2024-03-29T10:42:48Zhttp://repository.helmholtz-hzi.de/oai/requestoai:repository.helmholtz-hzi.de:10033/6211412019-08-30T11:28:12Zcom_10033_620968col_10033_620970col_10033_620969
Einzelzell-RNA-Sequenzierung beleuchtet den Infektionsprozess
Saliba, Antoine-Emmanuel
Westermann, Alexander J.
Vogel, Jörg
HIRI, Helmholtz-Institut für RNA-basierte Infektionsforschung, Josef-Schneider-Straße 2, 97080 Würzburg. Germany.
2017-10-23T14:17:43Z
2017-10-23T14:17:43Z
2017-10-11
Article
Einzelzell-RNA-Sequenzierung beleuchtet den Infektionsprozess 2017, 23 (5):525 BIOspektrum
0947-0867
1868-6249
10.1007/s12268-017-0836-y
http://hdl.handle.net/10033/621141
BIOspektrum
http://link.springer.com/10.1007/s12268-017-0836-y
http://creativecommons.org/licenses/by-nc-sa/4.0/
oai:repository.helmholtz-hzi.de:10033/6215762019-08-30T11:29:42Zcom_10033_620968col_10033_620970col_10033_620969
Genome organization and DNA accessibility control antigenic variation in trypanosomes.
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
HIRI, Helmholtz-Institut für RNA-basierte Infektionsforschung, Josef-Shneider Strasse 2, 97080 Würzburg, Germany.
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.
2018-11-20T14:22:49Z
2018-11-20T14:22:49Z
2018-01-01
Article
1476-4687
30333624
10.1038/s41586-018-0619-8
http://hdl.handle.net/10033/621576
Attribution-NonCommercial-ShareAlike 3.0 United States
http://creativecommons.org/licenses/by-nc-sa/3.0/us/
Nature
oai:repository.helmholtz-hzi.de:10033/6217412019-08-30T11:31:43Zcom_10033_620968col_10033_620970col_10033_620969col_10033_621391
Salmonella persisters undermine host immune defenses during antibiotic treatment.
Stapels, Daphne A C
Hill, Peter W S
Westermann, Alexander J
Fisher, Robert A
Thurston, Teresa L
Saliba, Antoine-Emmanuel
Blommestein, Isabelle
Vogel, Jörg
Helaine, Sophie
HIRI, Helmholtz-Institut für RNA-basierte Infektionsforschung, Josef-Shneider Strasse 2, 97080 Würzburg, Germany.
Many bacterial infections are hard to treat and tend to relapse, possibly due to the presence of antibiotic-tolerant persisters. In vitro, persister cells appear to be dormant. After uptake of Salmonella species by macrophages, nongrowing persisters also occur, but their physiological state is poorly understood. In this work, we show that Salmonella persisters arising during macrophage infection maintain a metabolically active state. Persisters reprogram macrophages by means of effectors secreted by the Salmonella pathogenicity island 2 type 3 secretion system. These effectors dampened proinflammatory innate immune responses and induced anti-inflammatory macrophage polarization. Such reprogramming allowed nongrowing Salmonella cells to survive for extended periods in their host. Persisters undermining host immune defenses might confer an advantage to the pathogen during relapse once antibiotic pressure is relieved.
2019-04-10T07:56:27Z
2019-04-10T07:56:27Z
2018-12-07
Article
Science. 2018 Dec 7;362(6419):1156-1160. doi: 10.1126/science.aat7148.
1095-9203
30523110
10.1126/science.aat7148
http://hdl.handle.net/10033/621741
Science
en
Attribution-NonCommercial-ShareAlike 4.0 International
http://creativecommons.org/licenses/by-nc-sa/4.0/
American Association for the Advancement of Science
Science (New York, N.Y.)
oai:repository.helmholtz-hzi.de:10033/6219252019-08-30T11:24:31Zcom_10033_620968col_10033_620970col_10033_620969
scSLAM-seq reveals core features of transcription dynamics in single cells.
