RAT for omicron compared to 1.32 × 105 to 2.05 × 106 for delta. To score positive in these point-of-care tests, up to 10-fold (LoD50) or 101-fold (LoD95) higher virus loads were required for omicron- compared to delta-containing samples. The rates of true positive test results for omicron samples in the highest virus load category (Ct values < 25) ranged between 31.4 and 77.8%, while they dropped to 0-8.3% for samples with intermediate Ct values (25-30). Of note, testing of expanded virus stocks suggested a comparable RAT sensitivity of both VoCs, questioning the predictive value of this type of in vitro-studies for clinical performance. Given their importance for national test strategies in the current omicron wave, awareness must be increased for the reduced detection rate of omicron infections by RATs and a short list of suitable RATs that fulfill the minimal requirements of performance should be rapidly disclosed.
Collapse
Affiliation(s)
- Andreas Osterman
- Max Von Pettenkofer Institute and Gene Center, Virology, National Reference Center for Retroviruses, LMU München, Feodor-Lynen-Str. 23, 81377, Munich, Germany
| | - Irina Badell
- Max Von Pettenkofer Institute and Gene Center, Virology, National Reference Center for Retroviruses, LMU München, Feodor-Lynen-Str. 23, 81377, Munich, Germany
| | - Elif Basara
- Max Von Pettenkofer Institute and Gene Center, Virology, National Reference Center for Retroviruses, LMU München, Feodor-Lynen-Str. 23, 81377, Munich, Germany
| | - Marcel Stern
- Max Von Pettenkofer Institute and Gene Center, Virology, National Reference Center for Retroviruses, LMU München, Feodor-Lynen-Str. 23, 81377, Munich, Germany
| | - Fabian Kriesel
- Max Von Pettenkofer Institute and Gene Center, Virology, National Reference Center for Retroviruses, LMU München, Feodor-Lynen-Str. 23, 81377, Munich, Germany
| | - Marwa Eletreby
- Max Von Pettenkofer Institute and Gene Center, Virology, National Reference Center for Retroviruses, LMU München, Feodor-Lynen-Str. 23, 81377, Munich, Germany
| | - Gamze Naz Öztan
- Max Von Pettenkofer Institute and Gene Center, Virology, National Reference Center for Retroviruses, LMU München, Feodor-Lynen-Str. 23, 81377, Munich, Germany
| | - Melanie Huber
- Max Von Pettenkofer Institute and Gene Center, Virology, National Reference Center for Retroviruses, LMU München, Feodor-Lynen-Str. 23, 81377, Munich, Germany
| | - Hanna Autenrieth
- Max Von Pettenkofer Institute and Gene Center, Virology, National Reference Center for Retroviruses, LMU München, Feodor-Lynen-Str. 23, 81377, Munich, Germany
| | - Ricarda Knabe
- Max Von Pettenkofer Institute and Gene Center, Virology, National Reference Center for Retroviruses, LMU München, Feodor-Lynen-Str. 23, 81377, Munich, Germany
| | - Patricia M Späth
- Max Von Pettenkofer Institute and Gene Center, Virology, National Reference Center for Retroviruses, LMU München, Feodor-Lynen-Str. 23, 81377, Munich, Germany
| | - Maximilian Muenchhoff
- Max Von Pettenkofer Institute and Gene Center, Virology, National Reference Center for Retroviruses, LMU München, Feodor-Lynen-Str. 23, 81377, Munich, Germany
- German Center for Infection Research (DZIF), Partner Site, Munich, Germany
- COVID-19 Registry of the LMU Munich (CORKUM), University Hospital, LMU Munich, Munich, Germany
| | - Alexander Graf
- Laboratory for Functional Genome Analysis, Gene Center, LMU München, Munich, Germany
| | - Stefan Krebs
- Laboratory for Functional Genome Analysis, Gene Center, LMU München, Munich, Germany
| | - Helmut Blum
- Laboratory for Functional Genome Analysis, Gene Center, LMU München, Munich, Germany
| | - Jürgen Durner
- Labor Becker MVZ GbR, Munich, Germany
- Department of Conservative Dentistry and Periodontology, University Hospital, LMU München, Goethestr. 70, 80336, Munich, Germany
| | | | - Christopher Dächert
- Max Von Pettenkofer Institute and Gene Center, Virology, National Reference Center for Retroviruses, LMU München, Feodor-Lynen-Str. 23, 81377, Munich, Germany
- German Center for Infection Research (DZIF), Partner Site, Munich, Germany
| | - Lars Kaderali
- Institute of Bioinformatics, University Medicine Greifswald, Felix-Hausdorff-Str. 8, 17475, Greifswald, Germany.
| | - Hanna-Mari Baldauf
- Max Von Pettenkofer Institute and Gene Center, Virology, National Reference Center for Retroviruses, LMU München, Feodor-Lynen-Str. 23, 81377, Munich, Germany.
| | - Oliver T Keppler
- Max Von Pettenkofer Institute and Gene Center, Virology, National Reference Center for Retroviruses, LMU München, Feodor-Lynen-Str. 23, 81377, Munich, Germany.
- German Center for Infection Research (DZIF), Partner Site, Munich, Germany.
- COVID-19 Registry of the LMU Munich (CORKUM), University Hospital, LMU Munich, Munich, Germany.
| |
Collapse
|
24
|
Schönborn L, Thiele T, Kaderali L, Günther A, Hoffmann T, Seck SE, Selleng K, Greinacher A. Most anti-PF4 antibodies in vaccine-induced immune thrombotic thrombocytopenia are transient. Blood 2022; 139:1903-1907. [PMID: 35113987 PMCID: PMC8816791 DOI: 10.1182/blood.2021014214] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2021] [Accepted: 01/26/2022] [Indexed: 11/20/2022] Open
Abstract
Vaccine-induced thrombotic thrombocytopenia (VITT) is triggered by vaccination against COVID-19 with adenovirus vector vaccines (ChAdOx1 nCoV-19; Ad26.COV2-S). In this observational study, we followed VITT patients for changes in their reactivity of platelet-activating antiplatelet factor 4 (PF4) immunoglobulin G (IgG) antibodies by an anti-PF4/heparin IgG enzyme immunoassay (EIA) and a functional test for PF4-dependent, platelet-activating antibodies, and new thrombotic complications. Sixty-five VITT patients (41 females; median, 51 years; range, 18-80 years) were followed for a median of 25 weeks (range, 3-36 weeks). In 48/65 patients (73.8%; CI, 62.0% to 83.0%) the functional assay became negative. The median time to negative functional test result was 15.5 weeks (range, 5-28 weeks). In parallel, EIA optical density (OD) values decreased from median 3.12 to 1.52 (P < .0001), but seroreversion to a negative result was seen in only 14 (21.5%) patients. Five (7.5%) patients showed persistent platelet-activating antibodies and high EIA ODs for >11 weeks. None of the 29 VITT patients who received a second vaccination dose with an mRNA COVID-19 vaccine developed new thromboses or relevant increase in anti-PF4/heparin IgG EIA OD, regardless of whether PF4-dependent platelet-activating antibodies were still present. PF4-dependent platelet-activating antibodies are transient in most patients with VITT. VITT patients can safely receive a second COVID-19 mRNA-vaccine shot.
Collapse
Affiliation(s)
| | - Thomas Thiele
- Institute of Immunology and Transfusion Medicine and
| | - Lars Kaderali
- Institute of Bioinformatics, University Medicine Greifswald, Greifswald, Germany
| | - Albrecht Günther
- Hans Berger Department of Neurology, Jena University Hospital-Friedrich Schiller University, Jena, Germany; and
| | - Till Hoffmann
- Institute for Transplantation Diagnostics and Cell Therapeutics, University Hospital Duesseldorf, Medical Faculty, Duesseldorf, Germany
| | | | | | | |
Collapse
|
25
|
Jayavelu AK, Wolf S, Buettner F, Alexe G, Häupl B, Comoglio F, Schneider C, Doebele C, Fuhrmann DC, Wagner S, Donato E, Andresen C, Wilke AC, Zindel A, Jahn D, Splettstoesser B, Plessmann U, Münch S, Abou-El-Ardat K, Makowka P, Acker F, Enssle JC, Cremer A, Schnütgen F, Kurrle N, Chapuy B, Löber J, Hartmann S, Wild PJ, Wittig I, Hübschmann D, Kaderali L, Cox J, Brüne B, Röllig C, Thiede C, Steffen B, Bornhäuser M, Trumpp A, Urlaub H, Stegmaier K, Serve H, Mann M, Oellerich T. The proteogenomic subtypes of acute myeloid leukemia. Cancer Cell 2022; 40:301-317.e12. [PMID: 35245447 DOI: 10.1016/j.ccell.2022.02.006] [Citation(s) in RCA: 39] [Impact Index Per Article: 19.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/21/2021] [Revised: 08/30/2021] [Accepted: 02/07/2022] [Indexed: 12/16/2022]
Abstract
Acute myeloid leukemia (AML) is an aggressive blood cancer with a poor prognosis. We report a comprehensive proteogenomic analysis of bone marrow biopsies from 252 uniformly treated AML patients to elucidate the molecular pathophysiology of AML in order to inform future diagnostic and therapeutic approaches. In addition to in-depth quantitative proteomics, our analysis includes cytogenetic profiling and DNA/RNA sequencing. We identify five proteomic AML subtypes, each reflecting specific biological features spanning genomic boundaries. Two of these proteomic subtypes correlate with patient outcome, but none is exclusively associated with specific genomic aberrations. Remarkably, one subtype (Mito-AML), which is captured only in the proteome, is characterized by high expression of mitochondrial proteins and confers poor outcome, with reduced remission rate and shorter overall survival on treatment with intensive induction chemotherapy. Functional analyses reveal that Mito-AML is metabolically wired toward stronger complex I-dependent respiration and is more responsive to treatment with the BCL2 inhibitor venetoclax.
Collapse
Affiliation(s)
- Ashok Kumar Jayavelu
- Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Martinsried, Germany; Clinical Cooperation Unit Pediatric Leukemia, DKFZ and Department of Pediatric Oncology, Hematology and Immunology, University of Heidelberg, Germany; Hopp Children's Cancer Center Heidelberg - KiTZ, Heidelberg, Germany
| | - Sebastian Wolf
- Department of Medicine II, Hematology/Oncology, University Hospital Frankfurt, Goethe University, Theodor-Stern-Kai 7, Frankfurt, Germany; Frankfurt Cancer Institute, Goethe University Frankfurt, Frankfurt, Germany
| | - Florian Buettner
- German Cancer Consortium (DKTK), Partner Site Frankfurt/Mainz and German Cancer Research Center (DKFZ), Heidelberg, Germany; Department of Medicine, University Hospital Frankfurt, Goethe University, Frankfurt, Germany; Frankfurt Cancer Institute, Goethe University Frankfurt, Frankfurt, Germany
| | - Gabriela Alexe
- Division of Hematology/Oncology, Department of Pediatric Oncology, Dana-Farber Cancer Institute and Boston Children's Hospital, Boston, MA, USA
| | - Björn Häupl
- Department of Medicine II, Hematology/Oncology, University Hospital Frankfurt, Goethe University, Theodor-Stern-Kai 7, Frankfurt, Germany; German Cancer Consortium (DKTK), Partner Site Frankfurt/Mainz and German Cancer Research Center (DKFZ), Heidelberg, Germany; Frankfurt Cancer Institute, Goethe University Frankfurt, Frankfurt, Germany
| | | | - Constanze Schneider
- Department of Medicine II, Hematology/Oncology, University Hospital Frankfurt, Goethe University, Theodor-Stern-Kai 7, Frankfurt, Germany
| | - Carmen Doebele
- Department of Medicine II, Hematology/Oncology, University Hospital Frankfurt, Goethe University, Theodor-Stern-Kai 7, Frankfurt, Germany; German Cancer Consortium (DKTK), Partner Site Frankfurt/Mainz and German Cancer Research Center (DKFZ), Heidelberg, Germany
| | | | - Sebastian Wagner
- Department of Medicine II, Hematology/Oncology, University Hospital Frankfurt, Goethe University, Theodor-Stern-Kai 7, Frankfurt, Germany
| | - Elisa Donato
- Division of Stem Cells and Cancer, German Cancer Research Center (DKFZ) and DKFZ-ZMBH Alliance, Heidelberg, Germany; Heidelberg Institute for Stem Cell Technology and Experimental Medicine (HI-STEM gGmbH), Heidelberg, Germany
| | - Carolin Andresen
- Division of Stem Cells and Cancer, German Cancer Research Center (DKFZ) and DKFZ-ZMBH Alliance, Heidelberg, Germany; Heidelberg Institute for Stem Cell Technology and Experimental Medicine (HI-STEM gGmbH), Heidelberg, Germany
| | - Anne C Wilke
- Department of Medicine II, Hematology/Oncology, University Hospital Frankfurt, Goethe University, Theodor-Stern-Kai 7, Frankfurt, Germany
| | - Alena Zindel
- Department of Medicine II, Hematology/Oncology, University Hospital Frankfurt, Goethe University, Theodor-Stern-Kai 7, Frankfurt, Germany; German Cancer Consortium (DKTK), Partner Site Frankfurt/Mainz and German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Dominique Jahn
- Department of Medicine II, Hematology/Oncology, University Hospital Frankfurt, Goethe University, Theodor-Stern-Kai 7, Frankfurt, Germany; German Cancer Consortium (DKTK), Partner Site Frankfurt/Mainz and German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Bianca Splettstoesser
- Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Uwe Plessmann
- Bioanalytical Mass Spectrometry Group, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
| | - Silvia Münch
- Department of Medicine II, Hematology/Oncology, University Hospital Frankfurt, Goethe University, Theodor-Stern-Kai 7, Frankfurt, Germany
| | - Khali Abou-El-Ardat
- Department of Medicine II, Hematology/Oncology, University Hospital Frankfurt, Goethe University, Theodor-Stern-Kai 7, Frankfurt, Germany
| | - Philipp Makowka
- Department of Medicine II, Hematology/Oncology, University Hospital Frankfurt, Goethe University, Theodor-Stern-Kai 7, Frankfurt, Germany
| | - Fabian Acker
- Department of Medicine II, Hematology/Oncology, University Hospital Frankfurt, Goethe University, Theodor-Stern-Kai 7, Frankfurt, Germany
| | - Julius C Enssle
- Department of Medicine II, Hematology/Oncology, University Hospital Frankfurt, Goethe University, Theodor-Stern-Kai 7, Frankfurt, Germany
| | - Anjali Cremer
- Department of Medicine II, Hematology/Oncology, University Hospital Frankfurt, Goethe University, Theodor-Stern-Kai 7, Frankfurt, Germany
| | - Frank Schnütgen
- Department of Medicine II, Hematology/Oncology, University Hospital Frankfurt, Goethe University, Theodor-Stern-Kai 7, Frankfurt, Germany; German Cancer Consortium (DKTK), Partner Site Frankfurt/Mainz and German Cancer Research Center (DKFZ), Heidelberg, Germany; Frankfurt Cancer Institute, Goethe University Frankfurt, Frankfurt, Germany
| | - Nina Kurrle
- Department of Medicine II, Hematology/Oncology, University Hospital Frankfurt, Goethe University, Theodor-Stern-Kai 7, Frankfurt, Germany; German Cancer Consortium (DKTK), Partner Site Frankfurt/Mainz and German Cancer Research Center (DKFZ), Heidelberg, Germany; Frankfurt Cancer Institute, Goethe University Frankfurt, Frankfurt, Germany
| | - Björn Chapuy
- Department of Medical Hematology and Oncology, University Medical Center Göttingen, Göttingen, Germany; Department of Hematology, Oncology and Tumor Immunology, Charité, Campus Benjamin Franklin, University Medicine Berlin, Berlin, Germany
| | - Jens Löber
- Department of Medical Hematology and Oncology, University Medical Center Göttingen, Göttingen, Germany; Department of Hematology, Oncology and Tumor Immunology, Charité, Campus Benjamin Franklin, University Medicine Berlin, Berlin, Germany
| | - Sylvia Hartmann
- Dr. Senckenberg Institute of Pathology, University Hospital Frankfurt, Frankfurt, Germany
| | - Peter J Wild
- Dr. Senckenberg Institute of Pathology, University Hospital Frankfurt, Frankfurt, Germany
| | - Ilka Wittig
- Functional Proteomics, Institute of Cardiovascular Physiology, Goethe University, Frankfurt, Germany
| | - Daniel Hübschmann
- Division of Stem Cells and Cancer, German Cancer Research Center (DKFZ) and DKFZ-ZMBH Alliance, Heidelberg, Germany; Heidelberg Institute for Stem Cell Technology and Experimental Medicine (HI-STEM gGmbH), Heidelberg, Germany; Pattern Recognition and Digital Medicine, Heidelberg Institute for Stem Cell Technology and Experimental Medicine (HI-STEM), Heidelberg, Germany; Computational Oncology, Molecular Precision Oncology Program, National Center for Tumor Diseases (NCT) Heidelberg and German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Lars Kaderali
- Institute of Bioinformatics, University Medicine Greifswald, Greifswald, Germany
| | - Jürgen Cox
- Computational Systems Biochemistry Research Group, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Bernhard Brüne
- Department of Biochemistry I, Goethe University, Frankfurt, Germany
| | - Christoph Röllig
- Department of Internal Medicine I, University Hospital Carl Gustav Carus TU Dresden, Dresden, Germany
| | - Christian Thiede
- Department of Internal Medicine I, University Hospital Carl Gustav Carus TU Dresden, Dresden, Germany
| | - Björn Steffen
- Department of Medicine II, Hematology/Oncology, University Hospital Frankfurt, Goethe University, Theodor-Stern-Kai 7, Frankfurt, Germany
| | - Martin Bornhäuser
- Department of Internal Medicine I, University Hospital Carl Gustav Carus TU Dresden, Dresden, Germany; National Center for Tumor Diseases, Dresden (NCT/UCC), Dresden, Germany
| | - Andreas Trumpp
- Division of Stem Cells and Cancer, German Cancer Research Center (DKFZ) and DKFZ-ZMBH Alliance, Heidelberg, Germany; Heidelberg Institute for Stem Cell Technology and Experimental Medicine (HI-STEM gGmbH), Heidelberg, Germany; German Cancer Consortium (DKTK), Heidelberg, Germany
| | - Henning Urlaub
- Bioanalytical Mass Spectrometry Group, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany; Bioanalytics, Institute for Clinical Chemistry, University Medical Center Göttingen, Göttingen, Germany
| | - Kimberly Stegmaier
- Division of Hematology/Oncology, Department of Pediatric Oncology, Dana-Farber Cancer Institute and Boston Children's Hospital, Boston, MA, USA; The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Hubert Serve
- Department of Medicine II, Hematology/Oncology, University Hospital Frankfurt, Goethe University, Theodor-Stern-Kai 7, Frankfurt, Germany; German Cancer Consortium (DKTK), Partner Site Frankfurt/Mainz and German Cancer Research Center (DKFZ), Heidelberg, Germany; Frankfurt Cancer Institute, Goethe University Frankfurt, Frankfurt, Germany.
