@article{BreitenbachLiangBeyersdorfetal.2019,
  author    = {Breitenbach, Tim and Liang, Chunguang and Beyersdorf, Niklas and Dandekar, Thomas},
  title     = {Analyzing pharmacological intervention points: A method to calculate external stimuli to switch between steady states in regulatory networks},
  series = {PLoS Computational Biology},
  volume    = {15},
  journal   = {PLoS Computational Biology},
  doi       = {10.1371/journal.pcbi.1007075},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-220385},
  year      = {2019},
  abstract  = {Once biological systems are modeled by regulatory networks, the next step is to include external stimuli, which model the experimental possibilities to affect the activity level of certain network's nodes, in a mathematical framework. Then, this framework can be interpreted as a mathematical optimal control framework such that optimization algorithms can be used to determine external stimuli which cause a desired switch from an initial state of the network to another final state. These external stimuli are the intervention points for the corresponding biological experiment to obtain the desired outcome of the considered experiment. In this work, the model of regulatory networks is extended to controlled regulatory networks. For this purpose, external stimuli are considered which can affect the activity of the network's nodes by activation or inhibition. A method is presented how to calculate a selection of external stimuli which causes a switch between two different steady states of a regulatory network. A software solution based on Jimena and Mathworks Matlab is provided. Furthermore, numerical examples are presented to demonstrate application and scope of the software on networks of 4 nodes, 11 nodes and 36 nodes. Moreover, we analyze the aggregation of platelets and the behavior of a basic T-helper cell protein-protein interaction network and its maturation towards Th0, Th1, Th2, Th17 and Treg cells in accordance with experimental data.},
  language  = {en}
}
@article{MarcuBichmannKuchenbeckeretal.2021,
  author    = {Marcu, Ana and Bichmann, Leon and Kuchenbecker, Leon and Kowalewski, Daniel Johannes and Freudenmann, Lena Katharina and Backert, Linus and M{\"u}hlenbruch, Lena and Szolek, Andr{\´a}s and L{\"u}bke, Maren and Wagner, Philipp and Engler, Tobias and Matovina, Sabine and Wang, Jian and Hauri-Hohl, Mathias and Martin, Roland and Kapolou, Konstantina and Walz, Juliane Sarah and Velz, Julia and Moch, Holger and Regli, Luca and Silginer, Manuela and Weller, Michael and L{\"o}ffler, Markus W. and Erhard, Florian and Schlosser, Andreas and Kohlbacher, Oliver and Stevanović, Stefan and Rammensee, Hans-Georg and Neidert, Marian Christoph},
  title     = {HLA Ligand Atlas: a benign reference of HLA-presented peptides to improve T-cell-based cancer immunotherapy},
  series = {Journal for ImmunoTherapy of Cancer},
  volume    = {9},
  journal   = {Journal for ImmunoTherapy of Cancer},
  doi       = {10.1136/jitc-2020-002071},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-370160},
  year      = {2021},
  abstract  = {Background The human leucocyte antigen (HLA) complex controls adaptive immunity by presenting defined fractions of the intracellular and extracellular protein content to immune cells. Understanding the benign HLA ligand repertoire is a prerequisite to define safe T-cell-based immunotherapies against cancer. Due to the poor availability of benign tissues, if available, normal tissue adjacent to the tumor has been used as a benign surrogate when defining tumor-associated antigens. However, this comparison has proven to be insufficient and even resulted in lethal outcomes. In order to match the tumor immunopeptidome with an equivalent counterpart, we created the HLA Ligand Atlas, the first extensive collection of paired HLA-I and HLA-II immunopeptidomes from 227 benign human tissue samples. This dataset facilitates a balanced comparison between tumor and benign tissues on HLA ligand level. Methods Human tissue samples were obtained from 16 subjects at autopsy, five thymus samples and two ovary samples originating from living donors. HLA ligands were isolated via immunoaffinity purification and analyzed in over 1200 liquid chromatography mass spectrometry