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- von Rahden, Burkhard H. A. (1)
- von Rintelen, Kristina (1)
- von Rintelen, Thomas (1)
- Öchsner, Konrad (1)
- Öckinger, Erik (1)
- Öner, Arman (1)
- Öztürk-Çolak, Arzu (1)
- Ødegaard, Frode (1)
- Üçeyler, Nurcan (1)
- Červenka, Jaroslav (1)
- Żmihorski, Michal (1)
Institute
- Theodor-Boveri-Institut für Biowissenschaften (1400) (remove)
Sonstige beteiligte Institutionen
- Mildred-Scheel-Nachwuchszentrum (2)
- Ökologische Station Fabrikschleichach (2)
- Core Unit Systemmedizin (1)
- DNA Analytics Core Facility, Biocenter, University of Wuerzburg, Wuerzburg, Germany (1)
- DNA Analytics Core Facility, Biocenter, University of Würzburg, Würzburg, Germany (1)
- Department of Animal Ecology and Tropical Biology, University of Würzburg, Würzburg, Germany (1)
- EMBL, Structural and Computational Biology Unit, Heidelberg, Germany (1)
- Forschungsstation Fabrikschleichach (1)
- Fraunhofer Institute Interfacial Engineering and Biotechnology (IGB) (1)
- IZKF (Interdisziplinäres Zentrum für Klinische Forschung), Universität Würzburg (1)
ResearcherID
- D-1221-2009 (1)
Tropical peat swamp forests sequester globally significant stores of carbon in deep layers of waterlogged, anoxic, acidic and nutrient-depleted peat. The roles of microbes in supporting these forests through the formation of peat, carbon sequestration and nutrient cycling are virtually unknown. This study investigated physicochemical peat properties and microbial diversity between three dominant tree species: Shorea uliginosa (Dipterocarpaceae), Koompassia malaccensis (legumes associated with nitrogen-fixing bacteria), Eleiodoxa conferta (palm) and depths (surface, 45 and 90 cm) using microbial 16S rRNA gene amplicon sequencing. Water pH, oxygen, nitrogen, phosphorus, total phenolic contents and C/N ratio differed significantly between depths, but not tree species. Depth also strongly influenced microbial diversity and composition, while both depth and tree species exhibited significant impact on the archaeal communities. Microbial diversity was highest at the surface, where fresh leaf litter accumulates, and nutrient supply is guaranteed. Nitrogen was the core parameter correlating to microbial communities, but the interactive effects from various environmental variables displayed significant correlation to relative abundance of major microbial groups. Proteobacteria was the dominant phylum and the most abundant genus, Rhodoplanes, might be involved in nitrogen fixation. The most abundant methanogens and methanotrophs affiliated, respectively, to families Methanomassiliicoccaceae and Methylocystaceae. Our results demonstrated diverse microbial communities and provide valuable insights on microbial ecology in these extreme ecosystems.
Prusty, Bhupesh K. ; Gulve, Nitish ; Govind, Sheila ; Krueger, Gerhard R. F. ; Feichtinger, Julia ; Larcombe, Lee ; Aspinall, Richard ; Ablashi, Dharam V. ; Toro, Carla T.
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.
Milanese, Alessio ; Mende, Daniel R ; Paoli, Lucas ; Salazar, Guillem ; Ruscheweyh, Hans-Joachim ; Cuenca, Miguelangel ; Hingamp, Pascal ; Alves, Renato ; Costea, Paul I ; Coelho, Luis Pedro ; Schmidt, Thomas S. B. ; Almeida, Alexandre ; Mitchell, Alex L ; Finn, Robert D. ; Huerta-Cepas, Jaime ; Bork, Peer ; Zeller, Georg ; Sunagawa, Shinichi
Metagenomic sequencing has greatly improved our ability to profile the composition of environmental and host-associated microbial communities. However, the dependency of most methods on reference genomes, which are currently unavailable for a substantial fraction of microbial species, introduces estimation biases. We present an updated and functionally extended tool based on universal (i.e., reference-independent), phylogenetic marker gene (MG)-based operational taxonomic units (mOTUs) enabling the profiling of >7700 microbial species. As more than 30% of them could not previously be quantified at this taxonomic resolution, relative abundance estimates based on mOTUs are more accurate compared to other methods. As a new feature, we show that mOTUs, which are based on essential housekeeping genes, are demonstrably well-suited for quantification of basal transcriptional activity of community members. Furthermore, single nucleotide variation profiles estimated using mOTUs reflect those from whole genomes, which allows for comparing microbial strain populations (e.g., across different human body sites).
Krah, Franz-Sebastian ; Büntgen, Ulf ; Schaefer, Hanno ; Müller, Jörg ; Andrew, Carrie ; Boddy, Lynne ; Diez, Jeffrey ; Egli, Simon ; Freckleton, Robert ; Gange, Alan C. ; Halvorsen, Rune ; Heegaard, Einar ; Heideroth, Antje ; Heibl, Christoph ; Heilmann-Clausen, Jacob ; Høiland, Klaus ; Kar, Ritwika ; Kauserud, Håvard ; Kirk, Paul M. ; Kuyper, Thomas W. ; Krisai-Greilhuber, Irmgard ; Norden, Jenni ; Papastefanou, Phillip ; Senn-Irlet, Beatrice ; Bässler, Claus
Thermal melanism theory states that dark-colored ectotherm organisms are at an advantage at low temperature due to increased warming. This theory is generally supported for ectotherm animals, however, the function of colors in the fungal kingdom is largely unknown. Here, we test whether the color lightness of mushroom assemblages is related to climate using a dataset of 3.2 million observations of 3,054 species across Europe. Consistent with the thermal melanism theory, mushroom assemblages are significantly darker in areas with cold climates. We further show differences in color phenotype between fungal lifestyles and a lifestyle differentiated response to seasonality. These results indicate a more complex ecological role of mushroom colors and suggest functions beyond thermal adaption. Because fungi play a crucial role in terrestrial carbon and nutrient cycles, understanding the links between the thermal environment, functional coloration and species’ geographical distributions will be critical in predicting ecosystem responses to global warming.
Woodcock, B. A. ; Garratt, M. P. D. ; Powney, G. D. ; Shaw, R. F. ; Osborne, J. L. ; Soroka, J. ; Lindström, S. A. M. ; Stanley, D. ; Ouvrard, P. ; Edwards, M. E. ; Jauker, F. ; McCracken, M. E. ; Zou, Y. ; Potts, S. G. ; Rundlöf, M. ; Noriega, J. A. ; Greenop, A. ; Smith, H. G. ; Bommarco, R. ; van der Werf, W. ; Stout, J. C. ; Steffan-Dewenter, I. ; Morandin, L. ; Bullock, J. M. ; Pywell, R. F.
How insects promote crop pollination remains poorly understood in terms of the contribution of functional trait differences between species. We used meta-analyses to test for correlations between community abundance, species richness and functional trait metrics with oilseed rape yield, a globally important crop. While overall abundance is consistently important in predicting yield, functional divergence between species traits also showed a positive correlation. This result supports the complementarity hypothesis that pollination function is maintained by non-overlapping trait distributions. In artificially constructed communities (mesocosms), species richness is positively correlated with yield, although this effect is not seen under field conditions. As traits of the dominant species do not predict yield above that attributed to the effect of abundance alone, we find no evidence in support of the mass ratio hypothesis. Management practices increasing not just pollinator abundance, but also functional divergence, could benefit oilseed rape agriculture.
Wegert, Jenny ; Vokuhl, Christian ; Collord, Grace ; Del Castillo Velasco-Herrera, Martin ; Farndon, Sarah J. ; Guzzo, Charlotte ; Jorgensen, Mette ; Anderson, John ; Slater, Olga ; Duncan, Catriona ; Bausenwein, Sabrina ; Streitenberger, Heike ; Ziegler, Barbara ; Furtwängler, Rhoikos ; Graf, Norbert ; Stratton, Michael R. ; Campbell, Peter J. ; Jones, David TW ; Koelsche, Christian ; Pfister, Stefan M. ; Mifsud, William ; Sebire, Neil ; Sparber-Sauer, Monika ; Koscielniak, Ewa ; Rosenwald, Andreas ; Gessler, Manfred ; Behjati, Sam
Soft tissue tumors of infancy encompass an overlapping spectrum of diseases that pose unique diagnostic and clinical challenges. We studied genomes and transcriptomes of cryptogenic congenital mesoblastic nephroma (CMN), and extended our findings to five anatomically or histologically related soft tissue tumors: infantile fibrosarcoma (IFS), nephroblastomatosis, Wilms tumor, malignant rhabdoid tumor, and clear cell sarcoma of the kidney. A key finding is recurrent mutation of EGFR in CMN by internal tandem duplication of the kinase domain, thus delineating CMN from other childhood renal tumors. Furthermore, we identify BRAF intragenic rearrangements in CMN and IFS. Collectively these findings reveal novel diagnostic markers and therapeutic strategies and highlight a prominent role of isolated intragenic rearrangements as drivers of infant tumors.
Vujanić, Gordan M. ; Gessler, Manfred ; Ooms, Ariadne H. A. G. ; Collini, Paola ; Coulomb-l'Hermine, Aurore ; D'Hooghe, Ellen ; de Krijger, Ronald R. ; Perotti, Daniela ; Pritchard-Jones, Kathy ; Vokuhl, Christian ; van den Heuvel-Eibrink, Marry M. ; Graf, Norbert
On the basis of the results of previous national and international trials and studies, the Renal Tumour Study Group of the International Society of Paediatric Oncology (SIOP–RTSG) has developed a new study protocol for paediatric renal tumours: the UMBRELLA SIOP–RTSG 2016 protocol (the UMBRELLA protocol). Currently, the overall outcomes of patients with Wilms tumour are excellent, but subgroups with poor prognosis and increased relapse rates still exist. The identification of these subgroups is of utmost importance to improve treatment stratification, which might lead to reduction of the direct and late effects of chemotherapy. The UMBRELLA protocol aims to validate new prognostic factors, such as blastemal tumour volume and molecular markers, to further improve outcome. To achieve this aim, large, international, high-quality databases are needed, which dictate optimization and international harmonization of specimen handling and comprehensive sampling of biological material, refine definitions and improve logistics for expert review. To promote broad implementation of the UMBRELLA protocol, the updated SIOP–RTSG pathology and molecular biology protocol for Wilms tumours has been outlined, which is a consensus from the SIOP–RTSG pathology panel.