| | - Matthias Mann
- Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Martinsried, Germany.
| | - Thomas Oellerich
- Department of Medicine II, Hematology/Oncology, University Hospital Frankfurt, Goethe University, Theodor-Stern-Kai 7, Frankfurt, Germany; German Cancer Consortium (DKTK), Partner Site Frankfurt/Mainz and German Cancer Research Center (DKFZ), Heidelberg, Germany; Frankfurt Cancer Institute, Goethe University Frankfurt, Frankfurt, Germany.
| |
Collapse
|
26
|
Nicolas AM, Pesic M, Engel E, Ziegler PK, Diefenhardt M, Kennel KB, Buettner F, Conche C, Petrocelli V, Elwakeel E, Weigert A, Zinoveva A, Fleischmann M, Häupl B, Karakütük C, Bohnenberger H, Mosa MH, Kaderali L, Gaedcke J, Ghadimi M, Rödel F, Arkan MC, Oellerich T, Rödel C, Fokas E, Greten FR. Inflammatory fibroblasts mediate resistance to neoadjuvant therapy in rectal cancer. Cancer Cell 2022; 40:168-184.e13. [PMID: 35120600 DOI: 10.1016/j.ccell.2022.01.004] [Citation(s) in RCA: 108] [Impact Index Per Article: 54.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/29/2021] [Revised: 10/12/2021] [Accepted: 01/11/2022] [Indexed: 12/14/2022]
Abstract
Standard cancer therapy targets tumor cells without considering possible damage on the tumor microenvironment that could impair therapy response. In rectal cancer patients we find that inflammatory cancer-associated fibroblasts (iCAFs) are associated with poor chemoradiotherapy response. Employing a murine rectal cancer model or patient-derived tumor organoids and primary stroma cells, we show that, upon irradiation, interleukin-1α (IL-1α) not only polarizes cancer-associated fibroblasts toward the inflammatory phenotype but also triggers oxidative DNA damage, thereby predisposing iCAFs to p53-mediated therapy-induced senescence, which in turn results in chemoradiotherapy resistance and disease progression. Consistently, IL-1 inhibition, prevention of iCAFs senescence, or senolytic therapy sensitizes mice to irradiation, while lower IL-1 receptor antagonist serum levels in rectal patients correlate with poor prognosis. Collectively, we unravel a critical role for iCAFs in rectal cancer therapy resistance and identify IL-1 signaling as an attractive target for stroma-repolarization and prevention of cancer-associated fibroblasts senescence.
Collapse
Affiliation(s)
- Adele M Nicolas
- Institute for Tumor Biology and Experimental Therapy, Georg-Speyer-Haus, 60596 Frankfurt/Main, Germany; Frankfurt Cancer Institute, Goethe University Frankfurt, Frankfurt/Main, Germany
| | - Marina Pesic
- Institute for Tumor Biology and Experimental Therapy, Georg-Speyer-Haus, 60596 Frankfurt/Main, Germany; Frankfurt Cancer Institute, Goethe University Frankfurt, Frankfurt/Main, Germany
| | - Esther Engel
- Institute for Tumor Biology and Experimental Therapy, Georg-Speyer-Haus, 60596 Frankfurt/Main, Germany; Frankfurt Cancer Institute, Goethe University Frankfurt, Frankfurt/Main, Germany; Department of Radiotherapy and Oncology, Goethe University Frankfurt, Frankfurt/Main, Germany
| | - Paul K Ziegler
- Dr. Senckenberg Institute of Pathology, University Hospital Frankfurt, Frankfurt/Main, Germany
| | - Markus Diefenhardt
- Frankfurt Cancer Institute, Goethe University Frankfurt, Frankfurt/Main, Germany; Department of Radiotherapy and Oncology, Goethe University Frankfurt, Frankfurt/Main, Germany; University Cancer Center Frankfurt Marburg (UCT), University Hospital Frankfurt, Frankfurt/Main, Germany
| | - Kilian B Kennel
- Institute for Tumor Biology and Experimental Therapy, Georg-Speyer-Haus, 60596 Frankfurt/Main, Germany; Frankfurt Cancer Institute, Goethe University Frankfurt, Frankfurt/Main, Germany
| | - Florian Buettner
- Frankfurt Cancer Institute, Goethe University Frankfurt, Frankfurt/Main, Germany; German Cancer Consortium (DKTK) and German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany; Department of Medicine, Goethe University Frankfurt, Frankfurt/Main, Germany
| | - Claire Conche
- Institute for Tumor Biology and Experimental Therapy, Georg-Speyer-Haus, 60596 Frankfurt/Main, Germany; Frankfurt Cancer Institute, Goethe University Frankfurt, Frankfurt/Main, Germany
| | - Valentina Petrocelli
- Institute for Tumor Biology and Experimental Therapy, Georg-Speyer-Haus, 60596 Frankfurt/Main, Germany; Frankfurt Cancer Institute, Goethe University Frankfurt, Frankfurt/Main, Germany
| | - Eiman Elwakeel
- Institute of Biochemistry I, Goethe University Frankfurt, Frankfurt/Main, Germany
| | - Andreas Weigert
- Frankfurt Cancer Institute, Goethe University Frankfurt, Frankfurt/Main, Germany; Institute of Biochemistry I, Goethe University Frankfurt, Frankfurt/Main, Germany
| | - Anna Zinoveva
- Institute for Tumor Biology and Experimental Therapy, Georg-Speyer-Haus, 60596 Frankfurt/Main, Germany; Frankfurt Cancer Institute, Goethe University Frankfurt, Frankfurt/Main, Germany
| | - Maximilian Fleischmann
- Frankfurt Cancer Institute, Goethe University Frankfurt, Frankfurt/Main, Germany; Department of Radiotherapy and Oncology, Goethe University Frankfurt, Frankfurt/Main, Germany; University Cancer Center Frankfurt Marburg (UCT), University Hospital Frankfurt, Frankfurt/Main, Germany
| | - Björn Häupl
- Frankfurt Cancer Institute, Goethe University Frankfurt, Frankfurt/Main, Germany; German Cancer Consortium (DKTK) and German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany; Department of Medicine, Goethe University Frankfurt, Frankfurt/Main, Germany
| | - Cem Karakütük
- Institute of Pathology, University Medical Center, Göttingen, Germany
| | | | - Mohammed H Mosa
- Institute for Tumor Biology and Experimental Therapy, Georg-Speyer-Haus, 60596 Frankfurt/Main, Germany; Frankfurt Cancer Institute, Goethe University Frankfurt, Frankfurt/Main, Germany
| | - Lars Kaderali
- Institute of Bioinformatics, University Medicine Greifswald, Greifswald, Germany
| | - Jochen Gaedcke
- Department of Surgery, University Medical Center, Göttingen, Germany
| | - Michael Ghadimi
- Department of Surgery, University Medical Center, Göttingen, Germany
| | - Franz Rödel
- Frankfurt Cancer Institute, Goethe University Frankfurt, Frankfurt/Main, Germany; Department of Radiotherapy and Oncology, Goethe University Frankfurt, Frankfurt/Main, Germany; University Cancer Center Frankfurt Marburg (UCT), University Hospital Frankfurt, Frankfurt/Main, Germany
| | - Melek C Arkan
- Institute for Tumor Biology and Experimental Therapy, Georg-Speyer-Haus, 60596 Frankfurt/Main, Germany; Frankfurt Cancer Institute, Goethe University Frankfurt, Frankfurt/Main, Germany; German Cancer Consortium (DKTK) and German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
| | - Thomas Oellerich
- Frankfurt Cancer Institute, Goethe University Frankfurt, Frankfurt/Main, Germany; German Cancer Consortium (DKTK) and German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany; Department of Medicine, Goethe University Frankfurt, Frankfurt/Main, Germany
| | - Claus Rödel
- Frankfurt Cancer Institute, Goethe University Frankfurt, Frankfurt/Main, Germany; Department of Radiotherapy and Oncology, Goethe University Frankfurt, Frankfurt/Main, Germany; University Cancer Center Frankfurt Marburg (UCT), University Hospital Frankfurt, Frankfurt/Main, Germany; German Cancer Consortium (DKTK) and German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
| | - Emmanouil Fokas
- Frankfurt Cancer Institute, Goethe University Frankfurt, Frankfurt/Main, Germany; Department of Radiotherapy and Oncology, Goethe University Frankfurt, Frankfurt/Main, Germany; University Cancer Center Frankfurt Marburg (UCT), University Hospital Frankfurt, Frankfurt/Main, Germany; German Cancer Consortium (DKTK) and German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
| | - Florian R Greten
- Institute for Tumor Biology and Experimental Therapy, Georg-Speyer-Haus, 60596 Frankfurt/Main, Germany; Frankfurt Cancer Institute, Goethe University Frankfurt, Frankfurt/Main, Germany; German Cancer Consortium (DKTK) and German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany.
| |
Collapse
|
27
|
Zanders L, Kny M, Hahn A, Schmidt S, Wundersitz S, Todiras M, Lahmann I, Bandyopadhyay A, Wollersheim T, Kaderali L, Luft FC, Birchmeier C, Weber-Carstens S, Fielitz J. Sepsis induces interleukin 6, gp130/JAK2/STAT3, and muscle wasting. J Cachexia Sarcopenia Muscle 2022; 13:713-727. [PMID: 34821076 PMCID: PMC8818599 DOI: 10.1002/jcsm.12867] [Citation(s) in RCA: 53] [Impact Index Per Article: 26.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/01/2021] [Revised: 10/18/2021] [Accepted: 10/20/2021] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND Sepsis and inflammation can cause intensive care unit-acquired weakness (ICUAW). Increased interleukin-6 (IL-6) plasma levels are a risk factor for ICUAW. IL-6 signalling involves the glycoprotein 130 (gp130) receptor and the JAK/STAT-pathway, but its role in sepsis-induced muscle wasting is uncertain. In a clinical observational study, we found that the IL-6 target gene, SOCS3, was increased in skeletal muscle of ICUAW patients indicative for JAK/STAT-pathway activation. We tested the hypothesis that the IL-6/gp130-pathway mediates ICUAW muscle atrophy. METHODS We sequenced RNA (RNAseq) from tibialis anterior (TA) muscle of cecal ligation and puncture-operated (CLP) and sham-operated wildtype (WT) mice. The effects of the IL-6/gp130/JAK2/STAT3-pathway were investigated by analysing the atrophy phenotype, gene expression, and protein contents of C2C12 myotubes. Mice lacking Il6st, encoding gp130, in myocytes (cKO) and WT controls, as well as mice treated with the JAK2 inhibitor AG490 or vehicle were exposed to CLP or sham surgery for 24 or 96 h. RESULTS Analyses of differentially expressed genes in RNAseq (≥2-log2-fold change, P < 0.01) revealed an activation of IL-6-signalling and JAK/STAT-signalling pathways in muscle of septic mice, which occurred after 24 h and lasted at least for 96 h during sepsis. IL-6 treatment of C2C12 myotubes induced STAT3 phosphorylation (three-fold, P < 0.01) and Socs3 mRNA expression (3.1-fold, P < 0.01) and caused myotube atrophy. Knockdown of Il6st diminished IL-6-induced STAT3 phosphorylation (-30.0%; P < 0.01), Socs3 mRNA expression, and myotube atrophy. JAK2 (- 29.0%; P < 0.01) or STAT3 inhibition (-38.7%; P < 0.05) decreased IL-6-induced Socs3 mRNA expression. Treatment with either inhibitor attenuated myotube atrophy in response to IL-6. CLP-operated septic mice showed an increased STAT3 phosphorylation and Socs3 mRNA expression in TA muscle, which was reduced in septic Il6st-cKO mice by 67.8% (P < 0.05) and 85.6% (P < 0.001), respectively. CLP caused a loss of TA muscle weight, which was attenuated in Il6st-cKO mice (WT: -22.3%, P < 0.001, cKO: -13.5%, P < 0.001; WT vs. cKO P < 0.001). While loss of Il6st resulted in a reduction of MuRF1 protein contents, Atrogin-1 remained unchanged between septic WT and cKO mice. mRNA expression of Trim63/MuRF1 and Fbxo32/Atrogin-1 were unaltered between CLP-treated WT and cKO mice. AG490 treatment reduced STAT3 phosphorylation (-22.2%, P < 0.05) and attenuated TA muscle atrophy in septic mice (29.6% relative reduction of muscle weight loss, P < 0.05). The reduction in muscle atrophy was accompanied by a reduction in Fbxo32/Atrogin-1-mRNA (-81.3%, P < 0.05) and Trim63/MuRF1-mRNA expression (-77.6%, P < 0.05) and protein content. CONCLUSIONS IL-6 via the gp130/JAK2/STAT3-pathway mediates sepsis-induced muscle atrophy possibly contributing to ICUAW.