runs. Experimentally and computationally reproducible protocols were employed for data acquisition and processing. Results The initial release covers 51 HLA-I and 86 HLA-II allotypes presenting 90,428 HLA-I- and 142,625 HLA-II ligands. The HLA allotypes are representative for the world population. We observe that immunopeptidomes differ considerably between tissues and individuals on source protein and HLA-ligand level. Moreover, we discover 1407 HLA-I ligands from non-canonical genomic regions. Such peptides were previously described in tumors, peripheral blood mononuclear cells (PBMCs), healthy lung tissues and cell lines. In a case study in glioblastoma, we show that potential on-target off-tumor adverse events in immunotherapy can be avoided by comparing tumor immunopeptidomes to the provided multi-tissue reference. Conclusion Given that T-cell-based immunotherapies, such as CAR-T cells, affinity-enhanced T cell transfer, cancer vaccines and immune checkpoint inhibition, have significant side effects, the HLA Ligand Atlas is the first step toward defining tumor-associated targets with an improved safety profile. The resource provides insights into basic and applied immune-associated questions in the context of cancer immunotherapy, infection, transplantation, allergy and autoimmunity. It is publicly available and can be browsed in an easy-to-use web interface at https://hla-ligand-atlas.org .},
  language  = {en}
}
@article{LiNagyLiuetal.2021,
  author    = {Li, Jinlin and Nagy, Noemi and Liu, Jiangnan and Gupta, Soham and Frisan, Teresa and Hennig, Thomas and Cameron, Donald P. and Baranello, Laura and Masucci, Maria G.},
  title     = {The Epstein-Barr virus deubiquitinating enzyme BPLF1 regulates the activity of topoisomerase II during productive infection},
  series = {PLOS Pathogens},
  volume    = {17},
  journal   = {PLOS Pathogens},
  doi       = {10.1371/journal.ppat.1009954},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-363841},
  year      = {2021},
  abstract  = {Topoisomerases are essential for the replication of herpesviruses but the mechanisms by which the viruses hijack the cellular enzymes are largely unknown. We found that topoisomerase-II (TOP2) is a substrate of the Epstein-Barr virus (EBV) ubiquitin deconjugase BPLF1. BPLF1 co-immunoprecipitated and deubiquitinated TOP2, and stabilized SUMOy-lated TOP2 trapped in cleavage complexes (TOP2ccs), which halted the DNA damage response to TOP2-induced double strand DNA breaks and promoted cell survival. Induction of the productive virus cycle in epithelial and lymphoid cell lines carrying recombinant EBV encoding the active enzyme was accompanied by TOP2 deubiquitination, accumulation of TOP2ccs and resistance to Etoposide toxicity. The protective effect of BPLF1 was dependent on the expression of tyrosyl-DNA phosphodiesterase 2 (TDP2) that releases DNA-trapped TOP2 and promotes error-free DNA repair. These findings highlight a previously unrecognized function of BPLF1 in supporting a non-proteolytic pathway for TOP2ccs debulking that favors cell survival and virus production.},
  language  = {en}
}
@article{BanasSteublRendersetal.2018,
  author    = {Banas, Bernhard and Steubl, Dominik and Renders, Lutz and Chittka, Dominik and Banas, Miriam C. and Wekerle, Thomas and Koch, Martina and Witzke, Oliver and M{\"u}hlfeld, Anja and Sommerer, Claudia and Habicht, Antje and Hugo, Christian and H{\"u}nig, Thomas and Lindemann, Monika and Schmidt, Traudel and Rascle, Anne and Barabas, Sascha and Deml, Ludwig and Wagner, Ralf and Kr{\"a}mer, Bernhard K. and Kr{\"u}ger, Bernd},
  title     = {Clinical validation of a novel enzyme-linked immunosorbent spot assay-based in vitro diagnostic assay to monitor cytomegalovirus-specific cell-mediated immunity in kidney transplant recipients: a multicenter, longitudinal, prospective, observational study},
  series = {Transplant International},
  volume    = {31},
  journal   = {Transplant International},
  doi       = {10.1111/tri.13110},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-221468},
  pages     = {436-450},
  year      = {2018},