Sommerfeld, Andreas ; Senf, Cornelius ; Buma, Brian ; D'Amato, Anthony W. ; Després, Tiphaine ; Díaz-Hormazábal, Ignacio ; Fraver, Shawn ; Frelich, Lee E. ; Gutiérrez, Álvaro G. ; Hart, Sarah J. ; Harvey, Brian J. ; He, Hong S. ; Hlásny, Tomáš ; Holz, Andrés ; Kitzberger, Thomas ; Kulakowski, Dominik ; Lindenmayer, David ; Mori, Akira S. ; Müller, Jörg ; Paritsis, Juan ; Perry, George L. W. ; Stephens, Scott L. ; Svoboda, Miroslav ; Turner, Monica G. ; Veblen, Thomas T. ; Seidl, Rupert
Increasing evidence indicates that forest disturbances are changing in response to global change, yet local variability in disturbance remains high. We quantified this considerable variability and analyzed whether recent disturbance episodes around the globe were consistently driven by climate, and if human influence modulates patterns of forest disturbance. We combined remote sensing data on recent (2001–2014) disturbances with in-depth local information for 50 protected landscapes and their surroundings across the temperate biome. Disturbance patterns are highly variable, and shaped by variation in disturbance agents and traits of prevailing tree species. However, high disturbance activity is consistently linked to warmer and drier than average conditions across the globe. Disturbances in protected areas are smaller and more complex in shape compared to their surroundings affected by human land use. This signal disappears in areas with high recent natural disturbance activity, underlining the potential of climate-mediated disturbance to transform forest landscapes.
The metabolic rewiring that occurs during cell transformation is a hallmark of cancer. It is diverse in different cancers as it reflects different combinations of oncogenic drivers, tumor suppressors, and the microenvironment. Metabolic rewiring is essential to cancer as it enables uncontrolled proliferation and adaptation to the fluctuating availability of nutrients and oxygen caused by poor access to the vasculature due to tumor growth and a foreign microenvironment encountered during metastasis. Increasing evidence now indicates that the metabolic state in cancer cells also plays a causal role in tumor growth and metastasis, for example through the action of oncometabolites, which modulate cell signaling and epigenetic pathways to promote malignancy. In addition to altering the metabolic state in cancer cells, some multifunctional enzymes possess non-metabolic functions that also contribute to cell transformation. Some multifunctional enzymes that are highly expressed in cancer, such as pyruvate kinase M2 (PKM2), have non-canonical functions that are co-opted by oncogenic signaling to drive proliferation and inhibit apoptosis. Other multifunctional enzymes that are frequently downregulated in cancer, such as fructose-bisphosphatase 1 (FBP1), are tumor suppressors, directly opposing mitogenic signaling via their non-canonical functions. In some cases, the enzymatic and non-canonical roles of these enzymes are functionally linked, making the modulation of non-metabolic cellular processes dependent on the metabolic state of the cell.
The Drosophila microbiome has a limited influence on sleep, activity, and courtship behaviors
(2018)
Selkrig, Joel ; Mohammad, Farhan ; Ng, Soon Hwee ; Chua, Jia Yi ; Tumkaya, Tayfun ; Ho, Joses ; Chiang, Yin Ning ; Rieger, Dirk ; Pettersson, Sven ; Helfrich-Förster, Charlotte ; Yew, Joanne Y. ; Claridge-Chang, Adam
In animals, commensal microbes modulate various physiological functions, including behavior. While microbiota exposure is required for normal behavior in mammals, it is not known how widely this dependency is present in other animal species. We proposed the hypothesis that the microbiome has a major influence on the behavior of the vinegar fly (Drosophila melanogaster), a major invertebrate model organism. Several assays were used to test the contribution of the microbiome on some well-characterized behaviors: defensive behavior, sleep, locomotion, and courtship in microbe-bearing, control flies and two generations of germ-free animals. None of the behaviors were largely influenced by the absence of a microbiome, and the small or moderate effects were not generalizable between replicates and/or generations. These results refute the hypothesis, indicating that the Drosophila microbiome does not have a major influence over several behaviors fundamental to the animal’s survival and reproduction. The impact of commensal microbes on animal behaviour may not be broadly conserved.
Nerreter, Thomas ; Letschert, Sebastian ; Götz, Ralph ; Doose, Sören ; Danhof, Sophia ; Einsele, Hermann ; Sauer, Markus ; Hudecek, Michael
Immunotherapy with chimeric antigen receptor-engineered T-cells (CAR-T) is under investigation in multiple myeloma. There are reports of myeloma remission after CD19 CAR-T therapy, although CD19 is hardly detectable on myeloma cells by flow cytometry (FC). We apply single molecule-sensitive direct stochastic optical reconstruction microscopy (dSTORM), and demonstrate CD19 expression on a fraction of myeloma cells (10.3–80%) in 10 out of 14 patients (density: 13–5,000 molecules per cell). In contrast, FC detects CD19 in only 2 of these 10 patients, on a smaller fraction of cells. Treatment with CD19 CAR-T in vitro results in elimination of CD19-positive myeloma cells, including those with <100 CD19 molecules per cell. Similar data are obtained by dSTORM analyses of CD20 expression on myeloma cells and CD20 CAR-T. These data establish a sensitivity threshold for CAR-T and illustrate how super-resolution microscopy can guide patient selection in immunotherapy to exploit ultra-low density antigens.
Müller, Laura S. M. ; Cosentino, Raúl O. ; Förstner, Konrad U. ; Guizetti, Julien ; Wedel, Carolin ; Kaplan, Noam ; Janzen, Christian J. ; Arampatzi, Panagiota ; Vogel, Jörg ; Steinbiss, Sascha ; Otto, Thomas D. ; Saliba, Antoine-Emmanuel ; Sebra, Robert P. ; Siegel, T. Nicolai
Many evolutionarily distant pathogenic organisms have evolved similar survival strategies to evade the immune responses of their hosts. These include antigenic variation, through which an infecting organism prevents clearance by periodically altering the identity of proteins that are visible to the immune system of the host1. Antigenic variation requires large reservoirs of immunologically diverse antigen genes, which are often generated through homologous recombination, as well as mechanisms to ensure the expression of one or very few antigens at any given time. Both homologous recombination and gene expression are affected by three-dimensional genome architecture and local DNA accessibility2,3. Factors that link three-dimensional genome architecture, local chromatin conformation and antigenic variation have, to our knowledge, not yet been identified in any organism. One of the major obstacles to studying the role of genome architecture in antigenic variation has been the highly repetitive nature and heterozygosity of antigen-gene arrays, which has precluded complete genome assembly in many pathogens. Here we report the de novo haplotype-specific assembly and scaffolding of the long antigen-gene arrays of the model protozoan parasite Trypanosoma brucei, using long-read sequencing technology and conserved features of chromosome folding4. Genome-wide chromosome conformation capture (Hi-C) reveals a distinct partitioning of the genome, with antigen-encoding subtelomeric regions that are folded into distinct, highly compact compartments. In addition, we performed a range of analyses—Hi-C, fluorescence in situ hybridization, assays for transposase-accessible chromatin using sequencing and single-cell RNA sequencing—that showed that deletion of the histone variants H3.V and H4.V increases antigen-gene clustering, DNA accessibility across sites of antigen expression and switching of the expressed antigen isoform, via homologous recombination. Our analyses identify histone variants as a molecular link between global genome architecture, local chromatin conformation and antigenic variation.
Mercier, Rebecca ; Wolmarans, Annemarie ; Schubert, Jonathan ; Neuweiler, Hannes ; Johnson, Jill L. ; LaPointe, Paul
Hsp90 is a dimeric molecular chaperone that is essential for the folding and activation of hundreds of client proteins. Co-chaperone proteins regulate the ATP-driven Hsp90 client activation cycle. Aha-type co-chaperones are the most potent stimulators of the Hsp90 ATPase activity but the relationship between ATPase regulation and in vivo activity is poorly understood. We report here that the most strongly conserved region of Aha-type co-chaperones, the N terminal NxNNWHW motif, modulates the apparent affinity of Hsp90 for nucleotide substrates. The ability of yeast Aha-type co-chaperones to act in vivo is ablated when the N terminal NxNNWHW motif is removed. This work suggests that nucleotide exchange during the Hsp90 functional cycle may be more important than rate of catalysis.
Periodontal treatment prevents arthritis in mice and methotrexate ameliorates periodontal bone loss
(2019)
Lübcke, Paul M. ; Ebbers, Meinolf N. B. ; Volzke, Johann ; Bull, Jana ; Kneitz, Susanne ; Engelmann, Robby ; Lang, Hermann ; Kreikemeyer, Bernd ; Müller-Hilke, Brigitte
Recent studies indicate a causal relationship between the periodontal pathogen P. gingivalis and rheumatoid arthritis involving the production of autoantibodies against citrullinated peptides. We therefore postulated that therapeutic eradication P. gingivalis may ameliorate rheumatoid arthritis development and here turned to a mouse model in order to challenge our hypothesis. F1 (DBA/1 x B10.Q) mice were orally inoculated with P. gingivalis before collagen-induced arthritis was provoked. Chlorhexidine or metronidazole were orally administered either before or during the induction phase of arthritis and their effects on arthritis progression and alveolar bone loss were compared to intraperitoneally injected methotrexate. Arthritis incidence and severity were macroscopically scored and alveolar bone loss was evaluated via microcomputed tomography. Serum antibody titres against P. gingivalis were quantified by ELISA and microbial dysbiosis following oral inoculation was monitored in stool samples via microbiome analyses. Both, oral chlorhexidine and metronidazole reduced the incidence and ameliorated the severity of collagen-induced arthritis comparable to methotrexate. Likewise, all three therapies attenuated alveolar bone loss. Relative abundance of Porphyromonadaceae was increased after oral inoculation with P. gingivalis and decreased after treatment. This is the first study to describe beneficial effects of non-surgical periodontal treatment on collagen-induced arthritis in mice and suggests that mouthwash with chlorhexidine or metronidazole may also be beneficial for patients with rheumatoid arthritis and a coexisting periodontitis. Methotrexate ameliorated periodontitis in mice, further raising the possibility that methotrexate may also positively impact on the tooth supporting tissues of patients with rheumatoid arthritis.