Collapse
Affiliation(s)
- Lukas Zanders
- Experimental and Clinical Research Center (ECRC), Charité-Universitätsmedizin Berlin, Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin, Germany.,DZHK (German Center for Cardiovascular Research), partner site Berlin, Berlin, Germany.,Department of Cardiology, Charité Campus Benjamin Franklin, Berlin, Germany
| | - Melanie Kny
- Experimental and Clinical Research Center (ECRC), Charité-Universitätsmedizin Berlin, Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin, Germany
| | - Alexander Hahn
- Experimental and Clinical Research Center (ECRC), Charité-Universitätsmedizin Berlin, Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin, Germany
| | - Sibylle Schmidt
- Experimental and Clinical Research Center (ECRC), Charité-Universitätsmedizin Berlin, Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin, Germany
| | - Sebastian Wundersitz
- Experimental and Clinical Research Center (ECRC), Charité-Universitätsmedizin Berlin, Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin, Germany
| | - Mihail Todiras
- Cardiovascular hormones, Max Delbrück Center (MDC) for Molecular Medicine in the Helmholtz Association, Berlin, Germany.,Nicolae Testemiţanu State University of Medicine and Pharmacy, Chișinău, Moldova
| | - Ines Lahmann
- Developmental Biology/Signal Transduction, Max-Delbrück-Center for Molecular Medicine, Berlin, Germany
| | - Arnab Bandyopadhyay
- Institute of Bioinformatics, University Medicine Greifswald, Greifswald, Germany
| | - Tobias Wollersheim
- Anesthesiology and operative Intensive Care Medicine, Charité Campus Virchow and Campus Mitte, Berlin, Germany.,Berlin Institute of Health (BIH), Berlin, Germany
| | - Lars Kaderali
- Institute of Bioinformatics, University Medicine Greifswald, Greifswald, Germany.,DZHK (German Center for Cardiovascular Research), partner site Greifswald, Greifswald, Germany
| | - Friedrich C Luft
- Experimental and Clinical Research Center (ECRC), Charité-Universitätsmedizin Berlin, Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin, Germany
| | - Carmen Birchmeier
- Developmental Biology/Signal Transduction, Max-Delbrück-Center for Molecular Medicine, Berlin, Germany.,Berlin Institute of Health (BIH), Berlin, Germany
| | - Steffen Weber-Carstens
- Anesthesiology and operative Intensive Care Medicine, Charité Campus Virchow and Campus Mitte, Berlin, Germany.,Berlin Institute of Health (BIH), Berlin, Germany
| | - Jens Fielitz
- Experimental and Clinical Research Center (ECRC), Charité-Universitätsmedizin Berlin, Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin, Germany.,Berlin Institute of Health (BIH), Berlin, Germany.,DZHK (German Center for Cardiovascular Research), partner site Greifswald, Greifswald, Germany.,Department of Internal Medicine B, Cardiology, University Medicine Greifswald, Greifswald, Germany
| |
Collapse
|
28
|
Wratil PR, Schmacke NA, Karakoc B, Dulovic A, Junker D, Becker M, Rothbauer U, Osterman A, Spaeth PM, Ruhle A, Gapp M, Schneider S, Muenchhoff M, Hellmuth JC, Scherer C, Mayerle J, Reincke M, Behr J, Kääb S, Zwissler B, von Bergwelt-Baildon M, Eberle J, Kaderali L, Schneiderhan-Marra N, Hornung V, Keppler OT. Evidence for increased SARS-CoV-2 susceptibility and COVID-19 severity related to pre-existing immunity to seasonal coronaviruses. Cell Rep 2021; 37:110169. [PMID: 34932974 PMCID: PMC8648802 DOI: 10.1016/j.celrep.2021.110169] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [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: 05/14/2021] [Revised: 10/27/2021] [Accepted: 12/03/2021] [Indexed: 11/30/2022] Open
Abstract
The importance of pre-existing immune responses to seasonal endemic coronaviruses (HCoVs) for the susceptibility to SARS-CoV-2 infection and the course of COVID-19 is the subject of an ongoing scientific debate. Recent studies postulate that immune responses to previous HCoV infections can either have a slightly protective or no effect on SARS-CoV-2 pathogenesis and, consequently, be neglected for COVID-19 risk stratification. Challenging this notion, we provide evidence that pre-existing, anti-nucleocapsid antibodies against endemic α-coronaviruses and S2 domain-specific anti-spike antibodies against β-coronavirus HCoV-OC43 are elevated in patients with COVID-19 compared to pre-pandemic donors. This finding is particularly pronounced in males and in critically ill patients. Longitudinal evaluation reveals that antibody cross-reactivity or polyclonal stimulation by SARS-CoV-2 infection are unlikely to be confounders. Thus, specific pre-existing immunity to seasonal coronaviruses may increase susceptibility to SARS-CoV-2 and predispose individuals to an adverse COVID-19 outcome, guiding risk management and supporting the development of universal coronavirus vaccines.
Collapse
Affiliation(s)
- Paul R Wratil
- Max von Pettenkofer Institute & Gene Center, Virology, National Reference Center for Retroviruses, Faculty of Medicine, LMU München, Pettenkoferstr. 9a, 80336 Munich, Bavaria, Germany; German Center for Infection Research (DZIF), partner site Munich, 80802 Munich, Bavaria, Germany
| | - Niklas A Schmacke
- Department of Biochemistry and Gene Center, LMU München, 81377 Munich, Bavaria, Germany
| | - Burak Karakoc
- Max von Pettenkofer Institute & Gene Center, Virology, National Reference Center for Retroviruses, Faculty of Medicine, LMU München, Pettenkoferstr. 9a, 80336 Munich, Bavaria, Germany
| | - Alex Dulovic
- Natural and Medical Sciences Institute at the University of Tübingen, 72770 Reutlingen, Baden-Württemberg, Germany
| | - Daniel Junker
- Natural and Medical Sciences Institute at the University of Tübingen, 72770 Reutlingen, Baden-Württemberg, Germany
| | - Matthias Becker
- Natural and Medical Sciences Institute at the University of Tübingen, 72770 Reutlingen, Baden-Württemberg, Germany
| | - Ulrich Rothbauer
- Natural and Medical Sciences Institute at the University of Tübingen, 72770 Reutlingen, Baden-Württemberg, Germany; Pharmaceutical Biotechnology, University of Tübingen, 72770 Reutlingen, Baden-Württemberg, Germany
| | - Andreas Osterman
- Max von Pettenkofer Institute & Gene Center, Virology, National Reference Center for Retroviruses, Faculty of Medicine, LMU München, Pettenkoferstr. 9a, 80336 Munich, Bavaria, Germany
| | - Patricia M Spaeth
- Max von Pettenkofer Institute & Gene Center, Virology, National Reference Center for Retroviruses, Faculty of Medicine, LMU München, Pettenkoferstr. 9a, 80336 Munich, Bavaria, Germany
| | - Adrian Ruhle
- Max von Pettenkofer Institute & Gene Center, Virology, National Reference Center for Retroviruses, Faculty of Medicine, LMU München, Pettenkoferstr. 9a, 80336 Munich, Bavaria, Germany
| | - Madeleine Gapp
- Max von Pettenkofer Institute & Gene Center, Virology, National Reference Center for Retroviruses, Faculty of Medicine, LMU München, Pettenkoferstr. 9a, 80336 Munich, Bavaria, Germany
| | - Stephanie Schneider
- Max von Pettenkofer Institute & Gene Center, Virology, National Reference Center for Retroviruses, Faculty of Medicine, LMU München, Pettenkoferstr. 9a, 80336 Munich, Bavaria, Germany
| | - Maximilian Muenchhoff
- Max von Pettenkofer Institute & Gene Center, Virology, National Reference Center for Retroviruses, Faculty of Medicine, LMU München, Pettenkoferstr. 9a, 80336 Munich, Bavaria, Germany; German Center for Infection Research (DZIF), partner site Munich, 80802 Munich, Bavaria, Germany; COVID-19 Registry of the LMU Munich (CORKUM), Klinikum der Universität München, LMU München, 81377 Munich, Bavaria, Germany
| | - Johannes C Hellmuth
- COVID-19 Registry of the LMU Munich (CORKUM), Klinikum der Universität München, LMU München, 81377 Munich, Bavaria, Germany; Department of Medicine III, Klinikum der Universität München, LMU München, 81377 Munich, Bavaria, Germany; German Cancer Consortium (DKTK), 81377 Munich, Bavaria, Germany
| | - Clemens Scherer
- COVID-19 Registry of the LMU Munich (CORKUM), Klinikum der Universität München, LMU München, 81377 Munich, Bavaria, Germany; Medizinische Klinik und Poliklinik I, Klinikum der Universität München, LMU München, 80336 Munich, Bavaria, Germany; Comprehensive Pneumology Center Munich (CPC-M), Member of the German Center for Lung Research, 85764 Neuherberg, Bavaria, Germany; DZHK (German Centre for Cardiovascular Research), partner site Munich Heart Alliance, 81377 Munich, Bavaria, Germany
| | - Julia Mayerle
- COVID-19 Registry of the LMU Munich (CORKUM), Klinikum der Universität München, LMU München, 81377 Munich, Bavaria, Germany; Department of Medicine II, Klinikum der Universität München, LMU München, 81377 Munich, Bavaria, Germany
| | - Martin Reincke
- COVID-19 Registry of the LMU Munich (CORKUM), Klinikum der Universität München, LMU München, 81377 Munich, Bavaria, Germany; Medizinische Klinik und Poliklinik IV, Klinikum der Universität München, LMU München, 80336 Munich, Bavaria, Germany
| | - Juergen Behr
- COVID-19 Registry of the LMU Munich (CORKUM), Klinikum der Universität München, LMU München, 81377 Munich, Bavaria, Germany; Comprehensive Pneumology Center Munich (CPC-M), Member of the German Center for Lung Research, 85764 Neuherberg, Bavaria, Germany; Department of Medicine V, Klinikum der Universität München, LMU München, 81377 Munich, Bavaria, Germany
| | - Stefan Kääb
- COVID-19 Registry of the LMU Munich (CORKUM), Klinikum der Universität München, LMU München, 81377 Munich, Bavaria, Germany; Medizinische Klinik und Poliklinik I, Klinikum der Universität München, LMU München, 80336 Munich, Bavaria, Germany; DZHK (German Centre for Cardiovascular Research), partner site Munich Heart Alliance, 81377 Munich, Bavaria, Germany
| | - Bernhard Zwissler
- COVID-19 Registry of the LMU Munich (CORKUM), Klinikum der Universität München, LMU München, 81377 Munich, Bavaria, Germany; Comprehensive Pneumology Center Munich (CPC-M), Member of the German Center for Lung Research, 85764 Neuherberg, Bavaria, Germany; Department of Anaesthesiology, Klinikum der Universität München, LMU München, 81377 Munich, Bavaria, Germany
| | - Michael von Bergwelt-Baildon
- COVID-19 Registry of the LMU Munich (CORKUM), Klinikum der Universität München, LMU München, 81377 Munich, Bavaria, Germany; Department of Medicine III, Klinikum der Universität München, LMU München, 81377 Munich, Bavaria, Germany; German Cancer Consortium (DKTK), 81377 Munich, Bavaria, Germany
| | - Josef Eberle
- Max von Pettenkofer Institute & Gene Center, Virology, National Reference Center for Retroviruses, Faculty of Medicine, LMU München, Pettenkoferstr. 9a, 80336 Munich, Bavaria, Germany
| | - Lars Kaderali
- Institute of Bioinformatics, University Medicine Greifswald, 17475 Greifswald, Mecklenburg-Vorpommern, Germany
| | - Nicole Schneiderhan-Marra
- Natural and Medical Sciences Institute at the University of Tübingen, 72770 Reutlingen, Baden-Württemberg, Germany
| | - Veit Hornung
- Department of Biochemistry and Gene Center, LMU München, 81377 Munich, Bavaria, Germany
| | - Oliver T Keppler
- Max von Pettenkofer Institute & Gene Center, Virology, National Reference Center for Retroviruses, Faculty of Medicine, LMU München, Pettenkoferstr. 9a, 80336 Munich, Bavaria, Germany; German Center for Infection Research (DZIF), partner site Munich, 80802 Munich, Bavaria, Germany.
| |
Collapse
|
29
|
Barbarics B, Eildermann K, Kaderali L, Cyganek L, Plessmann U, Bodemeyer J, Paul T, Ströbel P, Urlaub H, Tirilomis T, Lenz C, Bohnenberger H. Proteomic mapping of atrial and ventricular heart tissue in patients with aortic valve stenosis. Sci Rep 2021; 11:24389. [PMID: 34937869 PMCID: PMC8695579 DOI: 10.1038/s41598-021-03907-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2021] [Accepted: 12/06/2021] [Indexed: 11/20/2022] Open
Abstract
Aortic valve stenosis (AVS) is one of the most common valve diseases in the world. However, detailed biological understanding of the myocardial changes in AVS hearts on the proteome level is still lacking. Proteomic studies using high-resolution mass spectrometry of formalin-fixed and paraffin-embedded (FFPE) human myocardial tissue of AVS-patients are very rare due to methodical issues. To overcome these issues this study used high resolution mass spectrometry in combination with a stem cell-derived cardiac specific protein quantification-standard to profile the proteomes of 17 atrial and 29 left ventricular myocardial FFPE human myocardial tissue samples from AVS-patients. In our proteomic analysis we quantified a median of 1980 (range 1495–2281) proteins in every single sample and identified significant upregulation of 239 proteins in atrial and 54 proteins in ventricular myocardium. We compared the proteins with published data. Well studied proteins reflect disease-related changes in AVS, such as cardiac hypertrophy, development of fibrosis, impairment of mitochondria and downregulated blood supply. In summary, we provide both a workflow for quantitative proteomics of human FFPE heart tissue and a comprehensive proteomic resource for AVS induced changes in the human myocardium.
Collapse
|
30
|
Tabata K, Prasad V, Paul D, Lee JY, Pham MT, Twu WI, Neufeldt CJ, Cortese M, Cerikan B, Stahl Y, Joecks S, Tran CS, Lüchtenborg C, V'kovski P, Hörmann K, Müller AC, Zitzmann C, Haselmann U, Beneke J, Kaderali L, Erfle H, Thiel V, Lohmann V, Superti-Furga G, Brügger B, Bartenschlager R. Convergent use of phosphatidic acid for hepatitis C virus and SARS-CoV-2 replication organelle formation. Nat Commun 2021; 12:7276. [PMID: 34907161 PMCID: PMC8671429 DOI: 10.1038/s41467-021-27511-1] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [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: 05/06/2021] [Accepted: 11/22/2021] [Indexed: 11/09/2022] Open
Abstract
Double membrane vesicles (DMVs) serve as replication organelles of plus-strand RNA viruses such as hepatitis C virus (HCV) and SARS-CoV-2. Viral DMVs are morphologically analogous to DMVs formed during autophagy, but lipids driving their biogenesis are largely unknown. Here we show that production of the lipid phosphatidic acid (PA) by acylglycerolphosphate acyltransferase (AGPAT) 1 and 2 in the ER is important for DMV biogenesis in viral replication and autophagy. Using DMVs in HCV-replicating cells as model, we found that AGPATs are recruited to and critically contribute to HCV and SARS-CoV-2 replication and proper DMV formation. An intracellular PA sensor accumulated at viral DMV formation sites, consistent with elevated levels of PA in fractions of purified DMVs analyzed by lipidomics. Apart from AGPATs, PA is generated by alternative pathways and their pharmacological inhibition also impaired HCV and SARS-CoV-2 replication as well as formation of autophagosome-like DMVs. These data identify PA as host cell lipid involved in proper replication organelle formation by HCV and SARS-CoV-2, two phylogenetically disparate viruses causing very different diseases, i.e. chronic liver disease and COVID-19, respectively. Host-targeting therapy aiming at PA synthesis pathways might be suitable to attenuate replication of these viruses.
Collapse
Affiliation(s)
- Keisuke Tabata
- Department of Infectious Diseases, Molecular Virology, Heidelberg University, Heidelberg, Germany
- Department of Genetics, Graduate School of Medicine, Osaka University, Osaka, Japan
- Laboratory of Intracellular Membrane Dynamics, Graduate School of Frontier Biosciences, Osaka University, Osaka, Japan
| | - Vibhu Prasad
- Department of Infectious Diseases, Molecular Virology, Heidelberg University, Heidelberg, Germany
| | - David Paul
- Department of Infectious Diseases, Molecular Virology, Heidelberg University, Heidelberg, Germany
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge, CB2 0QH, UK
| | - Ji-Young Lee
- Department of Infectious Diseases, Molecular Virology, Heidelberg University, Heidelberg, Germany
| | - Minh-Tu Pham
- Department of Infectious Diseases, Molecular Virology, Heidelberg University, Heidelberg, Germany
| | - Woan-Ing Twu
- Department of Infectious Diseases, Molecular Virology, Heidelberg University, Heidelberg, Germany
| | - Christopher J Neufeldt
- Department of Infectious Diseases, Molecular Virology, Heidelberg University, Heidelberg, Germany
| | - Mirko Cortese
- Department of Infectious Diseases, Molecular Virology, Heidelberg University, Heidelberg, Germany
| | - Berati Cerikan
- Department of Infectious Diseases, Molecular Virology, Heidelberg University, Heidelberg, Germany
| | - Yannick Stahl
- Department of Infectious Diseases, Molecular Virology, Heidelberg University, Heidelberg, Germany
| | - Sebastian Joecks
- Department of Infectious Diseases, Molecular Virology, Heidelberg University, Heidelberg, Germany
- LI-COR Biosciences GmbH, Siemensstrasse 25A, Bad Homburg, Germany
| | - Cong Si Tran
- Department of Infectious Diseases, Molecular Virology, Heidelberg University, Heidelberg, Germany
| | | | - Philip V'kovski
- Institute of Virology and Immunology IVI, Bern, Switzerland
- Department of Infectious Diseases and Pathobiology, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | - Katrin Hörmann
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - André C Müller
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Carolin Zitzmann
- Institute of Bioinformatics and Center for Functional Genomics of Microbes, University Medicine Greifswald, Greifswald, Germany
- Los Alamos National Laboratory, Theoretical Biology and Biophysics, Los Alamos, NM, USA
| | - Uta Haselmann
- Department of Infectious Diseases, Molecular Virology, Heidelberg University, Heidelberg, Germany
| | - Jürgen Beneke
- BioQuant, Heidelberg University, Heidelberg, Germany
| | - Lars Kaderali
- Institute of Bioinformatics and Center for Functional Genomics of Microbes, University Medicine Greifswald, Greifswald, Germany
| | - Holger Erfle
- BioQuant, Heidelberg University, Heidelberg, Germany
| | - Volker Thiel
- Institute of Virology and Immunology IVI, Bern, Switzerland
- Department of Infectious Diseases and Pathobiology, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | - Volker Lohmann
- Department of Infectious Diseases, Molecular Virology, Heidelberg University, Heidelberg, Germany
| | - Giulio Superti-Furga
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
- Center for Physiology and Pharmacology, Medical University of Vienna, Vienna, Austria
| | - Britta Brügger
- Biochemistry Center Heidelberg, Heidelberg University, Heidelberg, Germany
| | - Ralf Bartenschlager
- Department of Infectious Diseases, Molecular Virology, Heidelberg University, Heidelberg, Germany.