Erhard, Florian
Baptista, Marisa A P
Krammer, Tobias
Hennig, Thomas
Lange, Marius
Arampatzi, Panagiota
Jürges, Christopher S
Theis, Fabian J
Saliba, Antoine-Emmanuel
Dölken, Lars
HIRI, Helmholtz-Institut für RNA-basierte Infektionsforschung, Josef-Shneider Strasse 2, 97080 Würzburg, Germany.
Single-cell RNA sequencing (scRNA-seq) has highlighted the important role of intercellular heterogeneity in phenotype variability in both health and disease1. However, current scRNA-seq approaches provide only a snapshot of gene expression and convey little information on the true temporal dynamics and stochastic nature of transcription. A further key limitation of scRNA-seq analysis is that the RNA profile of each individual cell can be analysed only once. Here we introduce single-cell, thiol-(SH)-linked alkylation of RNA for metabolic labelling sequencing (scSLAM-seq), which integrates metabolic RNA labelling2, biochemical nucleoside conversion3 and scRNA-seq to record transcriptional activity directly by differentiating between new and old RNA for thousands of genes per single cell. We use scSLAM-seq to study the onset of infection with lytic cytomegalovirus in single mouse fibroblasts. The cell-cycle state and dose of infection deduced from old RNA enable dose-response analysis based on new RNA. scSLAM-seq thereby both visualizes and explains differences in transcriptional activity at the single-cell level. Furthermore, it depicts 'on-off' switches and transcriptional burst kinetics in host gene expression with extensive gene-specific differences that correlate with promoter-intrinsic features (TBP-TATA-box interactions and DNA methylation). Thus, gene-specific, and not cell-specific, features explain the heterogeneity in transcriptomes between individual cells and the transcriptional response to perturbations.
2019-08-28T14:24:24Z
2019-08-28T14:24:24Z
2019-01-01
Article
Nature. 2019 Jul;571(7765):419-423. doi: 10.1038/s41586-019-1369-y. Epub 2019 Jul 10.
1476-4687
31292545
10.1038/s41586-019-1369-y
http://hdl.handle.net/10033/621925
Nature
en
Attribution-NonCommercial-ShareAlike 4.0 International
http://creativecommons.org/licenses/by-nc-sa/4.0/
Springer-Nature
Nature
oai:repository.helmholtz-hzi.de:10033/6221752020-03-12T03:28:58Zcom_10033_620968com_10033_620597col_10033_620970col_10033_620598
Eleven grand challenges in single-cell data science.
Lähnemann, David
Köster, Johannes
Szczurek, Ewa
McCarthy, Davis J
Hicks, Stephanie C
Robinson, Mark D
Vallejos, Catalina A
Campbell, Kieran R
Beerenwinkel, Niko
Mahfouz, Ahmed
Pinello, Luca
Skums, Pavel
Stamatakis, Alexandros
Attolini, Camille Stephan-Otto
Aparicio, Samuel
Baaijens, Jasmijn
Balvert, Marleen
Barbanson, Buys de
Cappuccio, Antonio
Corleone, Giacomo
Dutilh, Bas E
Florescu, Maria
Guryev, Victor
Holmer, Rens
Jahn, Katharina
Lobo, Thamar Jessurun
Keizer, Emma M
Khatri, Indu
Kielbasa, Szymon M
Korbel, Jan O
Kozlov, Alexey M
Kuo, Tzu-Hao
Lelieveldt, Boudewijn P F
Mandoiu, Ion I
Marioni, John C
Marschall, Tobias
Mölder, Felix
Niknejad, Amir
Raczkowski, Lukasz
Reinders, Marcel
Ridder, Jeroen de
Saliba, Antoine-Emmanuel
Somarakis, Antonios
Stegle, Oliver
Theis, Fabian J
Yang, Huan
Zelikovsky, Alex
McHardy, Alice C
Raphael, Benjamin J
Shah, Sohrab P
Schönhuth, Alexander
BRICS, Braunschweiger Zentrum für Systembiologie, Rebenring 56,38106 Braunschweig, Germany.;HIRI, Helmholtz-Institut für RNA-basierte Infektionsforschung, Josef-Shneider Strasse 2, 97080 Würzburg, Germany.