Lu, Yuan ; Boswell, Wiliam ; Boswell, Mikki ; Klotz, Barbara ; Kneitz, Susanne ; Regneri, Janine ; Savage, Markita ; Mendoza, Cristina ; Postlethwait, John ; Warren, Wesley C. ; Schartl, Manfred ; Walter, Ronald B.
Cell culture and protein target-based compound screening strategies, though broadly utilized in selecting candidate compounds, often fail to eliminate candidate compounds with non-target effects and/or safety concerns until late in the drug developmental process. Phenotype screening using intact research animals is attractive because it can help identify small molecule candidate compounds that have a high probability of proceeding to clinical use. Most FDA approved, first-in-class small molecules were identified from phenotypic screening. However, phenotypic screening using rodent models is labor intensive, low-throughput, and very expensive. As a novel alternative for small molecule screening, we have been developing gene expression disease profiles, termed the Transcriptional Disease Signature (TDS), as readout of small molecule screens for therapeutic molecules. In this concept, compounds that can reverse, or otherwise affect known disease-associated gene expression patterns in whole animals may be rapidly identified for more detailed downstream direct testing of their efficacy and mode of action. To establish proof of concept for this screening strategy, we employed a transgenic strain of a small aquarium fish, medaka (Oryzias latipes), that overexpresses the malignant melanoma driver gene xmrk, a mutant egfr gene, that is driven by a pigment cell-specific mitf promoter. In this model, melanoma develops with 100% penetrance. Using the transgenic medaka malignant melanoma model, we established a screening system that employs the NanoString nCounter platform to quantify gene expression within custom sets of TDS gene targets that we had previously shown to exhibit differential transcription among xmrk-transgenic and wild-type medaka. Compound-modulated gene expression was identified using an internet-accessible custom-built data processing pipeline. The effect of a given drug on the entire TDS profile was estimated by comparing compound-modulated genes in the TDS using an activation Z-score and Kolmogorov-Smirnov statistics. TDS gene probes were designed that target common signaling pathways that include proliferation, development, toxicity, immune function, metabolism and detoxification. These pathways may be utilized to evaluate candidate compounds for potential favorable, or unfavorable, effects on melanoma-associated gene expression. Here we present the logistics of using medaka to screen compounds, as well as, the development of a user-friendly NanoString data analysis pipeline to support feasibility of this novel TDS drug-screening strategy.
Despite their popularity as enzyme engineering targets structural information about Sucrose Phosphorylases remains scarce. We recently clarified that the Q345F variant of Bifidobacterium adolescentis Sucrose Phosphorylase is able to accept large polyphenolic substrates like resveratrol via a domain shift. Here we present a crystal structure of this variant in a conformation suitable for the accommodation of the donor substrate sucrose in excellent agreement with the wild type structure. Remarkably, this conformation does not feature the previously observed domain shift which is therefore reversible and part of a dynamic process rather than a static phenomenon. This crystallographic snapshot completes our understanding of the catalytic cycle of this useful variant and will allow for a more rational design of further generations of Sucrose Phosphorylase variants.
In most organisms, ribosomal RNA (rRNA) contributes to >85% of total RNA. Thus, to obtain useful information from RNA-sequencing (RNA-seq) analyses at reasonable sequencing depth, typically, mature polyadenylated transcripts are enriched or rRNA molecules are depleted. Targeted depletion of rRNA is particularly useful when studying transcripts lacking a poly(A) tail, such as some non-coding RNAs (ncRNAs), most bacterial RNAs and partially degraded or immature transcripts. While several commercially available kits allow effective rRNA depletion, their efficiency relies on a high degree of sequence homology between oligonucleotide probes and the target RNA. This restricts the use of such kits to a limited number of organisms with conserved rRNA sequences. In this study we describe the use of biotinylated oligos and streptavidin-coated paramagnetic beads for the efficient and specific depletion of trypanosomal rRNA. Our approach reduces the levels of the most abundant rRNA transcripts to less than 5% with minimal off-target effects. By adjusting the sequence of the oligonucleotide probes, our approach can be used to deplete rRNAs or other abundant transcripts independent of species. Thus, our protocol provides a useful alternative for rRNA removal where enrichment of polyadenylated transcripts is not an option and commercial kits for rRNA are not available.
Kim, Bo-Mi ; Amores, Angel ; Kang, Seunghyun ; Ahn, Do-Hwan ; Kim, Jin-Hyoung ; Kim, Il-Chan ; Lee, Jun Hyuck ; Lee, Sung Gu ; Lee, Hyoungseok ; Lee, Jungeun ; Kim, Han-Woo ; Desvignes, Thomas ; Batzel, Peter ; Sydes, Jason ; Titus, Tom ; Wilson, Catherine A. ; Catchen, Julian M. ; Warren, Wesley C. ; Schartl, Manfred ; Detrich, H. William III ; Postlethwait, John H. ; Park, Hyun
Icefishes (suborder Notothenioidei; family Channichthyidae) are the only vertebrates that lack functional haemoglobin genes and red blood cells. Here, we report a high-quality genome assembly and linkage map for the Antarctic blackfin icefish Chaenocephalus aceratus, highlighting evolved genomic features for its unique physiology. Phylogenomic analysis revealed that Antarctic fish of the teleost suborder Notothenioidei, including icefishes, diverged from the stickleback lineage about 77 million years ago and subsequently evolved cold-adapted phenotypes as the Southern Ocean cooled to sub-zero temperatures. Our results show that genes involved in protection from ice damage, including genes encoding antifreeze glycoprotein and zona pellucida proteins, are highly expanded in the icefish genome. Furthermore, genes that encode enzymes that help to control cellular redox state, including members of the sod3 and nqo1 gene families, are expanded, probably as evolutionary adaptations to the relatively high concentration of oxygen dissolved in cold Antarctic waters. In contrast, some crucial regulators of circadian homeostasis (cry and per genes) are absent from the icefish genome, suggesting compromised control of biological rhythms in the polar light environment. The availability of the icefish genome sequence will accelerate our understanding of adaptation to extreme Antarctic environments.
Hines, Rochelle M. ; Maric, Hans Michael ; Hines, Dustin J. ; Modgil, Amit ; Panzanelli, Patrizia ; Nakamura, Yasuko ; Nathanson, Anna J. ; Cross, Alan ; Deeb, Tarek ; Brandon, Nicholas J. ; Davies, Paul ; Fritschy, Jean-Marc ; Schindelin, Hermann ; Moss, Stephen J.
Fast inhibitory synaptic transmission is mediated by γ-aminobutyric acid type A receptors (GABAARs) that are enriched at functionally diverse synapses via mechanisms that remain unclear. Using isothermal titration calorimetry and complementary methods we demonstrate an exclusive low micromolar binding of collybistin to the α2-subunit of GABAARs. To explore the biological relevance of collybistin-α2-subunit selectivity, we generate mice with a mutation in the α2-subunit-collybistin binding region (Gabra2-1). The mutation results in loss of a distinct subset of inhibitory synapses and decreased amplitude of inhibitory synaptic currents. Gabra2–1 mice have a striking phenotype characterized by increased susceptibility to seizures and early mortality. Surviving Gabra2-1 mice show anxiety and elevations in electroencephalogram δ power, which are ameliorated by treatment with the α2/α3-selective positive modulator, AZD7325. Taken together, our results demonstrate an α2-subunit selective binding of collybistin, which plays a key role in patterned brain activity, particularly during development.
Hennrich, Marco L. ; Romanov, Natalie ; Horn, Patrick ; Jaeger, Samira ; Eckstein, Volker ; Steeples, Violetta ; Ye, Fei ; Ding, Ximing ; Poisa-Beiro, Laura ; Mang, Ching Lai ; Lang, Benjamin ; Boultwood, Jacqueline ; Luft, Thomas ; Zaugg, Judith B. ; Pellagatti, Andrea ; Bork, Peer ; Aloy, Patrick ; Gavin, Anne-Claude ; Ho, Anthony D.
Diminishing potential to replace damaged tissues is a hallmark for ageing of somatic stem cells, but the mechanisms remain elusive. Here, we present proteome-wide atlases of age-associated alterations in human haematopoietic stem and progenitor cells (HPCs) and five other cell populations that constitute the bone marrow niche. For each, the abundance of a large fraction of the ~12,000 proteins identified is assessed in 59 human subjects from different ages. As the HPCs become older, pathways in central carbon metabolism exhibit features reminiscent of the Warburg effect, where glycolytic intermediates are rerouted towards anabolism. Simultaneously, altered abundance of early regulators of HPC differentiation reveals a reduced functionality and a bias towards myeloid differentiation. Ageing causes alterations in the bone marrow niche too, and diminishes the functionality of the pathways involved in HPC homing. The data represent a valuable resource for further analyses, and for validation of knowledge gained from animal models.
Heil, Hannah S. ; Schreiber, Benjamin ; Götz, Ralph ; Emmerling, Monika ; Dabauvalle, Marie-Christine ; Krohne, Georg ; Höfling, Sven ; Kamp, Martin ; Sauer, Markus ; Heinze, Katrin G.
Single-molecule localization microscopy (SMLM) aims for maximized precision and a high signal-to-noise ratio1. Both features can be provided by placing the emitter in front of a metal-dielectric nanocoating that acts as a tuned mirror2,3,4. Here, we demonstrate that a higher photon yield at a lower background on biocompatible metal-dielectric nanocoatings substantially improves SMLM performance and increases the localization precision by up to a factor of two. The resolution improvement relies solely on easy-to-fabricate nanocoatings on standard glass coverslips and is spectrally and spatially tunable by the layer design and wavelength, as experimentally demonstrated for dual-color SMLM in cells.