- Division Virus-Associated Carcinogenesis, German Cancer Research Center, Heidelberg, Germany.
- German Center for Infection Research, Heidelberg Partner Site, Heidelberg, Germany.
| |
Collapse
|
31
|
|
32
|
Osterman A, Iglhaut M, Lehner A, Späth P, Stern M, Autenrieth H, Muenchhoff M, Graf A, Krebs S, Blum H, Baiker A, Grzimek-Koschewa N, Protzer U, Kaderali L, Baldauf HM, Keppler OT. Comparison of four commercial, automated antigen tests to detect SARS-CoV-2 variants of concern. Med Microbiol Immunol 2021; 210:263-275. [PMID: 34415422 PMCID: PMC8377707 DOI: 10.1007/s00430-021-00719-0] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [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: 08/08/2021] [Accepted: 08/13/2021] [Indexed: 12/23/2022]
Abstract
A versatile portfolio of diagnostic tests is essential for the containment of the severe acute respiratory syndrome coronavirus type 2 (SARS-CoV-2) pandemic. Besides nucleic acid-based test systems and point-of-care (POCT) antigen (Ag) tests, quantitative, laboratory-based nucleocapsid Ag tests for SARS-CoV-2 have recently been launched. Here, we evaluated four commercial Ag tests on automated platforms and one POCT to detect SARS-CoV-2. We evaluated PCR-positive (n = 107) and PCR-negative (n = 303) respiratory swabs from asymptomatic and symptomatic patients at the end of the second pandemic wave in Germany (February–March 2021) as well as clinical isolates EU1 (B.1.117), variant of concern (VOC) Alpha (B.1.1.7) or Beta (B.1.351), which had been expanded in a biosafety level 3 laboratory. The specificities of automated SARS-CoV-2 Ag tests ranged between 97.0 and 99.7% (Lumipulse G SARS-CoV-2 Ag (Fujirebio): 97.03%, Elecsys SARS-CoV-2 Ag (Roche Diagnostics): 97.69%; LIAISON® SARS-CoV-2 Ag (Diasorin) and SARS-CoV-2 Ag ELISA (Euroimmun): 99.67%). In this study cohort of hospitalized patients, the clinical sensitivities of tests were low, ranging from 17.76 to 52.34%, and analytical sensitivities ranged from 420,000 to 25,000,000 Geq/ml. In comparison, the detection limit of the Roche Rapid Ag Test (RAT) was 9,300,000 Geq/ml, detecting 23.58% of respiratory samples. Receiver-operating-characteristics (ROCs) and Youden’s index analyses were performed to further characterize the assays’ overall performance and determine optimal assay cutoffs for sensitivity and specificity. VOCs carrying up to four amino acid mutations in nucleocapsid were detected by all five assays with characteristics comparable to non-VOCs. In summary, automated, quantitative SARS-CoV-2 Ag tests show variable performance and are not necessarily superior to a standard POCT. The efficacy of any alternative testing strategies to complement nucleic acid-based assays must be carefully evaluated by independent laboratories prior to widespread implementation.
Collapse
Affiliation(s)
- Andreas Osterman
- Max Von Pettenkofer Institute and Gene Center, Virology, National Reference Center for Retroviruses, LMU München, Munich, Germany
| | - Maximilian Iglhaut
- Max Von Pettenkofer Institute and Gene Center, Virology, National Reference Center for Retroviruses, LMU München, Munich, Germany
| | - Andreas Lehner
- Max Von Pettenkofer Institute and Gene Center, Virology, National Reference Center for Retroviruses, LMU München, Munich, Germany
| | - Patricia Späth
- Max Von Pettenkofer Institute and Gene Center, Virology, National Reference Center for Retroviruses, LMU München, Munich, Germany
| | - Marcel Stern
- Max Von Pettenkofer Institute and Gene Center, Virology, National Reference Center for Retroviruses, LMU München, Munich, Germany
| | - Hanna Autenrieth
- Max Von Pettenkofer Institute and Gene Center, Virology, National Reference Center for Retroviruses, LMU München, Munich, Germany
| | - Maximilian Muenchhoff
- Max Von Pettenkofer Institute and Gene Center, Virology, National Reference Center for Retroviruses, LMU München, Munich, Germany
- German Center for Infection Research (DZIF), Partner Site, Munich, Germany
- COVID-19 Registry of the LMU Munich (CORKUM), University Hospital, LMU Munich, Munich, Germany
| | - Alexander Graf
- Laboratory for Functional Genome Analysis, Gene Center, LMU München, Munich, Germany
| | - Stefan Krebs
- Laboratory for Functional Genome Analysis, Gene Center, LMU München, Munich, Germany
| | - Helmut Blum
- Laboratory for Functional Genome Analysis, Gene Center, LMU München, Munich, Germany
| | - Armin Baiker
- Public Health Microbiology Unit, Bavarian Health and Food Safety Authority, Oberschleißheim, Germany
| | - Natascha Grzimek-Koschewa
- Max Von Pettenkofer Institute and Gene Center, Virology, National Reference Center for Retroviruses, LMU München, Munich, Germany
- German Center for Infection Research (DZIF), Partner Site, Munich, Germany
| | - Ulrike Protzer
- German Center for Infection Research (DZIF), Partner Site, Munich, Germany
- Institute of Virology, Technical University of Munich/Helmholtz Zentrum München, Munich, Germany
| | - Lars Kaderali
- Institute of Bioinformatics, University Medicine Greifswald, Greifswald, Germany
| | - Hanna-Mari Baldauf
- Max Von Pettenkofer Institute and Gene Center, Virology, National Reference Center for Retroviruses, LMU München, Munich, Germany.
- Max Von Pettenkofer Institute, Virology, National Reference Center for Retroviruses, LMU München, Feodor-Lynen-Str. 23, 81377, Munich, Germany.
| | - Oliver T Keppler
- Max Von Pettenkofer Institute and Gene Center, Virology, National Reference Center for Retroviruses, LMU München, Munich, Germany.
- German Center for Infection Research (DZIF), Partner Site, Munich, Germany.
- COVID-19 Registry of the LMU Munich (CORKUM), University Hospital, LMU Munich, Munich, Germany.
- Max Von Pettenkofer Institute, Virology, National Reference Center for Retroviruses, LMU München, Pettenkoferstr. 9a, 80336, Munich, Germany.
| |
Collapse
|
33
|
Wratil PR, Schmacke NA, Osterman A, Weinberger T, Rech J, Karakoc B, Zeilberger M, Steffen J, Mueller TT, Spaeth PM, Stern M, Albanese M, Thun H, Reinbold J, Sandmeyer B, Kressirer P, Grabein B, Falkai P, Adorjan K, Hornung V, Kaderali L, Klein M, Keppler OT. In-depth profiling of COVID-19 risk factors and preventive measures in healthcare workers. Infection 2021; 50:381-394. [PMID: 34379308 PMCID: PMC8354838 DOI: 10.1007/s15010-021-01672-z] [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: 06/22/2021] [Accepted: 07/17/2021] [Indexed: 12/12/2022]
Abstract
Purpose To determine risk factors for coronavirus disease 2019 (COVID-19) in healthcare workers (HCWs), characterize symptoms, and evaluate preventive measures against SARS-CoV-2 spread in hospitals. Methods In a cross-sectional study conducted between May 27 and August 12, 2020, after the first wave of the COVID-19 pandemic, we obtained serological, epidemiological, occupational as well as COVID-19-related data at a quaternary care, multicenter hospital in Munich, Germany. Results 7554 HCWs participated, 2.2% of whom tested positive for anti-SARS-CoV-2 antibodies. Multivariate analysis revealed increased COVID-19 risk for nurses (3.1% seropositivity, 95% CI 2.5–3.9%, p = 0.012), staff working on COVID-19 units (4.6% seropositivity, 95% CI 3.2–6.5%, p = 0.032), males (2.4% seropositivity, 95% CI 1.8–3.2%, p = 0.019), and HCWs reporting high-risk exposures to infected patients (5.5% seropositivity, 95% CI 4.0–7.5%, p = 0.0022) or outside of work (12.0% seropositivity, 95% CI 8.0–17.4%, p < 0.0001). Smoking was a protective factor (1.1% seropositivity, 95% CI 0.7–1.8% p = 0.00018) and the symptom taste disorder was strongly associated with COVID-19 (29.8% seropositivity, 95% CI 24.3–35.8%, p < 0.0001). An unbiased decision tree identified subgroups with different risk profiles. Working from home as a preventive measure did not protect against SARS-CoV-2 infection. A PCR-testing strategy focused on symptoms and high-risk exposures detected all larger COVID-19 outbreaks. Conclusion Awareness of the identified COVID-19 risk factors and successful surveillance strategies are key to protecting HCWs against SARS-CoV-2, especially in settings with limited vaccination capacities or reduced vaccine efficacy. Supplementary Information The online version contains supplementary material available at 10.1007/s15010-021-01672-z.
Collapse
Affiliation(s)
- Paul R Wratil
- Faculty of Medicine, National Reference Center for Retroviruses, Max Von Pettenkofer Institute and Gene Center, Virology, LMU München, Munich, Germany.
- German Center for Infection Research (DZIF), Partner site, Munich, Germany.
| | - Niklas A Schmacke
- Department of Biochemistry and Gene Center, LMU München, Munich, Germany
| | - Andreas Osterman
- Faculty of Medicine, National Reference Center for Retroviruses, Max Von Pettenkofer Institute and Gene Center, Virology, LMU München, Munich, Germany
| | - Tobias Weinberger
- Department of Medicine I, University Hospital, LMU München, Munich, Germany
- DZHK (German Centre for Cardiovascular Research), Partner Site Munich Heart Alliance, Munich, Germany
| | - Jochen Rech
- Department of Biochemistry and Gene Center, LMU München, Munich, Germany
| | - Burak Karakoc
- Faculty of Medicine, National Reference Center for Retroviruses, Max Von Pettenkofer Institute and Gene Center, Virology, LMU München, Munich, Germany
| | - Mira Zeilberger
- Department of Medicine IV, University Hospital, LMU München, Munich, Germany
| | - Julius Steffen
- Department of Medicine I, University Hospital, LMU München, Munich, Germany
- DZHK (German Centre for Cardiovascular Research), Partner Site Munich Heart Alliance, Munich, Germany
| | - Tonina T Mueller
- Department of Medicine I, University Hospital, LMU München, Munich, Germany
| | - Patricia M Spaeth
- Faculty of Medicine, National Reference Center for Retroviruses, Max Von Pettenkofer Institute and Gene Center, Virology, LMU München, Munich, Germany
| | - Marcel Stern
- Faculty of Medicine, National Reference Center for Retroviruses, Max Von Pettenkofer Institute and Gene Center, Virology, LMU München, Munich, Germany
| | - Manuel Albanese
- Faculty of Medicine, National Reference Center for Retroviruses, Max Von Pettenkofer Institute and Gene Center, Virology, LMU München, Munich, Germany
| | - Hella Thun
- Department of Communication and Media, University Hospital, LMU München, Munich, Germany
| | - Julia Reinbold
- Department of Communication and Media, University Hospital, LMU München, Munich, Germany
| | - Benedikt Sandmeyer
- Institute of Emergency Medicine and Management in Medicine, University Hospital, LMU Munich, Munich, Germany
| | - Philipp Kressirer
- Department of Communication and Media, University Hospital, LMU München, Munich, Germany
| | - Béatrice Grabein
- Department for Clinical Microbiology and Hospital Hygiene, University Hospital, LMU München, Munich, Germany
| | - Peter Falkai
- Department of Psychiatry and Psychotherapy, University Hospital, LMU München, Munich, Germany
| | - Kristina Adorjan
- Department of Psychiatry and Psychotherapy, University Hospital, LMU München, Munich, Germany
| | - Veit Hornung
- Department of Biochemistry and Gene Center, LMU München, Munich, Germany
| | - Lars Kaderali
- Institute of Bioinformatics, University Medicine Greifswald, Greifswald, Germany
| | - Matthias Klein
- Emergency Department and Department of Neurology, University Hospital, LMU München, Munich, Germany
| | - Oliver T Keppler
- Faculty of Medicine, National Reference Center for Retroviruses, Max Von Pettenkofer Institute and Gene Center, Virology, LMU München, Munich, Germany.
- German Center for Infection Research (DZIF), Partner site, Munich, Germany.
| |
Collapse
|
34
|
Friedrich S, Groß S, König IR, Engelhardt S, Bahls M, Heinz J, Huber C, Kaderali L, Kelm M, Leha A, Rühl J, Schaller J, Scherer C, Vollmer M, Seidler T, Friede T. Applications of artificial intelligence/machine learning approaches in cardiovascular medicine: a systematic review with recommendations. Eur Heart J Digit Health 2021; 2:424-436. [PMID: 36713608 PMCID: PMC9707954 DOI: 10.1093/ehjdh/ztab054] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/05/2021] [Revised: 04/21/2021] [Accepted: 06/07/2021] [Indexed: 02/01/2023]
Abstract
Aims Artificial intelligence (AI) and machine learning (ML) promise vast advances in medicine. The current state of AI/ML applications in cardiovascular medicine is largely unknown. This systematic review aims to close this gap and provides recommendations for future applications. Methods and results Pubmed and EMBASE were searched for applied publications using AI/ML approaches in cardiovascular medicine without limitations regarding study design or study population. The PRISMA statement was followed in this review. A total of 215 studies were identified and included in the final analysis. The majority (87%) of methods applied belong to the context of supervised learning. Within this group, tree-based methods were most commonly used, followed by network and regression analyses as well as boosting approaches. Concerning the areas of application, the most common disease context was coronary artery disease followed by heart failure and heart rhythm disorders. Often, different input types such as electronic health records and images were combined in one AI/ML application. Only a minority of publications investigated reproducibility and generalizability or provided a clinical trial registration. Conclusions A major finding is that methodology may overlap even with similar data. Since we observed marked variation in quality, reporting of the evaluation and transparency of data and methods urgently need to be improved.