  abstract  = {Impaired cytomegalovirus (CMV)-specific cell-mediated immunity (CMV-CMI) is a major cause of CMV reactivation and associated complications in solid-organ transplantation. Reliably assessing CMV-CMI is desirable to individually adjust antiviral and immunosuppressive therapy. This study aimed to evaluate the suitability of T-Track® CMV, a novel IFN-γ ELISpot assay based on the stimulation of peripheral blood mononuclear cells with pp65 and IE-I CMV proteins, to monitor CMV-CMI following kidney transplantation. A prospective longitudinal multicenter study was conducted in 86 intermediate-risk renal transplant recipients. CMV-CMI, CMV viral load, and clinical complications were monitored over 6 months post-transplantation. Ninety-five percent and 88-92\% ELISpot assays were positive pre- and post-transplantation, respectively. CMV-specific response was reduced following immunosuppressive treatment and increased in patients with graft rejection, indicating the ability of the ELISpot assay to monitor patients' immunosuppressive state. Interestingly, median pp65-specific response was ninefold higher in patients with self-clearing viral load compared to antivirally treated patients prior to first viral load detection (P < 0.001), suggesting that reactivity to pp65 represents a potential immunocompetence marker. Altogether, T-Track® CMV is a highly sensitive IFN-γ ELISpot assay, suitable for the immunomonitoring of CMV-seropositive renal transplant recipients, and with a potential use for the risk assessment of CMV-related clinical complications (ClinicalTrials.gov Identifier: NCT02083042).},
  language  = {en}
}
@article{KunzmannKremplSeidenspinneretal.2018,
  author    = {Kunzmann, Steffen and Krempl, Christine and Seidenspinner, Silvia and Glaser, Kirsten and Speer, Christian P. and Fehrholz, Markus},
  title     = {Increase in CTGF mRNA expression by respiratory syncytial virus infection is abrogated by caffeine in lung epithelial cells},
  series = {Influenza and Other Respiratory Viruses},
  volume    = {12},
  journal   = {Influenza and Other Respiratory Viruses},
  doi       = {10.1111/irv.12561},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-230909},
  pages     = {662-666},
  year      = {2018},
  abstract  = {Respiratory syncytial virus (RSV) is a leading cause of severe lower respiratory tract infection in early childhood. Underlying pathomechanisms of elevated pulmonary morbidity in later infancy are largely unknown. We found that RSV-infected H441 cells showed increased mRNA expression of connective tissue growth factor (CTGF), a key factor in airway remodeling. Additional dexamethasone treatment led to further elevated mRNA levels, indicating additive effects. Caffeine treatment prevented RSV-mediated increase in CTGF mRNA. RSV may be involved in airway remodeling processes by increasing CTGF mRNA expression. Caffeine might abrogate these negative effects and thereby help to restore lung homeostasis.},
  language  = {en}
}
@article{CounsellKardaDiazetal.2018,
  author    = {Counsell, John R. and Karda, Rajvinder and Diaz, Juan Antiano and Carey, Louise and Wiktorowicz, Tatiana and Buckley, Suzanne M. K. and Ameri, Shima and Ng, Joanne and Baruteau, Julien and Almeida, Filipa and de Silva, Rohan and Simone, Roberto and Lugar{\`a}, Eleonora and Lignani, Gabriele and Lindemann, Dirk and Rethwilm, Axel and Rahim, Ahad A. and Waddington, Simon N. and Howe, Steven J.},
  title     = {Foamy Virus Vectors Transduce Visceral Organs and Hippocampal Structures following In Vivo Delivery to Neonatal Mice},
  series = {Molecular Therapy: Nucleic Acids},
  volume    = {12},
  journal   = {Molecular Therapy: Nucleic Acids},
  doi       = {10.1016/j.omtn.2018.07.006},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-223379},
  pages     = {626-634},
  year      = {2018},
