@article{GoettschBeerenwinkelDengetal.2021, author = {Goettsch, Winfried and Beerenwinkel, Niko and Deng, Li and D{\"o}lken, Lars and Dutilh, Bas E. and Erhard, Florian and Kaderali, Lars and Kleist, Max von and Marquet, Roland and Matthijnssens, Jelle and McCallin, Shawna and McMahon, Dino and Rattei, Thomas and Van Rij, Ronald P. and Robertson, David L. and Schwemmle, Martin and Stern-Ginossar, Noam and Marz, Manja}, title = {ITN—VIROINF: Understanding (harmful) virus-host interactions by linking virology and bioinformatics}, series = {Viruses}, volume = {13}, journal = {Viruses}, number = {5}, issn = {1999-4915}, doi = {10.3390/v13050766}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-236687}, year = {2021}, 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.}, language = {en} } @article{KasangKalluvyaMajingeetal.2016, author = {Kasang, Christa and Kalluvya, Samuel and Majinge, Charles and Kongola, Gilbert and Mlewa, Mathias and Massawe, Irene and Kabyemera, Rogatus and Magambo, Kinanga and Ulmer, Albrecht and Klinker, Hartwig and Gschmack, Eva and Horn, Anne and Koutsilieri, Eleni and Preiser, Wolfgang and Hofmann, Daniela and Hain, Johannes and M{\"u}ller, Andreas and D{\"o}lken, Lars and Weissbrich, Benedikt and Rethwilm, Axel and Stich, August and Scheller, Carsten}, title = {Effects of Prednisolone on Disease Progression in Antiretroviral-Untreated HIV Infection: A 2-Year Randomized, Double-Blind Placebo-Controlled Clinical Trial}, series = {PLoS One}, volume = {11}, journal = {PLoS One}, number = {1}, doi = {10.1371/journal.pone.0146678}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-146479}, pages = {e0146678}, year = {2016}, abstract = {Background HIV-disease progression correlates with immune activation. Here we investigated whether corticosteroid treatment can attenuate HIV disease progression in antiretroviral-untreated patients. Methods Double-blind, placebo-controlled randomized clinical trial including 326 HIV-patients in a resource-limited setting in Tanzania (clinicaltrials.gov NCT01299948). Inclusion criteria were a CD4 count above 300 cells/μl, the absence of AIDS-defining symptoms and an ART-na{\"i}ve therapy status. Study participants received 5 mg prednisolone per day or placebo for 2 years. Primary endpoint was time to progression to an AIDS-defining condition or to a CD4-count below 200 cells/μl. Results No significant change in progression towards the primary endpoint was observed in the intent-to-treat (ITT) analysis (19 cases with prednisolone versus 28 cases with placebo, p = 0.1407). In a per-protocol (PP)-analysis, 13 versus 24 study participants progressed to the primary study endpoint (p = 0.0741). Secondary endpoints: Prednisolone-treatment decreased immune activation (sCD14, suPAR, CD38/HLA-DR/CD8+) and increased CD4-counts (+77.42 ± 5.70 cells/μl compared to -37.42 ± 10.77 cells/μl under placebo, p < 0.0001). Treatment with prednisolone was associated with a 3.2-fold increase in HIV viral load (p < 0.0001). In a post-hoc analysis stratifying for sex, females treated with prednisolone progressed significantly slower to the primary study endpoint than females treated with placebo (ITT-analysis: 11 versus 21 cases, p = 0.0567; PP-analysis: 5 versus 18 cases, p = 0.0051): No changes in disease progression were observed in men. Conclusions This study could not detect any significant effects of prednisolone on disease progression in antiretroviral-untreated HIV infection within the intent-to-treat population. However, significant effects were observed on CD4 counts, immune activation and HIV viral load. This study contributes to a better understanding of the role of immune activation in the pathogenesis of HIV infection.}, language = {en} } @article{HennigDjakovicDoelkenetal.2021, author = {Hennig, Thomas and Djakovic, Lara and D{\"o}lken, Lars and Whisnant, Adam W.}, title = {A Review of the Multipronged Attack of Herpes Simplex Virus 1 on the Host Transcriptional Machinery}, series = {Viruses}, volume = {13}, journal = {Viruses}, number = {9}, issn = {1999-4915}, doi = {10.3390/v13091836}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-246165}, year = {2021}, abstract = {During lytic infection, herpes simplex virus (HSV) 1 induces a rapid shutoff of host RNA synthesis while redirecting transcriptional machinery to viral genes. In addition to being a major human pathogen, there is burgeoning clinical interest in HSV as a vector in gene delivery and oncolytic therapies, necessitating research into transcriptional control. This review summarizes the array of impacts that HSV has on RNA Polymerase (Pol) II, which transcribes all mRNA in infected cells. We discuss alterations in Pol II holoenzymes, post-translational modifications, and how viral proteins regulate specific activities such as promoter-proximal pausing, splicing, histone repositioning, and termination with respect to host genes. Recent technological innovations that have reshaped our understanding of previous observations are summarized in detail, along with specific research directions and technical considerations for future studies.