Collapse
Affiliation(s)
- Sarah Friedrich
- Department of Medical Statistics, University Medical Center Göttingen, Humboldtallee 32, 37073 Göttingen, Germany,Corresponding author. Tel: +0049-551-3964064,
| | - Stefan Groß
- Department of Internal Medicine B, University Medicine Greifswald, Ferdinand-Sauerbruch-Straße, 17475 Greifswald, Germany,DZHK (German Centre for Cardiovascular Research), Partner Site Greifswald, Greifswald, Germany
| | - Inke R König
- Institute of Medical Biometry and Statistics, University of Lübeck, University Medical Center Schleswig-Holstein, Campus Lübeck, Ratzeburger Allee 160, 23562 Lübeck, Germany,DZHK (German Centre for Cardiovascular Research), Partner Site Hamburg/Kiel/Lübeck, Lübeck, Germany
| | - Sandy Engelhardt
- Department of Internal Medicine III, University Hospital Heidelberg, Im Neuenheimer Feld 420, 69120 Heidelberg, Germany,DZHK (German Centre for Cardiovascular Research), Partner Site Mannheim/Heidelberg, Heidelberg, Germany,Informatics for Life, Heidelberg, Germany
| | - Martin Bahls
- Department of Internal Medicine B, University Medicine Greifswald, Ferdinand-Sauerbruch-Straße, 17475 Greifswald, Germany,DZHK (German Centre for Cardiovascular Research), Partner Site Greifswald, Greifswald, Germany
| | - Judith Heinz
- Department of Medical Statistics, University Medical Center Göttingen, Humboldtallee 32, 37073 Göttingen, Germany
| | - Cynthia Huber
- Department of Medical Statistics, University Medical Center Göttingen, Humboldtallee 32, 37073 Göttingen, Germany
| | - Lars Kaderali
- DZHK (German Centre for Cardiovascular Research), Partner Site Greifswald, Greifswald, Germany,Institute of Bioinformatics, University Medicine Greifswald, Felix-Hausdorff-Str. 8, 17475 Greifswald, Germany
| | - Marcus Kelm
- Institute for Imaging Science and Computational Modelling in Cardiovascular Medicine, Charité Universitätsmedizin Berlin, Augustenburger Platz 1, 13353 Berlin, Germany,Department of Congenital Heart Disease, Deutsches Herzzentrum Berlin (DHZB), Berlin, Germany,Berlin Institute of Health (BIH), Anna-Louisa-Karsch-Str. 2, 10178 Berlin, Germany,DZHK (German Centre for Cardiovascular Research), Partner Site Berlin, Berlin, Germany
| | - Andreas Leha
- Department of Medical Statistics, University Medical Center Göttingen, Humboldtallee 32, 37073 Göttingen, Germany,DZHK (German Centre for Cardiovascular Research), Partner Site Göttingen, Göttingen, Germany
| | - Jasmin Rühl
- Department of Medical Statistics, University Medical Center Göttingen, Humboldtallee 32, 37073 Göttingen, Germany
| | - Jens Schaller
- Institute for Imaging Science and Computational Modelling in Cardiovascular Medicine, Charité Universitätsmedizin Berlin, Augustenburger Platz 1, 13353 Berlin, Germany,DZHK (German Centre for Cardiovascular Research), Partner Site Berlin, Berlin, Germany
| | - Clemens Scherer
- Department of Medicine I, University Hospital, LMU Munich, Marchioninistr. 15, 81377 München, Germany,DZHK (German Centre for Cardiovascular Research), Partner Site Munich, Munich, Germany
| | - Marcus Vollmer
- DZHK (German Centre for Cardiovascular Research), Partner Site Greifswald, Greifswald, Germany,Institute of Bioinformatics, University Medicine Greifswald, Felix-Hausdorff-Str. 8, 17475 Greifswald, Germany
| | - Tim Seidler
- DZHK (German Centre for Cardiovascular Research), Partner Site Göttingen, Göttingen, Germany,Clinic for Cardiology and Pneumology, University Medical Center Göttingen, Göttingen, Germany
| | - Tim Friede
- Department of Medical Statistics, University Medical Center Göttingen, Humboldtallee 32, 37073 Göttingen, Germany,DZHK (German Centre for Cardiovascular Research), Partner Site Göttingen, Göttingen, Germany
| |
Collapse
|
35
|
Trump S, Lukassen S, Anker MS, Chua RL, Liebig J, Thürmann L, Corman VM, Binder M, Loske J, Klasa C, Krieger T, Hennig BP, Messingschlager M, Pott F, Kazmierski J, Twardziok S, Albrecht JP, Eils J, Hadzibegovic S, Lena A, Heidecker B, Bürgel T, Steinfeldt J, Goffinet C, Kurth F, Witzenrath M, Völker MT, Müller SD, Liebert UG, Ishaque N, Kaderali L, Sander LE, Drosten C, Laudi S, Eils R, Conrad C, Landmesser U, Lehmann I. Hypertension delays viral clearance and exacerbates airway hyperinflammation in patients with COVID-19. Nat Biotechnol 2021; 39:705-716. [PMID: 33361824 DOI: 10.1038/s41587-020-00796-1] [Citation(s) in RCA: 109] [Impact Index Per Article: 36.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2020] [Accepted: 12/11/2020] [Indexed: 01/29/2023]
Abstract
In coronavirus disease 2019 (COVID-19), hypertension and cardiovascular diseases are major risk factors for critical disease progression. However, the underlying causes and the effects of the main anti-hypertensive therapies-angiotensin-converting enzyme inhibitors (ACEIs) and angiotensin receptor blockers (ARBs)-remain unclear. Combining clinical data (n = 144) and single-cell sequencing data of airway samples (n = 48) with in vitro experiments, we observed a distinct inflammatory predisposition of immune cells in patients with hypertension that correlated with critical COVID-19 progression. ACEI treatment was associated with dampened COVID-19-related hyperinflammation and with increased cell intrinsic antiviral responses, whereas ARB treatment related to enhanced epithelial-immune cell interactions. Macrophages and neutrophils of patients with hypertension, in particular under ARB treatment, exhibited higher expression of the pro-inflammatory cytokines CCL3 and CCL4 and the chemokine receptor CCR1. Although the limited size of our cohort does not allow us to establish clinical efficacy, our data suggest that the clinical benefits of ACEI treatment in patients with COVID-19 who have hypertension warrant further investigation.
Collapse
Affiliation(s)
- Saskia Trump
- Molecular Epidemiology Unit, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health (BIH), Berlin, Germany
| | - Soeren Lukassen
- Center for Digital Health, Berlin Institute of Health (BIH) and Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Markus S Anker
- Department of Cardiology, Campus Benjamin Franklin, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health (BIH), Berlin, Germany.,Division of Cardiology and Metabolism, Department of Cardiology Campus Virchow, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health (BIH), Berlin, Germany.,Centre for Cardiovascular Research (DZHK), Berlin, Germany.,Berlin Institute of Health Center for Regenerative Therapies (BCRT), Berlin, Germany
| | - Robert Lorenz Chua
- Center for Digital Health, Berlin Institute of Health (BIH) and Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Johannes Liebig
- Center for Digital Health, Berlin Institute of Health (BIH) and Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Loreen Thürmann
- Molecular Epidemiology Unit, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health (BIH), Berlin, Germany
| | - Victor Max Corman
- Institute of Virology, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health (BIH), Berlin, Germany
| | - Marco Binder
- Research group 'Dynamics of early viral infection and the innate antiviral response' (division F170), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Jennifer Loske
- Molecular Epidemiology Unit, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health (BIH), Berlin, Germany
| | - Christina Klasa
- Institute for Bioinformatics, University Medicine Greifswald, Greifswald, Germany
| | - Teresa Krieger
- Center for Digital Health, Berlin Institute of Health (BIH) and Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Bianca P Hennig
- Center for Digital Health, Berlin Institute of Health (BIH) and Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Marey Messingschlager
- Molecular Epidemiology Unit, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health (BIH), Berlin, Germany
| | - Fabian Pott
- Institute of Virology, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health (BIH), Berlin, Germany.,Berlin Institute of Health (BIH), Berlin, Germany
| | - Julia Kazmierski
- Institute of Virology, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health (BIH), Berlin, Germany.,Berlin Institute of Health (BIH), Berlin, Germany
| | - Sven Twardziok
- Center for Digital Health, Berlin Institute of Health (BIH) and Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Jan Philipp Albrecht
- Center for Digital Health, Berlin Institute of Health (BIH) and Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Jürgen Eils
- Center for Digital Health, Berlin Institute of Health (BIH) and Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Sara Hadzibegovic
- Department of Cardiology, Campus Benjamin Franklin, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health (BIH), Berlin, Germany.,Division of Cardiology and Metabolism, Department of Cardiology Campus Virchow, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health (BIH), Berlin, Germany.,Centre for Cardiovascular Research (DZHK), Berlin, Germany.,Berlin Institute of Health Center for Regenerative Therapies (BCRT), Berlin, Germany
| | - Alessia Lena
- Department of Cardiology, Campus Benjamin Franklin, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health (BIH), Berlin, Germany.,Division of Cardiology and Metabolism, Department of Cardiology Campus Virchow, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health (BIH), Berlin, Germany.,Centre for Cardiovascular Research (DZHK), Berlin, Germany.,Berlin Institute of Health Center for Regenerative Therapies (BCRT), Berlin, Germany
| | - Bettina Heidecker
- Department of Cardiology, Campus Benjamin Franklin, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health (BIH), Berlin, Germany
| | - Thore Bürgel
- Center for Digital Health, Berlin Institute of Health (BIH) and Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Jakob Steinfeldt
- Department of Cardiology, Campus Benjamin Franklin, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health (BIH), Berlin, Germany
| | - Christine Goffinet
- Institute of Virology, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health (BIH), Berlin, Germany.,Berlin Institute of Health (BIH), Berlin, Germany
| | - Florian Kurth
- Department of Infectious Diseases and Respiratory Medicine, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health (BIH), Berlin, Germany.,Department of Tropical Medicine, Bernhard Nocht Institute for Tropical Medicine & I. Department of Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Martin Witzenrath
- Department of Infectious Diseases and Respiratory Medicine, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health (BIH), Berlin, Germany
| | - Maria Theresa Völker
- Department of Anesthesiology and Intensive Care, University Hospital Leipzig, Leipzig, Germany
| | - Sarah Dorothea Müller
- Department of Anesthesiology and Intensive Care, University Hospital Leipzig, Leipzig, Germany
| | - Uwe Gerd Liebert
- Institute of Virology, University Hospital Leipzig, Leipzig, Germany
| | - Naveed Ishaque
- Center for Digital Health, Berlin Institute of Health (BIH) and Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Lars Kaderali
- Institute for Bioinformatics, University Medicine Greifswald, Greifswald, Germany
| | - Leif-Erik Sander
- Department of Infectious Diseases and Respiratory Medicine, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health (BIH), Berlin, Germany
| | - Christian Drosten
- Institute of Virology, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health (BIH), Berlin, Germany
| | - Sven Laudi
- Department of Anesthesiology and Intensive Care, University Hospital Leipzig, Leipzig, Germany.
| | - Roland Eils
- Center for Digital Health, Berlin Institute of Health (BIH) and Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Berlin, Germany. .,German Center for Lung Research (DZL), Berlin, Germany. .,Health Data Science Unit, Medical Faculty and BioQuant, University of Heidelberg, Heidelberg, Germany.
| | - Christian Conrad
- Center for Digital Health, Berlin Institute of Health (BIH) and Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Berlin, Germany.
| | - Ulf Landmesser
- Department of Cardiology, Campus Benjamin Franklin, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health (BIH), Berlin, Germany.
| | - Irina Lehmann
- Molecular Epidemiology Unit, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health (BIH), Berlin, Germany. .,German Center for Lung Research (DZL), Berlin, Germany.
| |
Collapse
|
36
|
Holzscheck N, Falckenhayn C, Söhle J, Kristof B, Siegner R, Werner A, Schössow J, Jürgens C, Völzke H, Wenck H, Winnefeld M, Grönniger E, Kaderali L. Modeling transcriptomic age using knowledge-primed artificial neural networks. NPJ Aging Mech Dis 2021; 7:15. [PMID: 34075044 PMCID: PMC8169742 DOI: 10.1038/s41514-021-00068-5] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [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: 08/12/2020] [Accepted: 04/26/2021] [Indexed: 02/04/2023] Open
Abstract
The development of 'age clocks', machine learning models predicting age from biological data, has been a major milestone in the search for reliable markers of biological age and has since become an invaluable tool in aging research. However, beyond their unquestionable utility, current clocks offer little insight into the molecular biological processes driving aging, and their inner workings often remain non-transparent. Here we propose a new type of age clock, one that couples predictivity with interpretability of the underlying biology, achieved through the incorporation of prior knowledge into the model design. The clock, an artificial neural network constructed according to well-described biological pathways, allows the prediction of age from gene expression data of skin tissue with high accuracy, while at the same time capturing and revealing aging states of the pathways driving the prediction. The model recapitulates known associations of aging gene knockdowns in simulation experiments and demonstrates its utility in deciphering the main pathways by which accelerated aging conditions such as Hutchinson-Gilford progeria syndrome, as well as pro-longevity interventions like caloric restriction, exert their effects.
Collapse
Affiliation(s)
- Nicholas Holzscheck
- grid.432589.10000 0001 2201 4639Front End Innovation, Beiersdorf AG, Hamburg, Germany ,grid.5603.0Institute for Bioinformatics, University Medicine Greifswald, Greifswald, Germany
| | - Cassandra Falckenhayn
- grid.432589.10000 0001 2201 4639Front End Innovation, Beiersdorf AG, Hamburg, Germany
| | - Jörn Söhle
- grid.432589.10000 0001 2201 4639Front End Innovation, Beiersdorf AG, Hamburg, Germany
| | - Boris Kristof
- grid.432589.10000 0001 2201 4639Front End Innovation, Beiersdorf AG, Hamburg, Germany
| | - Ralf Siegner
- grid.432589.10000 0001 2201 4639Front End Innovation, Beiersdorf AG, Hamburg, Germany
| | - André Werner
- grid.5603.0Institute for Community Medicine, University Medicine Greifswald, Greifswald, Germany
| | - Janka Schössow
- grid.5603.0Institute for Community Medicine, University Medicine Greifswald, Greifswald, Germany
| | - Clemens Jürgens
- grid.5603.0Institute for Community Medicine, University Medicine Greifswald, Greifswald, Germany
| | - Henry Völzke
- grid.5603.0Institute for Community Medicine, University Medicine Greifswald, Greifswald, Germany
| | - Horst Wenck
- grid.432589.10000 0001 2201 4639Front End Innovation, Beiersdorf AG, Hamburg, Germany
| | - Marc Winnefeld
- grid.432589.10000 0001 2201 4639Front End Innovation, Beiersdorf AG, Hamburg, Germany
| | - Elke Grönniger
- grid.432589.10000 0001 2201 4639Front End Innovation, Beiersdorf AG, Hamburg, Germany
| | - Lars Kaderali
- grid.5603.0Institute for Bioinformatics, University Medicine Greifswald, Greifswald, Germany
| |
Collapse
|
37
|
Lange T, Kuhn L, Böttcher MC, Simm S, Hammer E, Kaderali L, Völker U, Weber C, Endlich K, Endlich N. MO081THE INFLUENCE OF VITAMIN D3 ON PODOCYTE DIFFERENTIATION IN SITU AND IN VITRO. Nephrol Dial Transplant 2021. [DOI: 10.1093/ndt/gfab078.0017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Abstract
Background and Aims
Dedifferentiation of podocytes affects their complex 3 D morphology and is the main initiator for the development of chronic kidney disease (CKD). Unfortunately, there is no causal therapy for CKD until today. Thus, inadequate and late treatment lead to end-stage renal disease which subsequently makes renal replacement therapy inevitable. To address this, new treatment options are of high significance for CKD patients. Recently, vitamin D3 (VitD) became a promising candidate, but it is controversially discussed. In the present study, we investigated the influence of VitD on podocyte differentiation and the related pathways in situ and in vitro.
Method
We combined a podocyte dedifferentiation model (GlomAssay) with an automated imaging procedure (Aquifer Imaging Machine). We analyzed cultured glomeruli from transgenic mice expressing cyan-fluorescent protein (CFP) under the control of the nephrin promoter which were treated with VitD and its` analogue (calcipotriol). In this model, the decreasing CFP fluorescence is as a read out for podocyte (de)differentiation. Additionally, VitD-, calcipotriol- and VitD receptor (VDR) inhibitor (PS121912)-treated glomeruli were investigated by RNA-Seq and LC-MS/MS to reveal the molecular effects of VitD on podocyte differentiation. Furthermore, we treated cultured murine podocytes with VitD, calcipotriol and PS121912 to elucidate the morphological and molecular changes by immunofluorescence staining, RT-qPCR and Western blot.
Results
VitD- and calcipotriol-treated glomeruli showed a significantly higher intensity of CFP fluorescence after 9 days, indicating higher level of nephrin compared to the control. This was verified by RT-qPCR and Western blot for nephrin and CFP. Additionally, we found an upregulation of VDR in VitD- and calcipotriol-treated glomeruli compared to controls. By transcriptomic and proteomic analysis, we identified molecular patterns that are specific for the different treated groups. Thus, we observed differential gene expression in VitD- and Wnt-signaling pathway as well as regulated genes that are essential for the actin cytoskeleton, focal adhesion formation and the slit membrane. Beside this, cultured podocytes showed a significant upregulation of the slit membrane protein nephrin, VDR and CYP24A1 by VitD. This is accompanied by an altered morphology of the podocytes due to a reorganization of the actin cytoskeleton.
Conclusion
Our results show that VitD influences podocyte differentiation in situ and in vitro by the regulation of specific signaling pathways.