Gröbner, Susanne N. ; Worst, Barbara C. ; Weischenfeldt, Joachim ; Buchhalter, Ivo ; Kleinheinz, Kortine ; Rudneva, Vasilisa A. ; Johann, Pascal D. ; Balasubramanian, Gnana Prakash ; Segura-Wang, Maia ; Brabetz, Sebastian ; Bender, Sebastian ; Hutter, Barbara ; Sturm, Dominik ; Pfaff, Elke ; Hübschmann, Daniel ; Zipprich, Gideon ; Heinold, Michael ; Eils, Jürgen ; Lawerenz, Christian ; Erkek, Serap ; Lambo, Sander ; Waszak, Sebastian ; Blattmann, Claudia ; Borkhardt, Arndt ; Kuhlen, Michaela ; Eggert, Angelika ; Fulda, Simone ; Gessler, Manfred ; Wegert, Jenny ; Kappler, Roland ; Baumhoer, Daniel ; Stefan, Burdach ; Kirschner-Schwabe, Renate ; Kontny, Udo ; Kulozik, Andreas E. ; Lohmann, Dietmar ; Hettmer, Simone ; Eckert, Cornelia ; Bielack, Stefan ; Nathrath, Michaela ; Niemeyer, Charlotte ; Richter, Günther H. ; Schulte, Johannes ; Siebert, Reiner ; Westermann, Frank ; Molenaar, Jan J. ; Vassal, Gilles ; Witt, Hendrik ; Burkhardt, Birgit ; Kratz, Christian P. ; Witt, Olaf ; van Tilburg, Cornelis M. ; Kramm, Christof M. ; Fleischhack, Gudrun ; Dirksen, Uta ; Rutkowski, Stefan ; Frühwald, Michael ; Hoff, Katja von ; Wolf, Stephan ; Klingebeil, Thomas ; Koscielniak, Ewa ; Landgraf, Pablo ; Koster, Jan ; Resnick, Adam C. ; Zhang, Jinghui ; Liu, Yanling ; Zhou, Xin ; Waanders, Angela J. ; Zwijnenburg, Danny A. ; Raman, Pichai ; Brors, Benedikt ; Weber, Ursula D. ; Northcott, Paul A. ; Pajtler, Kristian W. ; Kool, Marcel ; Piro, Rosario M. ; Korbel, Jan O. ; Schlesner, Matthias ; Eils, Roland ; Jones, David T. W. ; Lichter, Peter ; Chavez, Lukas ; Zapatka, Marc ; Pfister, Stefan M.
Pan-cancer analyses that examine commonalities and differences among various cancer types have emerged as a powerful way to obtain novel insights into cancer biology. Here we present a comprehensive analysis of genetic alterations in a pan-cancer cohort including 961 tumours from children, adolescents, and young adults, comprising 24 distinct molecular types of cancer. Using a standardized workflow, we identified marked differences in terms of mutation frequency and significantly mutated genes in comparison to previously analysed adult cancers. Genetic alterations in 149 putative cancer driver genes separate the tumours into two classes: small mutation and structural/copy-number variant (correlating with germline variants). Structural variants, hyperdiploidy, and chromothripsis are linked to TP53 mutation status and mutational signatures. Our data suggest that 7–8% of the children in this cohort carry an unambiguous predisposing germline variant and that nearly 50% of paediatric neoplasms harbour a potentially druggable event, which is highly relevant for the design of future clinical trials.
Franchini, Paolo ; Jones, Julia C. ; Xiong, Peiwen ; Kneitz, Susanne ; Gompert, Zachariah ; Warren, Wesley C. ; Walter, Ronald B. ; Meyer, Axel ; Schartl, Manfred
The remarkable diversity of sex determination mechanisms known in fish may be fuelled by exceptionally high rates of sex chromosome turnovers or transitions. However, the evolutionary causes and genomic mechanisms underlying this variation and instability are yet to be understood. Here we report on an over 30-year evolutionary experiment in which we tested the genomic consequences of hybridisation and selection between two Xiphophorus fish species with different sex chromosome systems. We find that introgression and imposing selection for pigmentation phenotypes results in the retention of an unexpectedly large maternally derived genomic region. During the hybridisation process, the sex-determining region of the X chromosome from one parental species was translocated to an autosome in the hybrids leading to the evolution of a new sex chromosome. Our results highlight the complexity of factors contributing to patterns observed in hybrid genomes, and we experimentally demonstrate that hybridisation can catalyze rapid evolution of a new sex chromosome.
SMART (Simple Modular Architecture Research Tool) is a web resource (https://smart.embl.de) for the identification and annotation of protein domains and the analysis of protein domain architectures. SMART version 9 contains manually curatedmodels formore than 1300 protein domains, with a topical set of 68 new models added since our last update article (1). All the new models are for diverse recombinase families and subfamilies and as a set they provide a comprehensive overview of mobile element recombinases namely transposase, integrase, relaxase, resolvase, cas1 casposase and Xer like cellular recombinase. Further updates include the synchronization of the underlying protein databases with UniProt (2), Ensembl (3) and STRING (4), greatly increasing the total number of annotated domains and other protein features available in architecture analysis mode. Furthermore, SMART's vector-based protein display engine has been extended and updated to use the latest web technologies and the domain architecture analysis components have been optimized to handle the increased number of protein features available.
Loos, Jacqueline ; Krauss, Jochen ; Lyons, Ashley ; Föst, Stephanie ; Ohlendorf, Constanze ; Racky, Severin ; Röder, Marina ; Hudel, Lennart ; Herfert, Volker ; Tscharntke, Teja
Across Europe, calcareous grasslands become increasingly fragmented and their quality deteriorates through abandonment and land use intensification, both affecting biodiversity. Here, we investigated local and landscape effects on diversity patterns of several taxonomic groups in a landscape of highly fragmented calcareous grassland remnants. We surveyed 31 grassland fragments near Göttingen, Germany, in spring and summer 2017 for vascular plants, butterflies and birds, with sampling effort adapted to fragment area. Through regression modelling, we tested relationships between species richness and fragment size (from 314 to 51,395 m\(^2\)), successional stage, habitat connectivity and the per cent cover of arable land in the landscape at several radii. We detected 283 plant species, 53 butterfly species and 70 bird species. Of these, 59 plant species, 19 butterfly species and 9 bird species were grassland specialists. Larger fragments supported twice the species richness of plants than small ones, and hosted more species of butterflies, but not of birds. Larger grassland fragments contained more grassland specialist plants, but not butterfly or bird specialists. Increasing amounts of arable land in the landscape from 20 to 90% was related to the loss of a third of species of plants, and less so, of butterflies, but not of birds. Per cent cover of arable land negatively correlated to richness of grassland specialist plants and butterflies, but positively to grassland specialist birds. We found no effect by successional stages and habitat connectivity. Our multi-taxa approach highlights the need for conservation management at the local scale, complemented by measures at the landscape scale.
Quantitative information is omnipresent in the world and a wide range of species has been shown to use quantities to optimize their decisions. While most studies have focused on vertebrates, a growing body of research demonstrates that also insects such as honeybees possess basic quantitative abilities that might aid them in finding profitable flower patches. However, it remains unclear if for insects, quantity is a salient feature relative to other stimulus dimensions, or if it is only used as a “last resort” strategy in case other stimulus dimensions are inconclusive. Here, we tested the stingless bee Trigona fuscipennis, a species representative of a vastly understudied group of tropical pollinators, in a quantity discrimination task. In four experiments, we trained wild, free-flying bees on stimuli that depicted either one or four elements. Subsequently, bees were confronted with a choice between stimuli that matched the training stimulus either in terms of quantity or another stimulus dimension. We found that bees were able to discriminate between the two quantities, but performance differed depending on which quantity was rewarded. Furthermore, quantity was more salient than was shape. However, quantity did not measurably influence the bees' decisions when contrasted with color or surface area. Our results demonstrate that just as honeybees, small-brained stingless bees also possess basic quantitative abilities. Moreover, invertebrate pollinators seem to utilize quantity not only as "last resort" but as a salient stimulus dimension. Our study contributes to the growing body of knowledge on quantitative cognition in invertebrate species and adds to our understanding of the evolution of numerical cognition.
Dunce, James M. ; Milburn, Amy E. ; Gurusaran, Manickam ; da Cruz, Irene ; Sen, Lee T. ; Benavente, Ricardo ; Davies, Owen R.
Meiotic chromosomes undergo rapid prophase movements, which are thought to facilitate the formation of inter-homologue recombination intermediates that underlie synapsis, crossing over and segregation. The meiotic telomere complex (MAJIN, TERB1, TERB2) tethers telomere ends to the nuclear envelope and transmits cytoskeletal forces via the LINC complex to drive these rapid movements. Here, we report the molecular architecture of the meiotic telomere complex through the crystal structure of MAJIN-TERB2, together with light and X-ray scattering studies of wider complexes. The MAJIN-TERB2 2:2 hetero-tetramer binds strongly to DNA and is tethered through long flexible linkers to the inner nuclear membrane and two TRF1-binding 1:1 TERB2-TERB1 complexes. Our complementary structured illumination microscopy studies and biochemical findings reveal a telomere attachment mechanism in which MAJIN-TERB2-TERB1 recruits telomere-bound TRF1, which is then displaced during pachytene, allowing MAJIN-TERB2-TERB1 to bind telomeric DNA and form a mature attachment plate.