}, language = {en} } @article{ReuschWagenhaeuserGabeletal.2022, author = {Reusch, Julia and Wagenh{\"a}user, Isabell and Gabel, Alexander and Eggestein, Annika and H{\"o}hn, Anna and L{\^a}m, Thi{\^e}n-Tr{\´i} and Frey, Anna and Schubert-Unkmeir, Alexandra and D{\"o}lken, Lars and Frantz, Stefan and Kurzai, Oliver and Vogel, Ulrich and Krone, Manuel and Petri, Nils}, title = {Influencing factors of anti-SARS-CoV-2-spike-IgG antibody titers in healthcare workers: A cross-section study}, series = {Journal of Medical Virology}, volume = {95}, journal = {Journal of Medical Virology}, number = {1}, doi = {10.1002/jmv.28300}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-318659}, year = {2022}, abstract = {Against the background of the current COVID-19 infection dynamics with its rapid spread of SARS-CoV-2 variants of concern (VOC), the immunity and the vaccine prevention of healthcare workers (HCWs) against SARS-CoV-2 continues to be of high importance. This observational cross-section study assesses factors influencing the level of anti-SARS-CoV-2-spike IgG after SARS-CoV-2 infection or vaccination. One thousand seven hundred and fifty HCWs were recruited meeting the following inclusion criteria: age ≥18 years, PCR-confirmed SARS-CoV-2 infection convalescence and/or at least one dose of COVID-19 vaccination. anti-SARS-CoV-2-spike IgG titers were determined by SERION ELISA agile SARS-CoV-2 IgG. Mean anti-SARS-CoV-2-spike IgG levels increased significantly by number of COVID-19 vaccinations (92.2 BAU/ml for single, 140.9 BAU/ml for twice and 1144.3 BAU/ml for threefold vaccination). Hybrid COVID-19 immunized respondents (after infection and vaccination) had significantly higher antibody titers compared with convalescent only HCWs. Anti-SARS-CoV-2-spike IgG titers declined significantly with time after the second vaccination. Smoking and high age were associated with lower titers. Both recovered and vaccinated HCWs presented a predominantly good humoral immune response. Smoking and higher age limited the humoral SARS-CoV-2 immunity, adding to the risk of severe infections within this already health impaired collective.}, language = {en} } @article{RutkowskiErhardL'Hernaultetal.2015, author = {Rutkowski, Andrzej J. and Erhard, Florian and L'Hernault, Anne and Bonfert, Thomas and Schilhabel, Markus and Crump, Colin and Rosenstiel, Philip and Efstathiou, Stacey and Zimmer, Ralf and Friedel, Caroline C. and D{\"o}lken, Lars}, title = {Widespread disruption of host transcription termination in HSV-1 infection}, series = {Nature Communications}, volume = {6}, journal = {Nature Communications}, number = {7126}, doi = {10.1038/ncomms8126}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-148643}, year = {2015}, abstract = {Herpes simplex virus 1 (HSV-1) is an important human pathogen and a paradigm for virus-induced host shut-off. Here we show that global changes in transcription and RNA processing and their impact on translation can be analysed in a single experimental setting by applying 4sU-tagging of newly transcribed RNA and ribosome profiling to lytic HSV-1 infection. Unexpectedly, we find that HSV-1 triggers the disruption of transcription termination of cellular, but not viral, genes. This results in extensive transcription for tens of thousands of nucleotides beyond poly(A) sites and into downstream genes, leading to novel intergenic splicing between exons of neighbouring cellular genes. As a consequence, hundreds of cellular genes seem to be transcriptionally induced but are not translated. In contrast to previous reports, we show that HSV-1 does not inhibit co-transcriptional splicing. Our approach thus substantially advances our understanding of HSV-1 biology and establishes HSV-1 as a model system for studying transcription termination.