  abstract  = {Viral vectors are rapidly being developed for a range of applications in research and gene therapy. Prototype foamy virus (PFV) vectors have been described for gene therapy, although their use has mainly been restricted to ex vivo stem cell modification. Here we report direct in vivo transgene delivery with PFV vectors carrying reporter gene constructs. In our investigations, systemic PFV vector delivery to neonatal mice gave transgene expression in the heart, xiphisternum, liver, pancreas, and gut, whereas intracranial administration produced brain expression until animals were euthanized 49 days post-transduction. Immunostaining and confocal microscopy analysis of injected brains showed that transgene expression was highly localized to hippocampal architecture despite vector delivery being administered to the lateral ventricle. This was compared with intracranial biodistribution of lentiviral vectors and adeno-associated virus vectors, which gave a broad, non-specific spread through the neonatal mouse brain without regional localization, even when administered at lower copy numbers. Our work demonstrates that PFV can be used for neonatal gene delivery with an intracranial expression profile that localizes to hippocampal neurons, potentially because of the mitotic status of the targeted cells, which could be of use for research applications and gene therapy of neurological disorders.},
  language  = {en}
}
@article{BugaiQuaresmaFriedeletal.2019,
  author    = {Bugai, Andrii and Quaresma, Alexandre J. C. and Friedel, Caroline C. and Lenasi, Tina and D{\"u}ster, Robert and Sibley, Christopher R. and Fujinaga, Koh and Kukanja, Petra and Hennig, Thomas and Blasius, Melanie and Geyer, Matthias and Ule, Jernej and D{\"o}lken, Lars and Barborič, Matjaž},
  title     = {P-TEFb Activation by RBM7 Shapes a Pro-survival Transcriptional Response to Genotoxic Stress},
  series = {Molecular Cell},
  volume    = {74},
  journal   = {Molecular Cell},
  doi       = {10.1016/j.molcel.2019.01.033},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-221726},
  pages     = {254-267},
  year      = {2019},
  abstract  = {DNA damage response (DDR) involves dramatic transcriptional alterations, the mechanisms of which remain ill defined. Here, we show that following genotoxic stress, the RNA-binding motif protein 7 (RBM7) stimulates RNA polymerase II (Pol II) transcription and promotes cell viability by activating the positive transcription elongation factor b (P-TEFb) via its release from the inhibitory 7SK small nuclear ribonucleoprotein (7SK snRNP). This is mediated by activation of p38MAPK, which triggers enhanced binding of RBM7 with core subunits of 7SK snRNP. In turn, P-TEFb relocates to chromatin to induce transcription of short units, including key DDR genes and multiple classes of non-coding RNAs. Critically, interfering with the axis of RBM7 and P-TEFb provokes cellular hypersensitivity to DNA-damage-inducing agents due to activation of apoptosis. Our work uncovers the importance of stress-dependent stimulation of Pol II pause release, which enables a pro-survival transcriptional response that is crucial for cell fate upon genotoxic insult.},
  language  = {en}
}
@article{ChhatbarDetjeGrabskietal.2018,
  author    = {Chhatbar, Chintan and Detje, Claudia N. and Grabski, Elena and Borst, Katharina and Spanier, Julia and Ghita, Luca and Elliott, David A. and Jord{\~a}o, Marta Joana Costa and Mueller, Nora and Sutton, James and Prajeeth, Chittappen K. and Gudi, Viktoria and Klein, Michael A. and Prinz, Marco and Bradke, Frank and Stangel, Martin and Kalinke, Ulrich},
  title     = {Type I Interferon Receptor Signaling of Neurons and Astrocytes Regulates Microglia Activation during Viral Encephalitis},
  series = {Cell Reports},
  volume    = {25},
  journal   = {Cell Reports},
  doi       = {10.1016/j.celrep.2018.09.003},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-222456},
  pages     = {118-129},
  year      = {2018},
  abstract  = {In sterile neuroinflammation, a pathological role is proposed for microglia, whereas in viral encephalitis, their function is not entirely clear. Many viruses exploit the odorant system and enter the CNS via the olfactory bulb (OB). Upon intranasal vesicular stomatitis virus instillation, we show an accumulation of activated microglia and monocytes in the OB. Depletion of microglia during encephalitis results in enhanced virus spread and increased lethality. Activation, proliferation, and accumulation of microglia are regulated by type I IFN receptor signaling of neurons and astrocytes, but not of microglia. Morphological analysis of myeloid cells shows that type I IFN receptor signaling of neurons has a stronger impact on the activation of myeloid cells than of astrocytes. Thus, in the infected CNS, the cross talk among neurons, astrocytes, and microglia is critical for full microglia activation and protection from lethal encephalitis.},