Dörk, Thilo ; Peterlongo, Peter ; Mannermaa, Arto ; Bolla, Manjeet K. ; Wang, Qin ; Dennis, Joe ; Ahearn, Thomas ; Andrulis, Irene L. ; Anton-Culver, Hoda ; Arndt, Volker ; Aronson, Kristan J. ; Augustinsson, Annelie ; Beane Freeman, Laura E. ; Beckmann, Matthias W. ; Beeghly-Fadiel, Alicia ; Behrens, Sabine ; Bermisheva, Marina ; Blomqvist, Carl ; Bogdanova, Natalia V. ; Bojesen, Stig E. ; Brauch, Hiltrud ; Brenner, Hermann ; Burwinkel, Barbara ; Canzian, Federico ; Chan, Tsun L. ; Chang-Claude, Jenny ; Chanock, Stephen J. ; Choi, Ji-Yeob ; Christiansen, Hans ; Clarke, Christine L. ; Couch, Fergus J. ; Czene, Kamila ; Daly, Mary B. ; dos-Santos-Silva, Isabel ; Dwek, Miriam ; Eccles, Diana M. ; Ekici, Arif B. ; Eriksson, Mikael ; Evans, D. Gareth ; Fasching, Peter A. ; Figueroa, Jonine ; Flyger, Henrik ; Fritschi, Lin ; Gabrielson, Marike ; Gago-Dominguez, Manuela ; Gao, Chi ; Gapstur, Susan M. ; García-Closas, Montserrat ; García-Sáenz, José A. ; Gaudet, Mia M. ; Giles, Graham G. ; Goldberg, Mark S. ; Goldgar, David E. ; Guenél, Pascal ; Haeberle, Lothar ; Haimann, Christopher A. ; Håkansson, Niclas ; Hall, Per ; Hamann, Ute ; Hartman, Mikael ; Hauke, Jan ; Hein, Alexander ; Hillemanns, Peter ; Hogervorst, Frans B. L. ; Hooning, Maartje J. ; Hopper, John L. ; Howell, Tony ; Huo, Dezheng ; Ito, Hidemi ; Iwasaki, Motoki ; Jakubowska, Anna ; Janni, Wolfgang ; John, Esther M. ; Jung, Audrey ; Kaaks, Rudolf ; Kang, Daehee ; Kapoor, Pooja Middha ; Khusnutdinova, Elza ; Kim, Sung-Won ; Kitahara, Cari M. ; Koutros, Stella ; Kraft, Peter ; Kristensen, Vessela N. ; Kwong, Ava ; Lambrechts, Diether ; Le Marchand, Loic ; Li, Jingmei ; Lindström, Sara ; Linet, Martha ; Lo, Wing-Yee ; Long, Jirong ; Lophatananon, Artitaya ; Lubiński, Jan ; Manoochehri, Mehdi ; Manoukian, Siranoush ; Margolin, Sara ; Martinez, Elena ; Matsuo, Keitaro ; Mavroudis, Dimitris ; Meindl, Alfons ; Menon, Usha ; Milne, Roger L. ; Mohd Taib, Nur Aishah ; Muir, Kenneth ; Mulligan, Anna Marie ; Neuhausen, Susan L. ; Nevanlinna, Heli ; Neven, Patrick ; Newman, William G. ; Offit, Kenneth ; Olopade, Olufunmilayo I. ; Olshan, Andrew F. ; Olson, Janet E. ; Olsson, Håkan ; Park, Sue K. ; Park-Simon, Tjoung-Won ; Peto, Julian ; Plaseska-Karanfilska, Dijana ; Pohl-Rescigno, Esther ; Presneau, Nadege ; Rack, Brigitte ; Radice, Paolo ; Rashid, Muhammad U. ; Rennert, Gad ; Rennert, Hedy S. ; Romero, Atocha ; Ruebner, Matthias ; Saloustros, Emmanouil ; Schmidt, Marjanka K. ; Schmutzler, Rita K. ; Schneider, Michael O. ; Schoemaker, Minouk J. ; Scott, Christopher ; Shen, Chen-Yang ; Shu, Xiao-Ou ; Simard, Jaques ; Slager, Susan ; Smichkoska, Snezhana ; Southey, Melissa C. ; Spinelli, John J. ; Stone, Jennifer ; Surowy, Harald ; Swerdlow, Anthony J. ; Tamimi, Rulla M. ; Tapper, William J. ; Teo, Soo H. ; Terry, Mary Beth ; Toland, Amanda E. ; Tollenaar, Rob A. E. M. ; Torres, Diana ; Torres-Mejía, Gabriela ; Troester, Melissa A. ; Truong, Thérèse ; Tsugane, Shoichiro ; Untch, Michael ; Vachon, Celine M. ; van den Ouweland, Ans M. W. ; van Veen, Elke M. ; Vijai, Joseph ; Wendt, Camilla ; Wolk, Alicja ; Yu, Jyh-Cherng ; Zheng, Wei ; Ziogas, Argyrios ; Ziv, Elad ; Dunnig, Alison ; Pharaoh, Paul D. P. ; Schindler, Detlev ; Devilee, Peter ; Easton, Douglas F.
Fanconi anemia (FA) is a genetically heterogeneous disorder with 22 disease-causing genes reported to date. In some FA genes, monoallelic mutations have been found to be associated with breast cancer risk, while the risk associations of others remain unknown. The gene for FA type C, FANCC, has been proposed as a breast cancer susceptibility gene based on epidemiological and sequencing studies. We used the Oncoarray project to genotype two truncating FANCC variants (p.R185X and p.R548X) in 64,760 breast cancer cases and 49,793 controls of European descent. FANCC mutations were observed in 25 cases (14 with p.R185X, 11 with p.R548X) and 26 controls (18 with p.R185X, 8 with p.R548X). There was no evidence of an association with the risk of breast cancer, neither overall (odds ratio 0.77, 95%CI 0.44–1.33, p = 0.4) nor by histology, hormone receptor status, age or family history. We conclude that the breast cancer risk association of these two FANCC variants, if any, is much smaller than for BRCA1, BRCA2 or PALB2 mutations. If this applies to all truncating variants in FANCC it would suggest there are differences between FA genes in their roles on breast cancer risk and demonstrates the merit of large consortia for clarifying risk associations of rare variants.
Dammert, Marcel A. ; Brägelmann, Johannes ; Olsen, Rachelle R. ; Böhm, Stefanie ; Monhasery, Niloufar ; Whitney, Christopher P. ; Chalishazar, Milind D. ; Tumbrink, Hannah L. ; Guthrie, Matthew R. ; Klein, Sebastian ; Ireland, Abbie S. ; Ryan, Jeremy ; Schmitt, Anna ; Marx, Annika ; Ozretić, Luka ; Castiglione, Roberta ; Lorenz, Carina ; Jachimowicz, Ron D. ; Wolf, Elmar ; Thomas, Roman K. ; Poirier, John T. ; Büttner, Reinhard ; Sen, Triparna ; Byers, Lauren A. ; Reinhardt, H. Christian ; Letai, Anthony ; Oliver, Trudy G. ; Sos, Martin L.
MYC paralogs are frequently activated in small cell lung cancer (SCLC) but represent poor drug targets. Thus, a detailed mapping of MYC-paralog-specific vulnerabilities may help to develop effective therapies for SCLC patients. Using a unique cellular CRISPR activation model, we uncover that, in contrast to MYCN and MYCL, MYC represses BCL2 transcription via interaction with MIZ1 and DNMT3a. The resulting lack of BCL2 expression promotes sensitivity to cell cycle control inhibition and dependency on MCL1. Furthermore, MYC activation leads to heightened apoptotic priming, intrinsic genotoxic stress and susceptibility to DNA damage checkpoint inhibitors. Finally, combined AURK and CHK1 inhibition substantially prolongs the survival of mice bearing MYC-driven SCLC beyond that of combination chemotherapy. These analyses uncover MYC-paralog-specific regulation of the apoptotic machinery with implications for genotype-based selection of targeted therapeutics in SCLC patients.
Steuer Costa, Wagner ; Van der Auwera, Petrus ; Glock, Caspar ; Liewald, Jana F. ; Bach, Maximilian ; Schüler, Christina ; Wabnig, Sebastian ; Oranth, Alexandra ; Masurat, Florentin ; Bringmann, Henrik ; Schoofs, Liliane ; Stelzer, Ernst H. K. ; Fischer, Sabine C. ; Gottschalk, Alexander
Animals must slow or halt locomotion to integrate sensory inputs or to change direction. In Caenorhabditis elegans, the GABAergic and peptidergic neuron RIS mediates developmentally timed quiescence. Here, we show RIS functions additionally as a locomotion stop neuron. RIS optogenetic stimulation caused acute and persistent inhibition of locomotion and pharyngeal pumping, phenotypes requiring FLP-11 neuropeptides and GABA. RIS photoactivation allows the animal to maintain its body posture by sustaining muscle tone, yet inactivating motor neuron oscillatory activity. During locomotion, RIS axonal Ca2+ signals revealed functional compartmentalization: Activity in the nerve ring process correlated with locomotion stop, while activity in a branch correlated with induced reversals. GABA was required to induce, and FLP-11 neuropeptides were required to sustain locomotion stop. RIS attenuates neuronal activity and inhibits movement, possibly enabling sensory integration and decision making, and exemplifies dual use of one cell across development in a compact nervous system.
Osmanoglu, Özge ; Gupta, Shishir K. ; Almasi, Anna ; Yagci, Seray ; Srivastava, Mugdha ; Araujo, Gabriel H. M. ; Nagy, Zoltan ; Balkenhol, Johannes ; Dandekar, Thomas
Introduction
Pro-thrombotic events are one of the prevalent causes of intensive care unit (ICU) admissions among COVID-19 patients, although the signaling events in the stimulated platelets are still unclear.
Methods
We conducted a comparative analysis of platelet transcriptome data from healthy donors, ICU, and non-ICU COVID-19 patients to elucidate these mechanisms. To surpass previous analyses, we constructed models of involved networks and control cascades by integrating a global human signaling network with transcriptome data. We investigated the control of platelet hyperactivation and the specific proteins involved.
Results
Our study revealed that control of the platelet network in ICU patients is significantly higher than in non-ICU patients. Non-ICU patients require control over fewer proteins for managing platelet hyperactivity compared to ICU patients. Identification of indispensable proteins highlighted key subnetworks, that are targetable for system control in COVID-19-related platelet hyperactivity. We scrutinized FDA-approved drugs targeting indispensable proteins and identified fostamatinib as a potent candidate for preventing thrombosis in COVID-19 patients.