}, language = {en} } @article{MurakawaHinzMothesetal.2015, author = {Murakawa, Yasuhiro and Hinz, Michael and Mothes, Janina and Schuetz, Anja and Uhl, Michael and Wyler, Emanuel and Yasuda, Tomoharu and Mastrobuoni, Guido and Friedel, Caroline C. and D{\"o}lken, Lars and Kempa, Stefan and Schmidt-Supprian, Marc and Bl{\"u}thgen, Nils and Backofen, Rolf and Heinemann, Udo and Wolf, Jana and Scheidereit, Claus and Landthaler, Markus}, title = {RC3H1 post-transcriptionally regulates A20 mRNA and modulates the activity of the IKK/NF-\(\kappa\)B pathway}, series = {Nature Communications}, volume = {6}, journal = {Nature Communications}, number = {7367}, doi = {10.1038/ncomms8367}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-151596}, year = {2015}, abstract = {The RNA-binding protein RC3H1 (also known as ROQUIN) promotes TNF\(\alpha\) mRNA decay via a 3'UTR constitutive decay element (CDE). Here we applied PAR-CLIP to human RC3H1 to identify ~3,800 mRNA targets with >16,000 binding sites. A large number of sites are distinct from the consensus CDE and revealed a structure-sequence motif with U-rich sequences embedded in hairpins. RC3H1 binds preferentially short-lived and DNA damage-induced mRNAs, indicating a role of this RNA-binding protein in the post-transcriptional regulation of the DNA damage response. Intriguingly, RC3H1 affects expression of the NF-\(\kappa\)B pathway regulators such as I\(\kappa\)B\(\alpha\) and A20. RC3H1 uses ROQ and Zn-finger domains to contact a binding site in the A20 3'UTR, demonstrating a not yet recognized mode of RC3H1 binding. Knockdown of RC3H1 resulted in increased A20 protein expression, thereby interfering with I\(\kappa\)B kinase and NF-\(\kappa\)B activities, demonstrating that RC3H1 can modulate the activity of the IKK/NF-\(\kappa\)B pathway.}, language = {en} } @article{WylerMenegattiFrankeetal.2017, author = {Wyler, Emanuel and Menegatti, Jennifer and Franke, Vedran and Kocks, Christine and Boltengagen, Anastasiya and Hennig, Thomas and Theil, Kathrin and Rutkowski, Andrzej and Ferrai, Carmelo and Baer, Laura and Kermas, Lisa and Friedel, Caroline and Rajewsky, Nikolaus and Akalin, Altuna and D{\"o}lken, Lars and Gr{\"a}sser, Friedrich and Landthaler, Markus}, title = {Widespread activation of antisense transcription of the host genome during herpes simplex virus 1 infection}, series = {Genome Biology}, volume = {18}, journal = {Genome Biology}, doi = {10.1186/s13059-017-1329-5}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-173381}, year = {2017}, abstract = {Background Herpesviruses can infect a wide range of animal species. Herpes simplex virus 1 (HSV-1) is one of the eight herpesviruses that can infect humans and is prevalent worldwide. Herpesviruses have evolved multiple ways to adapt the infected cells to their needs, but knowledge about these transcriptional and post-transcriptional modifications is sparse. Results Here, we show that HSV-1 induces the expression of about 1000 antisense transcripts from the human host cell genome. A subset of these is also activated by the closely related varicella zoster virus. Antisense transcripts originate either at gene promoters or within the gene body, and they show different susceptibility to the inhibition of early and immediate early viral gene expression. Overexpression of the major viral transcription factor ICP4 is sufficient to turn on a subset of antisense transcripts. Histone marks around transcription start sites of HSV-1-induced and constitutively transcribed antisense transcripts are highly similar, indicating that the genetic loci are already poised to transcribe these novel RNAs. Furthermore, an antisense transcript overlapping with the BBC3 gene (also known as PUMA) transcriptionally silences this potent inducer of apoptosis in cis. Conclusions We show for the first time that a virus induces widespread antisense transcription of the host cell genome. We provide evidence that HSV-1 uses this to downregulate a strong inducer of apoptosis. Our findings open new perspectives on global and specific alterations of host cell transcription by viruses.}, language = {en} } @article{DoelkenStichSpinner2021, author = {D{\"o}lken, Lars and Stich, August and Spinner, Christoph D.}, title = {Remdesivir for Early COVID-19 Treatment of High-Risk Individuals Prior to or at Early Disease Onset — Lessons Learned}, series = {Viruses}, volume = {13}, journal = {Viruses}, number = {6}, issn = {1999-4915}, doi = {10.3390/v13060963}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-239648}, year = {2021}, abstract = {After more than one year of the COVID-19 pandemic, antiviral treatment options against SARS-CoV-2 are still severely limited. High hopes that had initially been placed on antiviral drugs like remdesivir have so far not been fulfilled. While individual case reports provide striking evidence for the clinical efficacy of remdesivir in the right clinical settings, major trials failed to demonstrate this. Here, we highlight and discuss the key findings of these studies and underlying reasons for their failure. We elaborate on how such shortcomings should be prevented in future clinical trials and pandemics. We suggest in conclusion that any novel antiviral agent that enters human trials should first be tested in a post-exposure setting to provide rapid and solid evidence for its clinical efficacy before initiating further time-consuming and costly clinical trials for more advanced disease. In the COVID-19 pandemic this might have established remdesivir early on as an efficient antiviral agent at a more suitable disease stage which would have saved many lives, in particular in large outbreaks within residential care homes.