  language  = {en}
}
@article{PrustyGulveGovindetal.2018,
  author    = {Prusty, Bhupesh K. and Gulve, Nitish and Govind, Sheila and Krueger, Gerhard R. F. and Feichtinger, Julia and Larcombe, Lee and Aspinall, Richard and Ablashi, Dharam V. and Toro, Carla T.},
  title     = {Active HHV-6 Infection of Cerebellar Purkinje Cells in Mood Disorders},
  series = {Frontiers in Microbiology},
  volume    = {9},
  journal   = {Frontiers in Microbiology},
  doi       = {10.3389/fmicb.2018.01955},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-369222},
  year      = {2018},
  abstract  = {Early-life infections and associated neuroinflammation is incriminated in the pathogenesis of various mood disorders. Infection with human roseoloviruses, HHV-6A and HHV-6B, allows viral latency in the central nervous system and other tissues, which can later be activated causing cognitive and behavioral disturbances. Hence, this study was designed to evaluate possible association of HHV-6A and HHV-6B activation with three different groups of psychiatric patients. DNA qPCR, immunofluorescence and FISH studies were carried out in post-mortem posterior cerebellum from 50 cases each of bipolar disorder (BPD), schizophrenia, 15 major depressive disorder (MDD) and 50 appropriate control samples obtained from two well-known brain collections (Stanley Medical Research Institute). HHV-6A and HHV-6B late proteins (indicating active infection) and viral DNA were detected more frequently (p < 0.001 for each virus) in human cerebellum in MDD and BPD relative to controls. These roseolovirus proteins and DNA were found less frequently in schizophrenia cases. Active HHV-6A and HHV-6B infection in cerebellar Purkinje cells were detected frequently in BPD and MDD cases. Furthermore, we found a significant association of HHV-6A infection with reduced Purkinje cell size, suggesting virus-mediated abnormal Purkinje cell function in these disorders. Finally, gene expression analysis of cerebellar tissue revealed changes in pathways reflecting an inflammatory response possibly to HHV-6A infection. Our results provide molecular evidence to support a role for active HHV-6A and HHV-6B infection in BPD and MDD.},
  language  = {en}
}
@article{JohnAbrantesPrustyetal.2019,
  author    = {John, Cathy N. and Abrantes, Pedro M. D. S. and Prusty, Bhupesh K. and Ablashi, Dharam V. and Africa, Charlene W. J.},
  title     = {K21 Compound, a Potent Antifungal Agent: Implications for the Treatment of Fluconazole-Resistant HIV-Associated Candida Species},
  series = {Frontiers in Microbiology},
  volume    = {10},
  journal   = {Frontiers in Microbiology},
  doi       = {10.3389/fmicb.2019.01021},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-323505},
  year      = {2019},
  abstract  = {Background/Objectives: With mucocutaneous candidiasis being highly prevalent in HIV patients, the emergence of fluconazole-resistant Candida species forms a major challenge in treating and eradicating these infections. The objective of this study was to establish the antifungal activity of K21, a membrane-rupturing antimicrobial compound derived from a silica quaternary ammonium compound (SiQAC) with tetraethoxysilane (TEOS). Methods: The study sample included 81 Candida species of which 9 were type strains and 72 were clinical isolates. Minimum inhibitory concentrations, synergy, fractional inhibitory concentration index (FICI), and time kill assays were determined by broth microdilution. Electron microscopy (EM) was used to determine the qualitative changes brought about after treatment with K21. Results: K21 inhibited the growth of all fluconazole-resistant and susceptible Candida strains with only 2 h of exposure required to effectively kill 99.9\% of the inoculum, and a definite synergistic effect was observed with a combination of K21 and fluconazole. EM demonstrated the presence of two forms of extracellular vesicles indicative of biofilm formation and cell lysis. Conclusion: The study established the efficacy of K21 as an antifungal agent and with fluconazole-resistant candidiasis on the increase, the development of K21 can provide a promising alternative to combat acquired drug resistance.},
  language  = {en}
}