Discussion
Our findings shed light on how SARS-CoV-2 efficiently affects host platelets by targeting indispensable and critical proteins involved in the control of platelet activity. We evaluated several drugs for specific control of platelet hyperactivity in ICU patients suffering from platelet hyperactivation. The focus of our approach is repurposing existing drugs for optimal control over the signaling network responsible for platelet hyperactivity in COVID-19 patients. Our study offers specific pharmacological recommendations, with drug prioritization tailored to the distinct network states observed in each patient condition. Interactive networks and detailed results can be accessed at https://fostamatinib.bioinfo-wuerz.eu/.
Carradec, Quentin ; Pelletier, Eric ; Da Silva, Corinne ; Alberti, Adriana ; Seeleuthner, Yoann ; Blanc-Mathieu, Romain ; Lima-Mendez, Gipsi ; Rocha, Fabio ; Tirichine, Leila ; Labadie, Karine ; Kirilovsky, Amos ; Bertrand, Alexis ; Engelen, Stefan ; Madoui, Mohammed-Amin ; Méheust, Raphaël ; Poulain, Julie ; Romac, Sarah ; Richter, Daniel J. ; Yoshikawa, Genki ; Dimier, Céline ; Kandels-Lewis, Stefanie ; Picheral, Marc ; Searson, Sarah ; Jaillon, Olivier ; Aury, Jean-Marc ; Karsenti, Eric ; Sullivan, Matthew B. ; Sunagawa, Shinichi ; Bork, Peer ; Not, Fabrice ; Hingamp, Pascal ; Raes, Jeroen ; Guidi, Lionel ; Ogata, Hiroyuki ; de Vargas, Colomban ; Iudicone, Daniele ; Bowler, Chris ; Wincker, Patrick
While our knowledge about the roles of microbes and viruses in the ocean has increased tremendously due to recent advances in genomics and metagenomics, research on marine microbial eukaryotes and zooplankton has benefited much less from these new technologies because of their larger genomes, their enormous diversity, and largely unexplored physiologies. Here, we use a metatranscriptomics approach to capture expressed genes in open ocean Tara Oceans stations across four organismal size fractions. The individual sequence reads cluster into 116 million unigenes representing the largest reference collection of eukaryotic transcripts from any single biome. The catalog is used to unveil functions expressed by eukaryotic marine plankton, and to assess their functional biogeography. Almost half of the sequences have no similarity with known proteins, and a great number belong to new gene families with a restricted distribution in the ocean. Overall, the resource provides the foundations for exploring the roles of marine eukaryotes in ocean ecology and biogeochemistry.
HyphaTracker: An ImageJ toolbox for time-resolved analysis of spore germination in filamentous fungi
(2018)
The dynamics of early fungal development and its interference with physiological signals and environmental factors is yet poorly understood. Especially computational analysis tools for the evaluation of the process of early spore germination and germ tube formation are still lacking. For the time-resolved analysis of conidia germination of the filamentous ascomycete Fusarium fujikuroi we developed a straightforward toolbox implemented in ImageJ. It allows for processing of microscopic acquisitions (movies) of conidial germination starting with drift correction and data reduction prior to germling analysis. From the image time series germling related region of interests (ROIs) are extracted, which are analysed for their area, circularity, and timing. ROIs originating from germlings crossing other hyphae or the image boundaries are omitted during analysis. Each conidium/hypha is identified and related to its origin, thus allowing subsequent categorization. The efficiency of HyphaTracker was proofed and the accuracy was tested on simulated germlings at different signal-to-noise ratios. Bright-field microscopic images of conidial germination of rhodopsin-deficient F. fujikuroi mutants and their respective control strains were analysed with HyphaTracker. Consistent with our observation in earlier studies the CarO deficient mutant germinated earlier and grew faster than other, CarO expressing strains.
Annunziata, Ida ; van de Vlekkert, Diantha ; Wolf, Elmar ; Finkelstein, David ; Neale, Geoffrey ; Machado, Eda ; Mosca, Rosario ; Campos, Yvan ; Tillman, Heather ; Roussel, Martine F. ; Weesner, Jason Andrew ; Fremuth, Leigh Ellen ; Qiu, Xiaohui ; Han, Min-Joon ; Grosveld, Gerard C. ; d'Azzo, Alessandra
Coordinated regulation of the lysosomal and autophagic systems ensures basal catabolism and normal cell physiology, and failure of either system causes disease. Here we describe an epigenetic rheostat orchestrated by c-MYC and histone deacetylases that inhibits lysosomal and autophagic biogenesis by concomitantly repressing the expression of the transcription factors MiT/TFE and FOXH1, and that of lysosomal and autophagy genes. Inhibition of histone deacetylases abates c-MYC binding to the promoters of lysosomal and autophagy genes, granting promoter occupancy to the MiT/TFE members, TFEB and TFE3, and/or the autophagy regulator FOXH1. In pluripotent stem cells and cancer, suppression of lysosomal and autophagic function is directly downstream of c-MYC overexpression and may represent a hallmark of malignant transformation. We propose that, by determining the fate of these catabolic systems, this hierarchical switch regulates the adaptive response of cells to pathological and physiological cues that could be exploited therapeutically.
Albrecht, Jörg ; Classen, Alice ; Vollstädt, Maximilian G.R. ; Mayr, Antonia ; Mollel, Neduvoto P. ; Schellenberger Costa, David ; Dulle, Hamadi I. ; Fischer, Markus ; Hemp, Andreas ; Howell, Kim M. ; Kleyer, Michael ; Nauss, Thomas ; Peters, Marcell K. ; Tschapka, Marco ; Steffan-Dewenter, Ingolf ; Böhning-Gaese, Katrin ; Schleuning, Matthias
Species' functional traits set the blueprint for pair-wise interactions in ecological networks. Yet, it is unknown to what extent the functional diversity of plant and animal communities controls network assembly along environmental gradients in real-world ecosystems. Here we address this question with a unique dataset of mutualistic bird-fruit, bird-flower and insect-flower interaction networks and associated functional traits of 200 plant and 282 animal species sampled along broad climate and land-use gradients on Mt. Kilimanjaro. We show that plant functional diversity is mainly limited by precipitation, while animal functional diversity is primarily limited by temperature. Furthermore, shifts in plant and animal functional diversity along the elevational gradient control the niche breadth and partitioning of the respective other trophic level. These findings reveal that climatic constraints on the functional diversity of either plants or animals determine the relative importance of bottom-up and top-down control in plant-animal interaction networks.
Andreska, Thomas ; Lüningschrör, Patrick ; Wolf, Daniel ; McFleder, Rhonda L. ; Ayon-Olivas, Maurilyn ; Rattka, Marta ; Drechsler, Christine ; Perschin, Veronika ; Blum, Robert ; Aufmkolk, Sarah ; Granado, Noelia ; Moratalla, Rosario ; Sauer, Markus ; Monoranu, Camelia ; Volkmann, Jens ; Ip, Chi Wang ; Stigloher, Christian ; Sendtner, Michael
Highlights
• Dopamine receptor-1 activation induces TrkB cell-surface expression in striatal neurons
• Dopaminergic deficits cause TrkB accumulation and clustering in the ER
• TrkB clusters colocalize with cargo receptor SORCS-2 in direct pathway striatal neurons
• Intracellular TrkB clusters fail to fuse with lysosomes after dopamine depletion
Summary
Disturbed motor control is a hallmark of Parkinson’s disease (PD). Cortico-striatal synapses play a central role in motor learning and adaption, and brain-derived neurotrophic factor (BDNF) from cortico-striatal afferents modulates their plasticity via TrkB in striatal medium spiny projection neurons (SPNs). We studied the role of dopamine in modulating the sensitivity of direct pathway SPNs (dSPNs) to BDNF in cultures of fluorescence-activated cell sorting (FACS)-enriched D1-expressing SPNs and 6-hydroxydopamine (6-OHDA)-treated rats. DRD1 activation causes enhanced TrkB translocation to the cell surface and increased sensitivity for BDNF. In contrast, dopamine depletion in cultured dSPN neurons, 6-OHDA-treated rats, and postmortem brain of patients with PD reduces BDNF responsiveness and causes formation of intracellular TrkB clusters. These clusters associate with sortilin related VPS10 domain containing receptor 2 (SORCS-2) in multivesicular-like structures, which apparently protects them from lysosomal degradation. Thus, impaired TrkB processing might contribute to disturbed motor function in PD.
The narrow escape theory (NET) predicts the escape time distribution of Brownian particles confined to a domain with reflecting borders except for one small window. Applications include molecular activation events in cell biology and biophysics. Specifically, the mean first passage time τ can be analytically calculated from the size of the domain, the escape window, and the diffusion coefficient of the particles. In this study, we systematically tested the NET in a disc by variation of the escape opening. Our model system consisted of micro-patterned lipid bilayers. For the measurement of τ, we imaged diffusing fluorescently-labeled lipids using single-molecule fluorescence microscopy. We overcame the lifetime limitation of fluorescent probes by re-scaling the measured time with the fraction of escaped particles. Experiments were complemented by matching stochastic numerical simulations. To conclude, we confirmed the NET prediction in vitro and in silico for the disc geometry in the limit of small escape openings, and we provide a straightforward solution to determine τ from incomplete experimental traces.