Collapse
Affiliation(s)
- Tim Lange
- Department of Anatomy and Cell Biology, University Medicine Greifswald, Greifswald, Germany
| | - Laura Kuhn
- Department of Anatomy and Cell Biology, University Medicine Greifswald, Greifswald, Germany
| | | | - Stefan Simm
- Institute of Bioinformatics, University Medicine Greifswald, Greifswald, Germany
| | - Elke Hammer
- Interfaculty Institute for Genetics and Functional Genomics, University Medicine Greifswald, Greifswald, Germany
| | - Lars Kaderali
- Institute of Bioinformatics, University Medicine Greifswald, Greifswald, Germany
| | - Uwe Völker
- Interfaculty Institute for Genetics and Functional Genomics, University Medicine Greifswald, Greifswald, Germany
| | - Claudia Weber
- Department of Anatomy and Cell Biology, University Medicine Greifswald, Greifswald, Germany
| | - Karlhans Endlich
- Department of Anatomy and Cell Biology, University Medicine Greifswald, Greifswald, Germany
| | - Nicole Endlich
- Department of Anatomy and Cell Biology, University Medicine Greifswald, Greifswald, Germany
| |
Collapse
|
38
|
Goettsch W, Beerenwinkel N, Deng L, Dölken L, Dutilh BE, Erhard F, Kaderali L, von Kleist M, Marquet R, Matthijnssens J, McCallin S, McMahon D, Rattei T, Van Rij RP, Robertson DL, Schwemmle M, Stern-Ginossar N, Marz M. ITN-VIROINF: Understanding (Harmful) Virus-Host Interactions by Linking Virology and Bioinformatics. Viruses 2021; 13:v13050766. [PMID: 33925452 PMCID: PMC8145447 DOI: 10.3390/v13050766] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [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: 03/05/2021] [Revised: 04/15/2021] [Accepted: 04/22/2021] [Indexed: 11/16/2022] Open
Abstract
Many recent studies highlight the fundamental importance of viruses. Besides their important role as human and animal pathogens, their beneficial, commensal or harmful functions are poorly understood. By developing and applying tailored bioinformatical tools in important virological models, the Marie Skłodowska-Curie Initiative International Training Network VIROINF will provide a better understanding of viruses and the interaction with their hosts. This will open the door to validate methods of improving viral growth, morphogenesis and development, as well as to control strategies against unwanted microorganisms. The key feature of VIROINF is its interdisciplinary nature, which brings together virologists and bioinformaticians to achieve common goals.
Collapse
Affiliation(s)
- Winfried Goettsch
- RNA Bioinformatics and High-Throughput Analysis, Friedrich Schiller University, 07743 Jena, Germany;
| | - Niko Beerenwinkel
- Department of Biosystems Science and Engineering, ETH Zurich, Mattenstrasse 26, 4058 Basel, Switzerland;
| | - Li Deng
- Institute of Virology, Helmholtz Centre Munich and Technical University Munich, Ingolstädter Landstraße 1, 85764 Neuherberg, Germany;
| | - Lars Dölken
- Institut für Virologie und Immunbiologie, Julius-Maximilians-Universität Würzburg, 97078 Würzburg, Germany; (L.D.); (F.E.)
| | - Bas E. Dutilh
- Theoretical Biology and Bioinformatics, Science for Life, Utrecht University, Hugo R. Kruytgebouw, Padualaan 8, 3584 CH Utrecht, The Netherlands;
| | - Florian Erhard
- Institut für Virologie und Immunbiologie, Julius-Maximilians-Universität Würzburg, 97078 Würzburg, Germany; (L.D.); (F.E.)
| | - Lars Kaderali
- Institute of Bioinformatics, University Medicine Greifswald, 17475 Greifswald, Germany;
| | - Max von Kleist
- MF1 Bioinformatics, Robert Koch-Institute, 13353 Berlin, Germany;
| | - Roland Marquet
- CNRS, Architecture et Réactivité de l’ARN, Université de Strasbourg, UPR 9002 Strasbourg, France;
| | - Jelle Matthijnssens
- Department of Microbiology and Immunology, Katholieke Universiteit Leuven, Herestraat 49 Box 1040, 3000 Leuven, Belgium;
| | - Shawna McCallin
- Department of Neuro-Urology, Balgrist University Hospital, University of Zürich, Forchstrasse 340, 8008 Zürich, Switzerland;
| | - Dino McMahon
- Institute of Biology, Freie Universität Berlin, Schwendenerstr. 1, 14195 Berlin, Germany;
| | - Thomas Rattei
- Division of Computational Systems Biology, Centre for Microbiology and Environmental Systems Science, University of Vienna, Althanstraße 14, 1090 Vienna, Austria;
| | - Ronald P. Van Rij
- Department of Medical Microbiology, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, P.O. Box 9101, 6500 HB Nijmegen, The Netherlands;
| | - David L. Robertson
- MRC, University of Glasgow Centre for Virus Research (CVR), 464 Bearsden Road, Glasgow G61 1QH, UK;
| | - Martin Schwemmle
- Institute of Virology, Medical Center—University of Freiburg, Hermann-Herder-Strasse 11, 79104 Freiburg, Germany;
| | - Noam Stern-Ginossar
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 7610001, Israel;
| | - Manja Marz
- RNA Bioinformatics and High-Throughput Analysis, Friedrich Schiller University, 07743 Jena, Germany;
- FLI Leibniz Institute for Age Research, 07745 Jena, Germany
- Correspondence: ; Tel.: +49-3641-9-46480
| |
Collapse
|
39
|
Hufsky F, Lamkiewicz K, Almeida A, Aouacheria A, Arighi C, Bateman A, Baumbach J, Beerenwinkel N, Brandt C, Cacciabue M, Chuguransky S, Drechsel O, Finn RD, Fritz A, Fuchs S, Hattab G, Hauschild AC, Heider D, Hoffmann M, Hölzer M, Hoops S, Kaderali L, Kalvari I, von Kleist M, Kmiecinski R, Kühnert D, Lasso G, Libin P, List M, Löchel HF, Martin MJ, Martin R, Matschinske J, McHardy AC, Mendes P, Mistry J, Navratil V, Nawrocki EP, O’Toole ÁN, Ontiveros-Palacios N, Petrov AI, Rangel-Pineros G, Redaschi N, Reimering S, Reinert K, Reyes A, Richardson L, Robertson DL, Sadegh S, Singer JB, Theys K, Upton C, Welzel M, Williams L, Marz M. Computational strategies to combat COVID-19: useful tools to accelerate SARS-CoV-2 and coronavirus research. Brief Bioinform 2021; 22:642-663. [PMID: 33147627 PMCID: PMC7665365 DOI: 10.1093/bib/bbaa232] [Citation(s) in RCA: 81] [Impact Index Per Article: 27.0] [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: 05/27/2020] [Revised: 07/28/2020] [Accepted: 08/26/2020] [Indexed: 12/16/2022] Open
Abstract
SARS-CoV-2 (severe acute respiratory syndrome coronavirus 2) is a novel virus of the family Coronaviridae. The virus causes the infectious disease COVID-19. The biology of coronaviruses has been studied for many years. However, bioinformatics tools designed explicitly for SARS-CoV-2 have only recently been developed as a rapid reaction to the need for fast detection, understanding and treatment of COVID-19. To control the ongoing COVID-19 pandemic, it is of utmost importance to get insight into the evolution and pathogenesis of the virus. In this review, we cover bioinformatics workflows and tools for the routine detection of SARS-CoV-2 infection, the reliable analysis of sequencing data, the tracking of the COVID-19 pandemic and evaluation of containment measures, the study of coronavirus evolution, the discovery of potential drug targets and development of therapeutic strategies. For each tool, we briefly describe its use case and how it advances research specifically for SARS-CoV-2. All tools are free to use and available online, either through web applications or public code repositories. Contact:evbc@unj-jena.de.
Collapse
Affiliation(s)
| | | | | | | | | | | | | | | | - Christian Brandt
- Institute of Infectious Disease and Infection Control at Jena University Hospital, Germany
| | - Marco Cacciabue
- Consejo Nacional de Investigaciones Científicas y Tócnicas (CONICET) working on FMDV virology at the Instituto de Agrobiotecnología y Biología Molecular (IABiMo, INTA-CONICET) and at the Departamento de Ciencias Básicas, Universidad Nacional de Luján (UNLu), Argentina
| | | | - Oliver Drechsel
- bioinformatics department at the Robert Koch-Institute, Germany
| | | | - Adrian Fritz
- Computational Biology of Infection Research group of Alice C. McHardy at the Helmholtz Centre for Infection Research, Germany
| | - Stephan Fuchs
- bioinformatics department at the Robert Koch-Institute, Germany
| | - Georges Hattab
- Bioinformatics Division at Philipps-University Marburg, Germany
| | | | - Dominik Heider
- Data Science in Biomedicine at the Philipps-University of Marburg, Germany
| | | | | | - Stefan Hoops
- Biocomplexity Institute and Initiative at the University of Virginia, USA
| | - Lars Kaderali
- Bioinformatics and head of the Institute of Bioinformatics at University Medicine Greifswald, Germany
| | | | - Max von Kleist
- bioinformatics department at the Robert Koch-Institute, Germany
| | - Renó Kmiecinski
- bioinformatics department at the Robert Koch-Institute, Germany
| | | | - Gorka Lasso
- Chandran Lab, Albert Einstein College of Medicine, USA
| | | | | | | | | | | | | | - Alice C McHardy
- Computational Biology of Infection Research Lab at the Helmholtz Centre for Infection Research in Braunschweig, Germany
| | - Pedro Mendes
- Center for Quantitative Medicine of the University of Connecticut School of Medicine, USA
| | | | - Vincent Navratil
- Bioinformatics and Systems Biology at the Rhône Alpes Bioinformatics core facility, Universitó de Lyon, France
| | | | | | | | | | | | - Nicole Redaschi
- Development of the Swiss-Prot group at the SIB for UniProt and SIB resources that cover viral biology (ViralZone)
| | - Susanne Reimering
- Computational Biology of Infection Research group of Alice C. McHardy at the Helmholtz Centre for Infection Research
| | | | | | | | | | - Sepideh Sadegh
- Chair of Experimental Bioinformatics at Technical University of Munich, Germany
| | - Joshua B Singer
- MRC-University of Glasgow Centre for Virus Research, Glasgow, Scotland, UK
| | | | - Chris Upton
- Department of Biochemistry and Microbiology, University of Victoria, Canada
| | | | | | - Manja Marz
- Friedrich Schiller University Jena, Germany
| |
Collapse
|
40
|
Becker AK, Dörr M, Felix SB, Frost F, Grabe HJ, Lerch MM, Nauck M, Völker U, Völzke H, Kaderali L. From heterogeneous healthcare data to disease-specific biomarker networks: A hierarchical Bayesian network approach. PLoS Comput Biol 2021; 17:e1008735. [PMID: 33577591 PMCID: PMC7906470 DOI: 10.1371/journal.pcbi.1008735] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2020] [Revised: 02/25/2021] [Accepted: 01/22/2021] [Indexed: 01/26/2023] Open
Abstract
In this work, we introduce an entirely data-driven and automated approach to reveal disease-associated biomarker and risk factor networks from heterogeneous and high-dimensional healthcare data. Our workflow is based on Bayesian networks, which are a popular tool for analyzing the interplay of biomarkers. Usually, data require extensive manual preprocessing and dimension reduction to allow for effective learning of Bayesian networks. For heterogeneous data, this preprocessing is hard to automatize and typically requires domain-specific prior knowledge. We here combine Bayesian network learning with hierarchical variable clustering in order to detect groups of similar features and learn interactions between them entirely automated. We present an optimization algorithm for the adaptive refinement of such group Bayesian networks to account for a specific target variable, like a disease. The combination of Bayesian networks, clustering, and refinement yields low-dimensional but disease-specific interaction networks. These networks provide easily interpretable, yet accurate models of biomarker interdependencies. We test our method extensively on simulated data, as well as on data from the Study of Health in Pomerania (SHIP-TREND), and demonstrate its effectiveness using non-alcoholic fatty liver disease and hypertension as examples. We show that the group network models outperform available biomarker scores, while at the same time, they provide an easily interpretable interaction network. High-dimensional and heterogeneous healthcare data, such as electronic health records or epidemiological study data, contain much information on yet unknown risk factors that are associated with disease development. The identification of these risk factors may help to improve prevention, diagnosis, and therapy. Bayesian networks are powerful statistical models that can decipher these complex relationships. However, high dimensionality and heterogeneity of data, together with missing values and high feature correlation, make it difficult to automatically learn a good model from data. To facilitate the use of network models, we present a novel, fully automated workflow that combines network learning with hierarchical clustering. The algorithm reveals groups of strongly related features and models the interactions among those groups. It results in simpler network models that are easier to analyze. We introduce a method of adaptive refinement of such models to ensure that disease-relevant parts of the network are modeled in great detail. Our approach makes it easy to learn compact, accurate, and easily interpretable biomarker interaction networks. We test our method extensively on simulated data as well as data from the Study of Health in Pomerania (SHIP-Trend) by learning models of hypertension and non-alcoholic fatty liver disease.
Collapse
Affiliation(s)
- Ann-Kristin Becker
- Institute of Bioinformatics, University Medicine Greifswald, Greifswald, Germany
| | - Marcus Dörr
- Department of Internal Medicine B, University Medicine Greifswald, Greifswald, Germany
- German Centre for Cardiovascular Research (DZHK), partner site Greifswald, Greifswald, Germany
| | - Stephan B. Felix
- Department of Internal Medicine B, University Medicine Greifswald, Greifswald, Germany
- German Centre for Cardiovascular Research (DZHK), partner site Greifswald, Greifswald, Germany
| | - Fabian Frost
- Department of Internal Medicine A, University Medicine Greifswald, Greifswald, Germany
| | - Hans J. Grabe
- Department of Psychiatry, University Medicine Greifswald, Greifswald, Germany
| | - Markus M. Lerch
- Department of Internal Medicine A, University Medicine Greifswald, Greifswald, Germany
| | - Matthias Nauck
- Institute of Clinical Chemistry and Laboratory Medicine, University Medicine Greifswald, Greifswald, Germany
| | - Uwe Völker
- Interfaculty Institute of Genetics and Functional Genomics, Department of Functional Genomics, University Medicine Greifswald, Greifswald, Germany
| | - Henry Völzke
- Institute of Community Medicine, SHIP/KEF, University Medicine Greifswald, Greifswald, Germany
| | - Lars Kaderali
- Institute of Bioinformatics, University Medicine Greifswald, Greifswald, Germany
- * E-mail:
| |
Collapse
|
41
|
Rüdebusch J, Benkner A, Nath N, Fleuch L, Kaderali L, Grube K, Klingel K, Eckstein G, Meitinger T, Fielitz J, Felix SB. Stimulation of soluble guanylyl cyclase (sGC) by riociguat attenuates heart failure and pathological cardiac remodelling. Br J Pharmacol 2020; 179:2430-2442. [PMID: 33247945 DOI: 10.1111/bph.15333] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2020] [Revised: 10/16/2020] [Accepted: 11/17/2020] [Indexed: 12/22/2022] Open
Abstract
BACKGROUND AND PURPOSE Heart failure is associated with an impaired NO-soluble guanylyl cyclase (sGC)-cGMP pathway and its augmentation is thought to be beneficial for its therapy. We hypothesized that stimulation of sGC by the sGC stimulator riociguat prevents pathological cardiac remodelling and heart failure in response to chronic pressure overload. EXPERIMENTAL APPROACH Transverse aortic constriction or sham surgery was performed in C57BL/6N mice. After 3 weeks of transverse aortic constriction when heart failure was established, animals receive either riociguat or its vehicle for 5 additional weeks. Cardiac function was evaluated weekly by echocardiography. Eight weeks after surgery, histological analyses were performed to evaluate remodelling and the transcriptome of the left ventricles (LVs) was analysed by RNA sequencing. Cell culture experiments were used for mechanistically studies. KEY RESULTS Transverse aortic constriction resulted in a continuous decrease of LV ejection fraction and an increase in LV mass until week 3. Five weeks of riociguat treatment resulted in an improved LV ejection fraction and a decrease in the ratio of left ventricular mass to total body weight (LVM/BW), myocardial fibrosis and myocyte cross-sectional area. RNA sequencing revealed that riociguat reduced the expression of myocardial stress and remodelling genes (e.g. Nppa, Nppb, Myh7 and collagen) and attenuated the activation of biological pathways associated with cardiac hypertrophy and heart failure. Riociguat reversed pathological stress response in cultivated myocytes and fibroblasts. CONCLUSION AND IMPLICATIONS Stimulation of the sGC reverses transverse aortic constriction-induced heart failure and remodelling, which is associated with improved myocardial gene expression.