}, language = {en} } @article{FuxArndtLangenmayeretal.2019, author = {Fux, Robert and Arndt, Daniela and Langenmayer, Martin C. and Schwaiger, Julia and Ferling, Hermann and Fischer, Nicole and Indenbirken, Daniela and Grundhoff, Adam and D{\"o}lken, Lars and Adamek, Mikolaj and Steinhagen, Dieter and Sutter, Gerd}, title = {Piscine orthoreovirus 3 is not the causative pathogen of proliferative darkening syndrome (PDS) of brown trout (Salmo trutta fario)}, series = {Viruses}, volume = {11}, journal = {Viruses}, number = {2}, issn = {1999-4915}, doi = {10.3390/v11020112}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-196991}, year = {2019}, abstract = {The proliferative darkening syndrome (PDS) is a lethal disease of brown trout (Salmo trutta fario) which occurs in several alpine Bavarian limestone rivers. Because mortality can reach 100\%, PDS is a serious threat for affected fish populations. Recently, Kuehn and colleagues reported that a high throughput RNA sequencing approach identified a piscine orthoreovirus (PRV) as a causative agent of PDS. We investigated samples from PDS-affected fish obtained from two exposure experiments performed at the river Iller in 2008 and 2009. Using a RT-qPCR and a well-established next-generation RNA sequencing pipeline for pathogen detection, PRV-specific RNA was not detectable in PDS fish from 2009. In contrast, PRV RNA was readily detectable in several organs from diseased fish in 2008. However, similar virus loads were detectable in the control fish which were not exposed to Iller water and did not show any signs of the disease. Therefore, we conclude that PRV is not the causative agent of PDS of brown trout in the rhithral region of alpine Bavarian limestone rivers. The abovementioned study by Kuehn used only samples from the exposure experiment from 2008 and detected a subclinical PRV bystander infection. Work is ongoing to identify the causative agent of PDS.}, language = {en} } @article{BoertleinSchumacherKleuseretal.2019, author = {B{\"o}rtlein, Charlene and Schumacher, Fabian and Kleuser, Burkhard and D{\"o}lken, Lars and Avota, Elita}, title = {Role of neutral sphingomyelinase-2 (NSM 2) in the control of T cell plasma membrane lipid composition and cholesterol homeostasis}, series = {Frontiers in Cell and Developmental Biology}, volume = {7}, journal = {Frontiers in Cell and Developmental Biology}, number = {226}, issn = {2296-634X}, doi = {10.3389/fcell.2019.00226}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-190596}, year = {2019}, abstract = {The activity of neutral sphingomyelinase-2 (NSM2) to catalyze the conversion of sphingomyelin (SM) to ceramide and phosphocholine at the cytosolic leaflet of plasma membrane (PM) is important in T cell receptor (TCR) signaling. We recently identified PKCζ as a major NSM2 downstream effector which regulates microtubular polarization. It remained, however, unclear to what extent NSM2 activity affected overall composition of PM lipids and downstream effector lipids in antigen stimulated T cells. Here, we provide a detailed lipidomics analyses on PM fractions isolated from TCR stimulated wild type and NSM2 deficient (ΔNSM) Jurkat T cells. This revealed that in addition to that of sphingolipids, NSM2 depletion also affected concentrations of many other lipids. In particular, NSM2 ablation resulted in increase of lyso-phosphatidylcholine (LPC) and lyso-phosphatidylethanolamine (LPE) which both govern PM biophysical properties. Crucially, TCR dependent upregulation of the important T cell signaling lipid diacylglycerol (DAG), which is fundamental for activation of conventional and novel PKCs, was abolished in ΔNSM cells. Moreover, NSM2 activity was found to play an important role in PM cholesterol transport to the endoplasmic reticulum (ER) and production of cholesteryl esters (CE) there. Most importantly, CE accumulation was essential to sustain human T cell proliferation. Accordingly, inhibition of CE generating enzymes, the cholesterol acetyltransferases ACAT1/SOAT1 and ACAT2/SOAT2, impaired TCR driven expansion of both CD4\(^+\) and CD8\(^+\) T cells. In summary, our study reveals an important role of NSM2 in regulating T cell functions by its multiple effects on PM lipids and cholesterol homeostasis.}, language = {en} }