Munawar, Umair ; Zhou, Xiang ; Prommersberger, Sabrina ; Nerreter, Silvia ; Vogt, Cornelia ; Steinhardt, Maximilian J. ; Truger, Marietta ; Mersi, Julia ; Teufel, Eva ; Han, Seungbin ; Haertle, Larissa ; Banholzer, Nicole ; Eiring, Patrick ; Danhof, Sophia ; Navarro-Aguadero, Miguel Angel ; Fernandez-Martin, Adrian ; Ortiz-Ruiz, Alejandra ; Barrio, Santiago ; Gallardo, Miguel ; Valeri, Antonio ; Castellano, Eva ; Raab, Peter ; Rudert, Maximilian ; Haferlach, Claudia ; Sauer, Markus ; Hudecek, Michael ; Martinez-Lopez, J. ; Waldschmidt, Johannes ; Einsele, Hermann ; Rasche, Leo ; Kortüm, K. Martin
The treatment landscape in multiple myeloma (MM) is shifting from genotoxic drugs to immunotherapies. Monoclonal antibodies, immunoconjugates, T-cell engaging antibodies and CART cells have been incorporated into routine treatment algorithms, resulting in improved response rates. Nevertheless, patients continue to relapse and the underlying mechanisms of resistance remain poorly understood. While Impaired death receptor signaling has been reported to mediate resistance to CART in acute lymphoblastic leukemia, this mechanism yet remains to be elucidated in context of novel immunotherapies for MM. Here, we describe impaired death receptor signaling as a novel mechanism of resistance to T-cell mediated immunotherapies in MM. This resistance seems exclusive to novel immunotherapies while sensitivity to conventional anti-tumor therapies being preserved in vitro. As a proof of concept, we present a confirmatory clinical case indicating that the FADD/BID axis is required for meaningful responses to novel immunotherapies thus we report impaired death receptor signaling as a novel resistance mechanism to T-cell mediated immunotherapy in MM.
Reuter, Christian ; Hauf, Laura ; Imdahl, Fabian ; Sen, Rituparno ; Vafadarnejad, Ehsan ; Fey, Philipp ; Finger, Tamara ; Jones, Nicola G. ; Walles, Heike ; Barquist, Lars ; Saliba, Antoine-Emmanuel ; Groeber-Becker, Florian ; Engstler, Markus
Transmission of Trypanosoma brucei by tsetse flies involves the deposition of the cell cycle-arrested metacyclic life cycle stage into mammalian skin at the site of the fly’s bite. We introduce an advanced human skin equivalent and use tsetse flies to naturally infect the skin with trypanosomes. We detail the chronological order of the parasites’ development in the skin by single-cell RNA sequencing and find a rapid activation of metacyclic trypanosomes and differentiation to proliferative parasites. Here we show that after the establishment of a proliferative population, the parasites enter a reversible quiescent state characterized by slow replication and a strongly reduced metabolism. We term these quiescent trypanosomes skin tissue forms, a parasite population that may play an important role in maintaining the infection over long time periods and in asymptomatic infected individuals.
Meinert, Madlen ; Jessen, Christina ; Hufnagel, Anita ; Kreß, Julia Katharina Charlotte ; Burnworth, Mychal ; Däubler, Theo ; Gallasch, Till ; Da Xavier Silva, Thamara Nishida ; Dos Santos, Ancély Ferreira ; Ade, Carsten Patrick ; Schmitz, Werner ; Kneitz, Susanne ; Friedmann Angeli, José Pedro ; Meierjohann, Svenja
The cystine/glutamate antiporter xCT is an important source of cysteine for cancer cells. Once taken up, cystine is reduced to cysteine and serves as a building block for the synthesis of glutathione, which efficiently protects cells from oxidative damage and prevents ferroptosis. As melanomas are particularly exposed to several sources of oxidative stress, we investigated the biological role of cysteine and glutathione supply by xCT in melanoma. xCT activity was abolished by genetic depletion in the Tyr::CreER; Braf\(^{CA}\); Pten\(^{lox/+}\) melanoma model and by acute cystine withdrawal in melanoma cell lines. Both interventions profoundly impacted melanoma glutathione levels, but they were surprisingly well tolerated by murine melanomas in vivo and by most human melanoma cell lines in vitro. RNA sequencing of human melanoma cells revealed a strong adaptive upregulation of NRF2 and ATF4 pathways, which orchestrated the compensatory upregulation of genes involved in antioxidant defence and de novo cysteine biosynthesis. In addition, the joint activation of ATF4 and NRF2 triggered a phenotypic switch characterized by a reduction of differentiation genes and induction of pro-invasive features, which was also observed after erastin treatment or the inhibition of glutathione synthesis. NRF2 alone was capable of inducing the phenotypic switch in a transient manner. Together, our data show that cystine or glutathione levels regulate the phenotypic plasticity of melanoma cells by elevating ATF4 and NRF2.
Kreß, Julia Katharina Charlotte ; Jessen, Christina ; Hufnagel, Anita ; Schmitz, Werner ; Da Xavier Silva, Thamara Nishida ; Ferreira Dos Santos, Ancély ; Mosteo, Laura ; Goding, Colin R. ; Friedmann Angeli, José Pedro ; Meierjohann, Svenja
Highlights
• The integrated stress response leads to a general ATF4-dependent activation of NRF2
• ATF4 causes a CHAC1-dependent GSH depletion, resulting in NRF2 stabilization
• An elevation of NRF2 transcript levels fosters this effect
• NRF2 supports the ISR/ATF4 pathway by improving cystine and antioxidant supply
Summary
The redox regulator NRF2 becomes activated upon oxidative and electrophilic stress and orchestrates a response program associated with redox regulation, metabolism, tumor therapy resistance, and immune suppression. Here, we describe an unrecognized link between the integrated stress response (ISR) and NRF2 mediated by the ISR effector ATF4. The ISR is commonly activated after starvation or ER stress and plays a central role in tissue homeostasis and cancer plasticity. ATF4 increases NRF2 transcription and induces the glutathione-degrading enzyme CHAC1, which we now show to be critically important for maintaining NRF2 activation. In-depth analyses reveal that NRF2 supports ATF4-induced cells by increasing cystine uptake via the glutamate-cystine antiporter xCT. In addition, NRF2 upregulates genes mediating thioredoxin usage and regeneration, thus balancing the glutathione decrease. In conclusion, we demonstrate that the NRF2 response serves as second layer of the ISR, an observation highly relevant for the understanding of cellular resilience in health and disease.
Maihoff, Fabienne ; Sahler, Simone ; Schoger, Simon ; Brenzinger, Kristof ; Kallnik, Katharina ; Sauer, Nikki ; Bofinger, Lukas ; Schmitt, Thomas ; Nooten, Sabine S. ; Classen, Alice
Alpine bumble bees are the most important pollinators in temperate mountain ecosystems. Although they are used to encounter small-scale successions of very different climates in the mountains, many species respond sensitively to climatic changes, reflected in spatial range shifts and declining populations worldwide. Cuticular hydrocarbons (CHCs) mediate climate adaptation in some insects. However, whether they predict the elevational niche of bumble bees or their responses to climatic changes remains poorly understood. Here, we used three different approaches to study the role of bumble bees’ CHCs in the context of climate adaptation: using a 1,300 m elevational gradient, we first investigated whether the overall composition of CHCs, and two potentially climate-associated chemical traits (proportion of saturated components, mean chain length) on the cuticle of six bumble bee species were linked to the species’ elevational niches. We then analyzed intraspecific variation in CHCs of Bombus pascuorum along the elevational gradient and tested whether these traits respond to temperature. Finally, we used a field translocation experiment to test whether CHCs of Bombus lucorum workers change, when translocated from the foothill of a cool and wet mountain region to (a) higher elevations, and (b) a warm and dry region. Overall, the six species showed distinctive, species-specific CHC profiles. We found inter- and intraspecific variation in the composition of CHCs and in chemical traits along the elevational gradient, but no link to the elevational distribution of species and individuals. According to our expectations, bumble bees translocated to a warm and dry region tended to express longer CHC chains than bumble bees translocated to cool and wet foothills, which could reflect an acclimatization to regional climate. However, chain lengths did not further decrease systematically along the elevational gradient, suggesting that other factors than temperature also shape chain lengths in CHC profiles. We conclude that in alpine bumble bees, CHC profiles and traits respond at best secondarily to the climate conditions tested in this study. While the functional role of species-specific CHC profiles in bumble bees remains elusive, limited plasticity in this trait could restrict species’ ability to adapt to climatic changes.
Liu, Ruiqi ; Friedrich, Mike ; Hemmen, Katherina ; Jansen, Kerstin ; Adolfi, Mateus C. ; Schartl, Manfred ; Heinze, Katrin G.
Xiphophorus fish exhibit a clear phenotypic polymorphism in puberty onset and reproductive strategies of males. In X. nigrensis and X. multilineatus, puberty onset is genetically determined and linked to a melanocortin 4 receptor (Mc4r) polymorphism of wild-type and mutant alleles on the sex chromosomes. We hypothesized that Mc4r mutant alleles act on wild-type alleles by a dominant negative effect through receptor dimerization, leading to differential intracellular signaling and effector gene activation. Depending on signaling strength, the onset of puberty either occurs early or is delayed. Here, we show by Förster Resonance Energy Transfer (FRET) that wild-type Xiphophorus Mc4r monomers can form homodimers, but also heterodimers with mutant receptors resulting in compromised signaling which explains the reduced Mc4r signaling in large males. Thus, hetero- vs. homo- dimerization seems to be the key molecular mechanism for the polymorphism in puberty onset and body size in male fish.
Luther, Christian H. ; Brandt, Philipp ; Vylkova, Slavena ; Dandekar, Thomas ; Müller, Tobias ; Dittrich, Marcus
Fungal infections are a major global health burden where Candida albicans is among the most common fungal pathogen in humans and is a common cause of invasive candidiasis. Fungal phenotypes, such as those related to morphology, proliferation and virulence are mainly driven by gene expression, which is primarily regulated by kinase signaling cascades. Serine-arginine (SR) protein kinases are highly conserved among eukaryotes and are involved in major transcriptional processes in human and S. cerevisiae. Candida albicans harbors two SR protein kinases, while Sky2 is important for metabolic adaptation, Sky1 has similar functions as in S. cerevisiae. To investigate the role of these SR kinases for the regulation of transcriptional responses in C. albicans, we performed RNA sequencing of sky1Δ and sky2Δ and integrated a comprehensive phosphoproteome dataset of these mutants. Using a Systems Biology approach, we study transcriptional regulation in the context of kinase signaling networks. Transcriptomic enrichment analysis indicates that pathways involved in the regulation of gene expression are downregulated and mitochondrial processes are upregulated in sky1Δ. In sky2Δ, primarily metabolic processes are affected, especially for arginine, and we observed that arginine-induced hyphae formation is impaired in sky2Δ. In addition, our analysis identifies several transcription factors as potential drivers of the transcriptional response. Among these, a core set is shared between both kinase knockouts, but it appears to regulate different subsets of target genes. To elucidate these diverse regulatory patterns, we created network modules by integrating the data of site-specific protein phosphorylation and gene expression with kinase-substrate predictions and protein-protein interactions. These integrated signaling modules reveal shared parts but also highlight specific patterns characteristic for each kinase. Interestingly, the modules contain many proteins involved in fungal morphogenesis and stress response. Accordingly, experimental phenotyping shows a higher resistance to Hygromycin B for sky1Δ. Thus, our study demonstrates that a combination of computational approaches with integration of experimental data can offer a new systems biological perspective on the complex network of signaling and transcription. With that, the investigation of the interface between signaling and transcriptional regulation in C. albicans provides a deeper insight into how cellular mechanisms can shape the phenotype.