Collapse
Affiliation(s)
- Julia Rüdebusch
- Department of Internal Medicine B, University Medicine Greifswald, Greifswald, Germany.,DZHK (German Centre for Cardiovascular Research, partner site Greifswald), Greifswald, Germany
| | - Alexander Benkner
- Department of Internal Medicine B, University Medicine Greifswald, Greifswald, Germany.,DZHK (German Centre for Cardiovascular Research, partner site Greifswald), Greifswald, Germany
| | - Neetika Nath
- Institute of Bioinformatics, University Medicine Greifswald, Greifswald, Germany
| | - Lina Fleuch
- Department of Internal Medicine B, University Medicine Greifswald, Greifswald, Germany.,DZHK (German Centre for Cardiovascular Research, partner site Greifswald), Greifswald, Germany
| | - Lars Kaderali
- DZHK (German Centre for Cardiovascular Research, partner site Greifswald), Greifswald, Germany.,Institute of Bioinformatics, University Medicine Greifswald, Greifswald, Germany
| | - Karina Grube
- Department of Internal Medicine B, University Medicine Greifswald, Greifswald, Germany.,DZHK (German Centre for Cardiovascular Research, partner site Greifswald), Greifswald, Germany
| | - Karin Klingel
- Cardiopathology, Institute for Pathology, University Hospital Tübingen, Tübingen, Germany
| | - Gertrud Eckstein
- Institute of Human Genetics, Helmholtz Zentrum München, Neuherberg, Germany
| | - Thomas Meitinger
- Institute of Human Genetics, Helmholtz Zentrum München, Neuherberg, Germany
| | - Jens Fielitz
- Department of Internal Medicine B, University Medicine Greifswald, Greifswald, Germany.,DZHK (German Centre for Cardiovascular Research, partner site Greifswald), Greifswald, Germany
| | - Stephan B Felix
- Department of Internal Medicine B, University Medicine Greifswald, Greifswald, Germany.,DZHK (German Centre for Cardiovascular Research, partner site Greifswald), Greifswald, Germany
| |
Collapse
|
42
|
Zitzmann C, Kaderali L, Perelson AS. Mathematical modeling of hepatitis C RNA replication, exosome secretion and virus release. PLoS Comput Biol 2020; 16:e1008421. [PMID: 33151933 PMCID: PMC7671504 DOI: 10.1371/journal.pcbi.1008421] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2020] [Revised: 11/17/2020] [Accepted: 10/06/2020] [Indexed: 01/04/2023] Open
Abstract
Hepatitis C virus (HCV) causes acute hepatitis C and can lead to life-threatening complications if it becomes chronic. The HCV genome is a single plus strand of RNA. Its intracellular replication is a spatiotemporally coordinated process of RNA translation upon cell infection, RNA synthesis within a replication compartment, and virus particle production. While HCV is mainly transmitted via mature infectious virus particles, it has also been suggested that HCV-infected cells can secrete HCV RNA carrying exosomes that can infect cells in a receptor independent manner. In order to gain insight into these two routes of transmission, we developed a series of intracellular HCV replication models that include HCV RNA secretion and/or virus assembly and release. Fitting our models to in vitro data, in which cells were infected with HCV, suggests that initially most secreted HCV RNA derives from intracellular cytosolic plus-strand RNA, but subsequently secreted HCV RNA derives equally from the cytoplasm and the replication compartments. Furthermore, our model fits to the data suggest that the rate of virus assembly and release is limited by host cell resources. Including the effects of direct acting antivirals in our models, we found that in spite of decreasing intracellular HCV RNA and extracellular virus concentration, low level HCV RNA secretion may continue as long as intracellular RNA is available. This may possibly explain the presence of detectable levels of plasma HCV RNA at the end of treatment even in patients that ultimately attain a sustained virologic response. Approximately 70 million people are chronically infected with hepatitis C virus (HCV), which if left untreated may lead to cirrhosis and liver cancer. However, modern drug therapy is highly effective and hepatitis C is the first chronic virus infection that can be cured with short-term therapy in almost all infected individuals. The within-host transmission of HCV occurs mainly via infectious virus particles, but experimental studies suggest that there may be additional receptor-independent cell-to-cell transmission by exosomes that carry the HCV genome. In order to understand the intracellular HCV lifecycle and HCV RNA spread, we developed a series of mathematical models that take both exosomal secretion and viral secretion into account. By fitting these models to in vitro data, we found that secretion of both HCV RNA as well as virus probably occurs and that the rate of virus assembly is likely limited by cellular co-factors on which the virus strongly depends for its own replication. Furthermore, our modeling predicted that the parameters governing the processes in the viral lifecycle that are targeted by direct acting antivirals are the most sensitive to perturbations, which may help explain their ability to cure this infection.
Collapse
Affiliation(s)
- Carolin Zitzmann
- University Medicine Greifswald, Institute of Bioinformatics and Center for Functional Genomics of Microbes, Greifswald, Germany
- Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos, New Mexico, United States of America
| | - Lars Kaderali
- University Medicine Greifswald, Institute of Bioinformatics and Center for Functional Genomics of Microbes, Greifswald, Germany
| | - Alan S. Perelson
- Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos, New Mexico, United States of America
- * E-mail:
| |
Collapse
|
43
|
Palma Medina LM, Becker AK, Michalik S, Surmann K, Hildebrandt P, Gesell Salazar M, Mekonnen SA, Kaderali L, Völker U, van Dijl JM. Interaction of Staphylococcus aureus and Host Cells upon Infection of Bronchial Epithelium during Different Stages of Regeneration. ACS Infect Dis 2020; 6:2279-2290. [PMID: 32579327 PMCID: PMC7432605 DOI: 10.1021/acsinfecdis.0c00403] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [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] [Indexed: 12/12/2022]
Abstract
![]()
The
primary barrier that protects our lungs against infection by
pathogens is a tightly sealed layer of epithelial cells. When the
integrity of this barrier is disrupted as a consequence of chronic
pulmonary diseases or viral insults, bacterial pathogens will gain
access to underlying tissues. A major pathogen that can take advantage
of such conditions is Staphylococcus aureus, thereby
causing severe pneumonia. In this study, we investigated how S. aureus responds to different conditions of the human
epithelium, especially nonpolarization and fibrogenesis during regeneration
using an in vitro infection model. The infective
process was monitored by quantification of the epithelial cell and
bacterial populations, fluorescence microscopy, and mass spectrometry.
The results uncover differences in bacterial internalization and population
dynamics that correlate with the outcome of infection. Protein profiling
reveals that, irrespective of the polarization state of the epithelial
cells, the invading bacteria mount similar responses to adapt to the
intracellular milieu. Remarkably, a bacterial adaptation that was
associated with the regeneration state of the epithelial cells concerned
the early upregulation of proteins controlled by the redox-responsive
regulator Rex when bacteria were confronted with a polarized cell
layer. This is indicative of the modulation of the bacterial cytoplasmic
redox state to maintain homeostasis early during infection even before
internalization. Our present observations provide a deeper insight
into how S. aureus can take advantage of a breached
epithelial barrier and show that infected epithelial cells have limited
ability to respond adequately to staphylococcal insults.
Collapse
Affiliation(s)
- Laura M. Palma Medina
- Interfaculty Institute for Genetics and Functional Genomics, University Medicine Greifswald, 17475 Greifswald, Germany
- University of Groningen, University Medical Center Groningen, Department of Medical Microbiology, 9700 RB Groningen, The Netherlands
| | - Ann-Kristin Becker
- Institute of Bioinformatics, University Medicine Greifswald, 17475 Greifswald, Germany
| | - Stephan Michalik
- Interfaculty Institute for Genetics and Functional Genomics, University Medicine Greifswald, 17475 Greifswald, Germany
| | - Kristin Surmann
- Interfaculty Institute for Genetics and Functional Genomics, University Medicine Greifswald, 17475 Greifswald, Germany
| | - Petra Hildebrandt
- Interfaculty Institute for Genetics and Functional Genomics, University Medicine Greifswald, 17475 Greifswald, Germany
| | - Manuela Gesell Salazar
- Interfaculty Institute for Genetics and Functional Genomics, University Medicine Greifswald, 17475 Greifswald, Germany
| | - Solomon A. Mekonnen
- Interfaculty Institute for Genetics and Functional Genomics, University Medicine Greifswald, 17475 Greifswald, Germany
- University of Groningen, University Medical Center Groningen, Department of Medical Microbiology, 9700 RB Groningen, The Netherlands
| | - Lars Kaderali
- Institute of Bioinformatics, University Medicine Greifswald, 17475 Greifswald, Germany
| | - Uwe Völker
- Interfaculty Institute for Genetics and Functional Genomics, University Medicine Greifswald, 17475 Greifswald, Germany
| | - Jan Maarten van Dijl
- University of Groningen, University Medical Center Groningen, Department of Medical Microbiology, 9700 RB Groningen, The Netherlands
| |
Collapse
|
44
|
Nath N, Hagenau L, Weiss S, Tzvetkova A, Jensen LR, Kaderali L, Port M, Scherthan H, Kuss AW. Genome-Wide DNA Alterations in X-Irradiated Human Gingiva Fibroblasts. Int J Mol Sci 2020; 21:E5778. [PMID: 32806598 PMCID: PMC7460866 DOI: 10.3390/ijms21165778] [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] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2020] [Revised: 07/30/2020] [Accepted: 07/31/2020] [Indexed: 01/04/2023] Open
Abstract
While ionizing radiation (IR) is a powerful tool in medical diagnostics, nuclear medicine, and radiology, it also is a serious threat to the integrity of genetic material. Mutagenic effects of IR to the human genome have long been the subject of research, yet still comparatively little is known about the genome-wide effects of IR exposure on the DNA-sequence level. In this study, we employed high throughput sequencing technologies to investigate IR-induced DNA alterations in human gingiva fibroblasts (HGF) that were acutely exposed to 0.5, 2, and 10 Gy of 240 kV X-radiation followed by repair times of 16 h or 7 days before whole-genome sequencing (WGS). Our analysis of the obtained WGS datasets revealed patterns of IR-induced variant (SNV and InDel) accumulation across the genome, within chromosomes as well as around the borders of topologically associating domains (TADs). Chromosome 19 consistently accumulated the highest SNVs and InDels events. Translocations showed variable patterns but with recurrent chromosomes of origin (e.g., Chr7 and Chr16). IR-induced InDels showed a relative increase in number relative to SNVs and a characteristic signature with respect to the frequency of triplet deletions in areas without repetitive or microhomology features. Overall experimental conditions and datasets the majority of SNVs per genome had no or little predicted functional impact with a maximum of 62, showing damaging potential. A dose-dependent effect of IR was surprisingly not apparent. We also observed a significant reduction in transition/transversion (Ti/Tv) ratios for IR-dependent SNVs, which could point to a contribution of the mismatch repair (MMR) system that strongly favors the repair of transitions over transversions, to the IR-induced DNA-damage response in human cells. Taken together, our results show the presence of distinguishable characteristic patterns of IR-induced DNA-alterations on a genome-wide level and implicate DNA-repair mechanisms in the formation of these signatures.
Collapse
Affiliation(s)
- Neetika Nath
- Human Molecular Genetics Group, Department of Functional Genomics, Interfaculty Institute for Genetics and Functional Genomics, University Medicine Greifswald, 17475 Greifswald, Germany; (N.N.); (L.H.); (S.W.); (A.T.); (L.R.J.)
- Institute of Bioinformatics, University Medicine Greifswald, 17475 Greifswald, Germany;
| | - Lisa Hagenau
- Human Molecular Genetics Group, Department of Functional Genomics, Interfaculty Institute for Genetics and Functional Genomics, University Medicine Greifswald, 17475 Greifswald, Germany; (N.N.); (L.H.); (S.W.); (A.T.); (L.R.J.)
| | - Stefan Weiss
- Human Molecular Genetics Group, Department of Functional Genomics, Interfaculty Institute for Genetics and Functional Genomics, University Medicine Greifswald, 17475 Greifswald, Germany; (N.N.); (L.H.); (S.W.); (A.T.); (L.R.J.)
| | - Ana Tzvetkova
- Human Molecular Genetics Group, Department of Functional Genomics, Interfaculty Institute for Genetics and Functional Genomics, University Medicine Greifswald, 17475 Greifswald, Germany; (N.N.); (L.H.); (S.W.); (A.T.); (L.R.J.)
- Institute of Bioinformatics, University Medicine Greifswald, 17475 Greifswald, Germany;
| | - Lars R. Jensen
- Human Molecular Genetics Group, Department of Functional Genomics, Interfaculty Institute for Genetics and Functional Genomics, University Medicine Greifswald, 17475 Greifswald, Germany; (N.N.); (L.H.); (S.W.); (A.T.); (L.R.J.)
| | - Lars Kaderali
- Institute of Bioinformatics, University Medicine Greifswald, 17475 Greifswald, Germany;
| | - Matthias Port
- Bundeswehr Institute for Radiobiology Affiliated to the University of Ulm, 80937 München, Germany; (M.P.); (H.S.)
| | - Harry Scherthan
- Bundeswehr Institute for Radiobiology Affiliated to the University of Ulm, 80937 München, Germany; (M.P.); (H.S.)
| | - Andreas W. Kuss
- Human Molecular Genetics Group, Department of Functional Genomics, Interfaculty Institute for Genetics and Functional Genomics, University Medicine Greifswald, 17475 Greifswald, Germany; (N.N.); (L.H.); (S.W.); (A.T.); (L.R.J.)
| |
Collapse
|
45
|
Cortese M, Kumar A, Matula P, Kaderali L, Scaturro P, Erfle H, Acosta EG, Buehler S, Ruggieri A, Chatel-Chaix L, Rohr K, Bartenschlager R. Reciprocal Effects of Fibroblast Growth Factor Receptor Signaling on Dengue Virus Replication and Virion Production. Cell Rep 2020; 27:2579-2592.e6. [PMID: 31141684 DOI: 10.1016/j.celrep.2019.04.105] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2018] [Revised: 03/27/2019] [Accepted: 04/23/2019] [Indexed: 12/11/2022] Open
Abstract
Dengue virus (DENV) is a human arboviral pathogen accounting for 390 million infections every year. The available vaccine has limited efficacy, and DENV-specific drugs have not been generated. To better understand DENV-host cell interaction, we employed RNA interference-based screening of the human kinome and identified fibroblast growth factor receptor 4 (FGFR4) to control the DENV replication cycle. Pharmacological inhibition of FGFR exerts a reciprocal effect by reducing DENV RNA replication and promoting the production of infectious virus particles. Addressing the latter effect, we found that the FGFR signaling pathway modulates intracellular distribution of DENV particles in a PI3K-dependent manner. Upon FGFR inhibition, virions accumulate in the trans-Golgi network compartment, where they undergo enhanced maturation cleavage of the envelope protein precursor membrane (prM), rendering virus particles more infectious. This study reveals an unexpected reciprocal role of a cellular receptor tyrosine kinase regulating DENV RNA replication and the production of infectious virions.
Collapse
Affiliation(s)
- Mirko Cortese
- Department of Infectious Diseases, Molecular Virology, Heidelberg University, Im Neuenheimer Feld 344, Heidelberg 69120, Germany
| | - Anil Kumar
- Department of Infectious Diseases, Molecular Virology, Heidelberg University, Im Neuenheimer Feld 344, Heidelberg 69120, Germany
| | - Petr Matula
- Biomedical Computer Vision Group, Heidelberg University, BioQuant, IPMB, and German Cancer Research Center, Im Neuenheimer Feld 267, Heidelberg 69120, Germany
| | - Lars Kaderali
- ViroQuant Research Group Modeling, BioQuant, Heidelberg University, Heidelberg, Germany
| | - Pietro Scaturro
- Department of Infectious Diseases, Molecular Virology, Heidelberg University, Im Neuenheimer Feld 344, Heidelberg 69120, Germany
| | - Holger Erfle
- Advanced Biological Screening Facility, BioQuant, Heidelberg University, Heidelberg 69120, Germany
| | - Eliana Gisela Acosta
- Department of Infectious Diseases, Molecular Virology, Heidelberg University, Im Neuenheimer Feld 344, Heidelberg 69120, Germany
| | - Sandra Buehler
- Department of Infectious Diseases, Molecular Virology, Heidelberg University, Im Neuenheimer Feld 344, Heidelberg 69120, Germany
| | - Alessia Ruggieri
- Department of Infectious Diseases, Molecular Virology, Heidelberg University, Im Neuenheimer Feld 344, Heidelberg 69120, Germany
| | - Laurent Chatel-Chaix
- Department of Infectious Diseases, Molecular Virology, Heidelberg University, Im Neuenheimer Feld 344, Heidelberg 69120, Germany; Institut National de la Recherche Scientifique, Institut Armand-Frappier, 531, Boulevard des Prairies Laval, Québec, QC H7V 1B7, Canada
| | - Karl Rohr
- Biomedical Computer Vision Group, Heidelberg University, BioQuant, IPMB, and German Cancer Research Center, Im Neuenheimer Feld 267, Heidelberg 69120, Germany
| | - Ralf Bartenschlager
- Department of Infectious Diseases, Molecular Virology, Heidelberg University, Im Neuenheimer Feld 344, Heidelberg 69120, Germany; German Center for Infection Research, Heidelberg Partner Site, Im Neuenheimer Feld 344, Heidelberg 69120, Germany.
| |
Collapse
|
46
|
Haralambiev L, Bandyophadyay A, Suchy B, Weiss M, Kramer A, Bekeschus S, Ekkernkamp A, Mustea A, Kaderali L, Stope MB. Determination of Immediate vs. Kinetic Growth Retardation in Physically Plasma-treated Cells by Experimental and Modelling Data. Anticancer Res 2020; 40:3743-3749. [PMID: 32620613 DOI: 10.21873/anticanres.14363] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2020] [Revised: 06/15/2020] [Accepted: 06/16/2020] [Indexed: 11/10/2022]
Abstract
BACKGROUND/AIM The antiproliferative effects of cold atmospheric plasma (CAP) make it a promising application option in oncology. The aim of the present study was to examine whether short-term CAP treatment leads to an initial partial elimination of the treated cells or to long-term impairement and inhibition of cell growth. MATERIALS AND METHODS Cells were treated with CAP and biostatistical modelling was used to estimate growth rates over the incubation time. Four cell lines (U2-OS and MNNG osteosarcoma cells, 3T3 fibroblasts, HaCaT keratinocytes) and three CAP sources (MiniJet-R, kINPen MED, Maxium) were used. RESULTS The antiproliferative efficacy of CAP was due to a significant reduction in cell count during treatment and the long-lasting inhibition of growth rate in the remaining cells, detectable in all cell lines and after treatment using all three CAP devices. CONCLUSION Induction of cell death and inhibition of cell growth are part of a general mechanism of biological CAP efficacy. However, data contradict the hypothesis that cancer cells respond more sensitively to CAP treatment compared to non-malignant cells.
Collapse
Affiliation(s)
- Lyubomir Haralambiev
- Department of Trauma, Reconstructive Surgery and Rehabilitation Medicine, University Medicine Greifswald, Greifswald, Germany.,Department of Trauma and Orthopaedic Surgery, BG Klinikum Unfallkrankenhaus Berlin gGmbH, Berlin, Germany
| | - Arnab Bandyophadyay
- Institute of Bioinformatics, University Medicine Greifswald, Greifswald, Germany
| | - Bettina Suchy
- Department of Trauma, Reconstructive Surgery and Rehabilitation Medicine, University Medicine Greifswald, Greifswald, Germany
| | - Martin Weiss
- Department of Women's Health Tübingen, Tübingen, Germany
| | - Axel Kramer
- Institute of Hygiene and Environmental Medicine, University Medicine Greifswald, Greifswald, Germany
| | - Sander Bekeschus
- ZIK plasmatis, Leibniz Institute for Plasma Science and Technology (INP Greifswald), Greifswald, Germany
| | - Axel Ekkernkamp
- Department of Trauma, Reconstructive Surgery and Rehabilitation Medicine, University Medicine Greifswald, Greifswald, Germany.,Department of Trauma and Orthopaedic Surgery, BG Klinikum Unfallkrankenhaus Berlin gGmbH, Berlin, Germany
| | - Alexander Mustea
- Department of Gynecology and Gynecological Oncology, University Hospital Bonn, Bonn, Germany
| | - Lars Kaderali
- Institute of Bioinformatics, University Medicine Greifswald, Greifswald, Germany
| | - Matthias B Stope
- Department of Gynecology and Gynecological Oncology, University Hospital Bonn, Bonn, Germany
| |
Collapse
|
47
|
Nath N, Hagenau L, Weiss S, Tzvetkova A, Jensen LR, Kaderali L, Port M, Scherthan H, Kuss AW. Ionizing Radiation Alters the Transition/Transversion Ratio in the Exome of Human Gingiva Fibroblasts. Health Phys 2020; 119:109-117. [PMID: 32483046 DOI: 10.1097/hp.0000000000001251] [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] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Little is known about the mutational impact of ionizing radiation (IR) exposure on a genome-wide level in mammalian tissues. Recent advancements in sequencing technology have provided powerful tools to perform exome-wide analyses of genetic variation. This also opened up new avenues for studying and characterizing global genomic IR-induced effects. However, genotypes generated by next generation sequencing (NGS) studies can contain errors, which may significantly impact the power to detect signals in common and rare variant analyses. These genotyping errors are not explicitly detected by the standard Genotype Analysis ToolKit (GATK) and Variant Quality Score Recalibration (VQSR) tool and thus remain a potential source of false-positive variants in whole exome sequencing (WES) datasets. In this context, the transition-transversion ratio (Ti/Tv) is commonly used as an additional quality check. In case of IR experiments, this is problematic when Ti/Tv itself might be influenced by IR treatment. It was the aim of this study to determine a suitable threshold for variant filters for NGS datasets from irradiated cells in order to achieve high data quality using Ti/Tv, while at the same time being able to investigate radiation-specific effects on the Ti/Tv ratio for different radiation doses. By testing a variety of filter settings and comparing the obtained results with publicly available datasets, we observe that a coverage filter setting of depth (DP) 3 and genotype quality (GQ) 20 is sufficient for high quality single nucleotide variants (SNVs) calling in an analysis combining GATK and VSQR and that Ti/Tv values are a consistent and useful indicator for data quality assessment for all tested NGS platforms. Furthermore, we report a reduction in Ti/Tv in IR-induced mutations in primary human gingiva fibroblasts (HGFs), which points to an elevated proportion of transversions among IR-induced SNVs and thus might imply that mismatch repair (MMR) plays a role in the cellular damage response to IR-induced DNA lesions.
Collapse
Affiliation(s)
| | - Lisa Hagenau
- Department of Functional Genomics, Interfaculty Institute for Genetics and Functional Genomics, University Medicine Greifswald, Greifswald, Germany
| | - Stefan Weiss
- Department of Functional Genomics, Interfaculty Institute for Genetics and Functional Genomics, University Medicine Greifswald, Greifswald, Germany
| | | | - Lars R Jensen
- Department of Functional Genomics, Interfaculty Institute for Genetics and Functional Genomics, University Medicine Greifswald, Greifswald, Germany
| | - Lars Kaderali
- Institute of Bioinformatics, University Medicine Greifswald, Greifswald, Germany
| | - Matthias Port
- Bundeswehr Institute for Radiobiology, University of Ulm, München, Germany
| | - Harry Scherthan
- Bundeswehr Institute for Radiobiology, University of Ulm, München, Germany
| | - Andreas W Kuss
- Department of Functional Genomics, Interfaculty Institute for Genetics and Functional Genomics, University Medicine Greifswald, Greifswald, Germany
| |
Collapse
|
48
|
Schweinoch D, Bachmann P, Clausznitzer D, Binder M, Kaderali L. Mechanistic modeling explains the dsRNA length-dependent activation of the RIG-I mediated immune response. J Theor Biol 2020; 500:110336. [PMID: 32446742 DOI: 10.1016/j.jtbi.2020.110336] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2019] [Revised: 05/13/2020] [Accepted: 05/15/2020] [Indexed: 12/25/2022]
Abstract
In cell-intrinsic antiviral immunity, cytoplasmic receptors such as retinoic acid-inducible gene I (RIG-I) detect viral double-stranded RNA (dsRNA) and trigger a signaling cascade activating the interferon (IFN) system. This leads to the transcription of hundreds of interferon-stimulated genes (ISGs) with a wide range of antiviral effects. This recognition of dsRNA not only has to be very specific to discriminate foreign from self but also highly sensitive to detect even very low numbers of pathogenic dsRNA molecules. Previous work indicated an influence of the dsRNA length on the binding behavior of RIG-I and its potential to elicit antiviral signaling. However, the molecular mechanisms behind the binding process are still under debate. We compare two hypothesized RIG-I binding mechanisms by translating them into mathematical models and analyzing their potential to describe published experimental data. The models consider the length of the dsRNA as well as known RIG-I binding motifs and describe RIG-I pathway activation after stimulation with dsRNA. We show that internal RIG-I binding sites in addition to cooperative RIG-I oligomerization are essential to describe the experimentally observed RIG-I binding behavior and immune response activation for different dsRNA lengths and concentrations. The combination of RIG-I binding to internal sites on the dsRNA and cooperative oligomerization compensates for a lack of high-affinity binding motifs and triggers a strong antiviral response for long dsRNAs. Model analysis reveals dsRNA length-dependency as a potential mechanism to discriminate between different types of dsRNAs: It allows for sensitive detection of small numbers of long dsRNAs, a typical by-product of viral replication, while ensuring tolerance against non-harming small dsRNAs.
Collapse
Affiliation(s)
- Darius Schweinoch
- University Medicine Greifswald, Institute of Bioinformatics and Center for Functional Genomics of Microbes (C_FunGene), Felix-Hausdorff-Str. 8, 17475 Greifswald, Germany
| | - Pia Bachmann
- University Medicine Greifswald, Institute of Bioinformatics and Center for Functional Genomics of Microbes (C_FunGene), Felix-Hausdorff-Str. 8, 17475 Greifswald, Germany
| | - Diana Clausznitzer
- Technische Universität Dresden, Faculty of Medicine Carl-Gustav Carus, Institute for Medical Informatics and Biometry, Dresden, Germany
| | - Marco Binder
- Research Group "Dynamics of Early Viral Infection and the Innate Antiviral Response", Division Virus-Associated Carcinogenesis (F170), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Lars Kaderali
- University Medicine Greifswald, Institute of Bioinformatics and Center for Functional Genomics of Microbes (C_FunGene), Felix-Hausdorff-Str. 8, 17475 Greifswald, Germany.
| |
Collapse
|
49
|
Zitzmann C, Schmid B, Ruggieri A, Perelson AS, Binder M, Bartenschlager R, Kaderali L. A Coupled Mathematical Model of the Intracellular Replication of Dengue Virus and the Host Cell Immune Response to Infection. Front Microbiol 2020; 11:725. [PMID: 32411105 PMCID: PMC7200986 DOI: 10.3389/fmicb.2020.00725] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [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: 07/21/2019] [Accepted: 03/27/2020] [Indexed: 12/15/2022] Open
Abstract
Dengue virus (DV) is a positive-strand RNA virus of the Flavivirus genus. It is one of the most prevalent mosquito-borne viruses, infecting globally 390 million individuals per year. The clinical spectrum of DV infection ranges from an asymptomatic course to severe complications such as dengue hemorrhagic fever (DHF) and dengue shock syndrome (DSS), the latter because of severe plasma leakage. Given that the outcome of infection is likely determined by the kinetics of viral replication and the antiviral host cell immune response (HIR) it is of importance to understand the interaction between these two parameters. In this study, we use mathematical modeling to characterize and understand the complex interplay between intracellular DV replication and the host cells' defense mechanisms. We first measured viral RNA, viral protein, and virus particle production in Huh7 cells, which exhibit a notoriously weak intrinsic antiviral response. Based on these measurements, we developed a detailed intracellular DV replication model. We then measured replication in IFN competent A549 cells and used this data to couple the replication model with a model describing IFN activation and production of IFN stimulated genes (ISGs), as well as their interplay with DV replication. By comparing the cell line specific DV replication, we found that host factors involved in replication complex formation and virus particle production are crucial for replication efficiency. Regarding possible modes of action of the HIR, our model fits suggest that the HIR mainly affects DV RNA translation initiation, cytosolic DV RNA degradation, and naïve cell infection. We further analyzed the potential of direct acting antiviral drugs targeting different processes of the DV lifecycle in silico and found that targeting RNA synthesis and virus assembly and release are the most promising anti-DV drug targets.
Collapse
Affiliation(s)
- Carolin Zitzmann
- Center for Functional Genomics of Microbes, Institute of Bioinformatics, University Medicine Greifswald, Greifswald, Germany.,Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos, NM, United States
| | - Bianca Schmid
- Department of Infectious Diseases, Molecular Virology, Heidelberg University, Heidelberg, Germany
| | - Alessia Ruggieri
- Department of Infectious Diseases, Molecular Virology, Heidelberg University, Heidelberg, Germany
| | - Alan S Perelson
- Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos, NM, United States
| | - Marco Binder
- Research Group "Dynamics of Early Viral Infection and the Innate Antiviral Response", Division Virus-Associated Carcinogenesis (F170), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Ralf Bartenschlager
- Department of Infectious Diseases, Molecular Virology, Heidelberg University, Heidelberg, Germany
| | - Lars Kaderali
- Center for Functional Genomics of Microbes, Institute of Bioinformatics, University Medicine Greifswald, Greifswald, Germany
| |
Collapse
|
50
|
Gholizadeh M, Fayazi J, Asgari Y, Zali H, Kaderali L. Reconstruction and Analysis of Cattle Metabolic Networks in Normal and Acidosis Rumen Tissue. Animals (Basel) 2020; 10:ani10030469. [PMID: 32168900 PMCID: PMC7142512 DOI: 10.3390/ani10030469] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [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: 01/05/2020] [Revised: 02/21/2020] [Accepted: 02/27/2020] [Indexed: 12/29/2022] Open
Abstract
Simple Summary Economics of feedlot beef production dictate that beef cattle must gain weight at their maximum potential rate; this involves getting them quickly onto a full feed of high fermentable diet which can induce the ruminal acidosis disease. The molecular host mechanisms that occur as a response to the acidosis, are mostly unknown. For answering this question, the rumen epithelial transcriptome in acidosis and control fattening steers were obtained. By RNA sequencing we found the different expression profiles of genes in normal and acidosis induced steers. Then we constructed two metabolic networks for normal and acidosis tissue based on gene expression profile. Our results suggest that rapid shifts to diets rich in fermentable carbohydrates cause an increased concentration of ruminal volatile fatty acids (VFA) and toxins and significant changes in transcriptome profiles and metabolites of rumen epithelial tissue, with negative effects on economic consequences of poor performance and animal health. Abstract The objective of this study was to develop a system-level understanding of acidosis biology. Therefore, the genes expression differences between the normal and acidosis rumen epithelial tissues were first examined using the RNA-seq data in order to understand the molecular mechanisms involved in the disease and then their corresponding metabolic networks constructed. A number of 1074 genes, 978 isoforms, 1049 transcription start sites (TSS), 998 coding DNA sequence (CDS) and 2 promoters were identified being differentially expressed in the rumen tissue between the normal and acidosis samples (p < 0.05). The functional analysis of 627 up-regulated genes revealed their involvement in ion transmembrane transport, filament organization, regulation of cell adhesion, regulation of the actin cytoskeleton, ATP binding, glucose transmembrane transporter activity, carbohydrate binding, growth factor binding and cAMP metabolic process. Additionally, 111 differentially expressed enzymes were identified between the rumen epithelial tissue of the normal and acidosis steers with 46 up-regulated and 65 down-regulated ones in the acidosis group. The pathways and reactions analyses associated with the up-regulated enzymes indicate that most of these enzymes are involved in the fatty acid metabolism, biosynthesis of amino acids, pyruvate and carbon metabolism while most of the down-regulated ones are involved in purine and pyrimidine, vitamin B6 and antibiotics metabolisms. The degree distribution of both metabolic networks follows a power-law one, hence displaying a scale-free property. The top 15 hub metabolites were determined in the acidosis metabolic network with most of them involved in the fatty acid oxidation, VFA biosynthesis, amino acid biogenesis and glutathione metabolism which plays an important role in the stress condition. The limitations of this study were low number of animals and using only epithelial tissue (ventral sac) for RNA-seq.
Collapse
Affiliation(s)
- Maryam Gholizadeh
- Department of Animal Science, Faculty of Animal Science and Food Technology, Agricultural Sciences and Natural Resources University of Khuzestan, Mollasani, Ahvaz 6341773637, Iran;
| | - Jamal Fayazi
- Department of Animal Science, Faculty of Animal Science and Food Technology, Agricultural Sciences and Natural Resources University of Khuzestan, Mollasani, Ahvaz 6341773637, Iran;
- Correspondence: ; Tel.: +98-91-6612-4162
| | - Yazdan Asgari
- Department of Medical Biotechnology, School of Advanced Technologies in Medicine, Tehran University of Medical Sciences, Tehran 1416753955, Iran;
| | - Hakimeh Zali
- School of Advanced Technologies in Medicine, Shahid Beheshti University of Medical Sciences, Tehran 1416753955, Iran;
| | - Lars Kaderali
- Institute of Bioinformatics, University Medicine Greifswald, Felix-Hausdorff-Str. 8, 17475 Greifswald, Germany;
| |
Collapse
|