Wu, Hao ; Zhao, Xiufeng ; Hochrein, Sophia M. ; Eckstein, Miriam ; Gubert, Gabriela F. ; Knöpper, Konrad ; Mansilla, Ana Maria ; Öner, Arman ; Doucet-Ladevèze, Remi ; Schmitz, Werner ; Ghesquière, Bart ; Theurich, Sebastian ; Dudek, Jan ; Gasteiger, Georg ; Zernecke, Alma ; Kobold, Sebastian ; Kastenmüller, Wolfgang ; Vaeth, Martin
T cell exhaustion is a hallmark of cancer and persistent infections, marked by inhibitory receptor upregulation, diminished cytokine secretion, and impaired cytolytic activity. Terminally exhausted T cells are steadily replenished by a precursor population (Tpex), but the metabolic principles governing Tpex maintenance and the regulatory circuits that control their exhaustion remain incompletely understood. Using a combination of gene-deficient mice, single-cell transcriptomics, and metabolomic analyses, we show that mitochondrial insufficiency is a cell-intrinsic trigger that initiates the functional exhaustion of T cells. At the molecular level, we find that mitochondrial dysfunction causes redox stress, which inhibits the proteasomal degradation of hypoxia-inducible factor 1α (HIF-1α) and promotes the transcriptional and metabolic reprogramming of Tpex cells into terminally exhausted T cells. Our findings also bear clinical significance, as metabolic engineering of chimeric antigen receptor (CAR) T cells is a promising strategy to enhance the stemness and functionality of Tpex cells for cancer immunotherapy.
Müller, Jörg ; Mitesser, Oliver ; Schaefer, H. Martin ; Seibold, Sebastian ; Busse, Annika ; Kriegel, Peter ; Rabl, Dominik ; Gelis, Rudy ; Arteaga, Alejandro ; Freile, Juan ; Leite, Gabriel Augusto ; de Melo, Tomaz Nascimento ; LeBien, Jack ; Campos-Cerqueira, Marconi ; Blüthgen, Nico ; Tremlett, Constance J. ; Böttger, Dennis ; Feldhaar, Heike ; Grella, Nina ; Falconí-López, Ana ; Donoso, David A. ; Moriniere, Jerome ; Buřivalová, Zuzana
Tropical forest recovery is fundamental to addressing the intertwined climate and biodiversity loss crises. While regenerating trees sequester carbon relatively quickly, the pace of biodiversity recovery remains contentious. Here, we use bioacoustics and metabarcoding to measure forest recovery post-agriculture in a global biodiversity hotspot in Ecuador. We show that the community composition, and not species richness, of vocalizing vertebrates identified by experts reflects the restoration gradient. Two automated measures – an acoustic index model and a bird community composition derived from an independently developed Convolutional Neural Network - correlated well with restoration (adj-R² = 0.62 and 0.69, respectively). Importantly, both measures reflected composition of non-vocalizing nocturnal insects identified via metabarcoding. We show that such automated monitoring tools, based on new technologies, can effectively monitor the success of forest recovery, using robust and reproducible data.
Neural processing of a desired moving direction requires the continuous comparison between the current heading and the goal direction. While the neural basis underlying the current heading is well-studied, the coding of the goal direction remains unclear in insects. Here, we used tetrode recordings in tethered flying monarch butterflies to unravel how a goal direction is represented in the insect brain. While recording, the butterflies maintained robust goal directions relative to a virtual sun. By resetting their goal directions, we found neurons whose spatial tuning was tightly linked to the goal directions. Importantly, their tuning was unaffected when the butterflies changed their heading after compass perturbations, showing that these neurons specifically encode the goal direction. Overall, we here discovered invertebrate goal-direction neurons that share functional similarities to goal-direction cells reported in mammals. Our results give insights into the evolutionarily conserved principles of goal-directed spatial orientation in animals.
Djakovic, Lara ; Hennig, Thomas ; Reinisch, Katharina ; Milić, Andrea ; Whisnant, Adam W. ; Wolf, Katharina ; Weiß, Elena ; Haas, Tobias ; Grothey, Arnhild ; Jürges, Christopher S. ; Kluge, Michael ; Wolf, Elmar ; Erhard, Florian ; Friedel, Caroline C. ; Dölken, Lars
Herpes simplex virus 1 (HSV-1) infection and stress responses disrupt transcription termination by RNA Polymerase II (Pol II). In HSV-1 infection, but not upon salt or heat stress, this is accompanied by a dramatic increase in chromatin accessibility downstream of genes. Here, we show that the HSV-1 immediate-early protein ICP22 is both necessary and sufficient to induce downstream open chromatin regions (dOCRs) when transcription termination is disrupted by the viral ICP27 protein. This is accompanied by a marked ICP22-dependent loss of histones downstream of affected genes consistent with impaired histone repositioning in the wake of Pol II. Efficient knock-down of the ICP22-interacting histone chaperone FACT is not sufficient to induce dOCRs in ΔICP22 infection but increases dOCR induction in wild-type HSV-1 infection. Interestingly, this is accompanied by a marked increase in chromatin accessibility within gene bodies. We propose a model in which allosteric changes in Pol II composition downstream of genes and ICP22-mediated interference with FACT activity explain the differential impairment of histone repositioning downstream of genes in the wake of Pol II in HSV-1 infection.
Haake, Markus ; Haack, Beatrice ; Schäfer, Tina ; Harter, Patrick N. ; Mattavelli, Greta ; Eiring, Patrick ; Vashist, Neha ; Wedekink, Florian ; Genssler, Sabrina ; Fischer, Birgitt ; Dahlhoff, Julia ; Mokhtari, Fatemeh ; Kuzkina, Anastasia ; Welters, Marij J. P. ; Benz, Tamara M. ; Sorger, Lena ; Thiemann, Vincent ; Almanzar, Giovanni ; Selle, Martina ; Thein, Klara ; Späth, Jacob ; Gonzalez, Maria Cecilia ; Reitinger, Carmen ; Ipsen-Escobedo, Andrea ; Wistuba-Hamprecht, Kilian ; Eichler, Kristin ; Filipski, Katharina ; Zeiner, Pia S. ; Beschorner, Rudi ; Goedemans, Renske ; Gogolla, Falk Hagen ; Hackl, Hubert ; Rooswinkel, Rogier W. ; Thiem, Alexander ; Romer Roche, Paula ; Joshi, Hemant ; Pühringer, Dirk ; Wöckel, Achim ; Diessner, Joachim E. ; Rüdiger, Manfred ; Leo, Eugen ; Cheng, Phil F. ; Levesque, Mitchell P. ; Goebeler, Matthias ; Sauer, Markus ; Nimmerjahn, Falk ; Schuberth-Wagner, Christine ; Felten, Stefanie von ; Mittelbronn, Michel ; Mehling, Matthias ; Beilhack, Andreas ; van der Burg, Sjoerd H. ; Riedel, Angela ; Weide, Benjamin ; Dummer, Reinhard ; Wischhusen, Jörg
Immune checkpoint blockade therapy is beneficial and even curative for some cancer patients. However, the majority don’t respond to immune therapy. Across different tumor types, pre-existing T cell infiltrates predict response to checkpoint-based immunotherapy. Based on in vitro pharmacological studies, mouse models and analyses of human melanoma patients, we show that the cytokine GDF-15 impairs LFA-1/β2-integrin-mediated adhesion of T cells to activated endothelial cells, which is a pre-requisite of T cell extravasation. In melanoma patients, GDF-15 serum levels strongly correlate with failure of PD-1-based immune checkpoint blockade therapy. Neutralization of GDF-15 improves both T cell trafficking and therapy efficiency in murine tumor models. Thus GDF-15, beside its known role in cancer-related anorexia and cachexia, emerges as a regulator of T cell extravasation into the tumor microenvironment, which provides an even stronger rationale for therapeutic anti-GDF-15 antibody development.
Salehi, Saeede ; Zare, Abdolhossein ; Prezza, Gianluca ; Bader, Jakob ; Schneider, Cornelius ; Fischer, Utz ; Meissner, Felix ; Mann, Matthias ; Briese, Michael ; Sendtner, Michael
The neuronal RNA-binding protein Ptbp2 regulates neuronal differentiation by modulating alternative splicing programs in the nucleus. Such programs contribute to axonogenesis by adjusting the levels of protein isoforms involved in axon growth and branching. While its functions in alternative splicing have been described in detail, cytosolic roles of Ptbp2 for axon growth have remained elusive. Here, we show that Ptbp2 is located in the cytosol including axons and growth cones of motoneurons, and that depletion of cytosolic Ptbp2 affects axon growth. We identify Ptbp2 as a major interactor of the 3’ UTR of Hnrnpr mRNA encoding the RNA-binding protein hnRNP R. Axonal localization of Hnrnpr mRNA and local synthesis of hnRNP R protein are strongly reduced when Ptbp2 is depleted, leading to defective axon growth. Ptbp2 regulates hnRNP R translation by mediating the association of Hnrnpr with ribosomes in a manner dependent on the translation factor eIF5A2. Our data thus suggest a mechanism whereby cytosolic Ptbp2 modulates axon growth by fine-tuning the mRNA transport and local synthesis of an RNA-binding protein.