The recent boom in microfluidics and combinatorial indexing strategies, combined with low sequencing costs, has empowered single-cell sequencing technology. Thousands-or even millions-of cells analyzed in a single experiment amount to a data revolution in single-cell biology and pose unique data science problems. Here, we outline eleven challenges that will be central to bringing this emerging field of single-cell data science forward. For each challenge, we highlight motivating research questions, review prior work, and formulate open problems. This compendium is for established researchers, newcomers, and students alike, highlighting interesting and rewarding problems for the coming years.
2020-02-26T10:38:33Z
2020-02-26T10:38:33Z
2020-02-07
Article
Genome Biol. 2020 Feb 7;21(1):31. doi: 10.1186/s13059-020-1926-6.
1474-760X
32033589
10.1186/s13059-020-1926-6
http://hdl.handle.net/10033/622175
Genome Biology
en
Attribution-NonCommercial-ShareAlike 4.0 International
http://creativecommons.org/licenses/by-nc-sa/4.0/
BMC
Genome biology
oai:repository.helmholtz-hzi.de:10033/6222492020-05-15T11:46:19Zcom_10033_620968col_10033_620970
Atlas of the Immune Cell Repertoire in Mouse Atherosclerosis Defined by Single-Cell RNA-Sequencing and Mass Cytometry.
Winkels, Holger
Ehinger, Erik
Vassallo, Melanie
Buscher, Konrad
Dinh, Huy Q
Kobiyama, Kouji
Hamers, Anouk A J
Cochain, Clément
Vafadarnejad, Ehsan
Saliba, Antoine-Emmanuel
Zernecke, Alma
Pramod, Akula Bala
Ghosh, Amlan K
Anto Michel, Nathaly
Hoppe, Natalie
Hilgendorf, Ingo
Zirlik, Andreas
Hedrick, Catherine C
Ley, Klaus
Wolf, Dennis
HIRI, Helmholtz-Institut für RNA-basierte Infektionsforschung, Josef-Schneider-Straße 2, 97080 Würzburg, Germany.
atherosclerosis
flow cytometry
immune system
leukocytes
lymphocytes
macrophages
mass cytometry
single-cell RNA-sequencing
Using single-cell RNA-sequencing of aortic leukocytes from chow diet- and Western diet-fed Apoe-/- and Ldlr-/- mice, we detected 11 principal leukocyte clusters with distinct phenotypic and spatial characteristics while the cellular repertoire in healthy aortas was less diverse. Gene set enrichment analysis on the single-cell level established that multiple pathways, such as for lipid metabolism, proliferation, and cytokine secretion, were confined to particular leukocyte clusters. Leukocyte populations were differentially regulated in atherosclerotic Apoe-/- and Ldlr-/- mice. We confirmed the phenotypic diversity of these clusters with a novel mass cytometry 35-marker panel with metal-labeled antibodies and conventional flow cytometry. Cell populations retrieved by these protein-based approaches were highly correlated to transcriptionally defined clusters. In an integrated screening strategy of single-cell RNA-sequencing, mass cytometry, and fluorescence-activated cell sorting, we detected 3 principal B-cell subsets with alterations in surface markers, functional pathways, and in vitro cytokine secretion. Leukocyte cluster gene signatures revealed leukocyte frequencies in 126 human plaques by a genetic deconvolution strategy. This approach revealed that human carotid plaques and microdissected mouse plaques were mostly populated by macrophages, T-cells, and monocytes. In addition, the frequency of genetically defined leukocyte populations in carotid plaques predicted cardiovascular events in patients.
2020-05-07T15:18:46Z
2020-05-07T15:18:46Z
2018-03-15
Article
Other
Circ Res. 2018 Jun 8;122(12):1675-1688. doi: 10.1161/CIRCRESAHA.117.312513. Epub 2018 Mar 15.
29545366
10.1161/CIRCRESAHA.117.312513
http://hdl.handle.net/10033/622249
1524-4571
Circulation research
MC5993603
en
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5993603/
Attribution-NonCommercial-ShareAlike 4.0 International
http://creativecommons.org/licenses/by-nc-sa/4.0/
Amercan Heart Association
122
12
1675
1688
Circulation research
United States
United States
United States
United States
United States
United States
United States
oai:repository.helmholtz-hzi.de:10033/6224312020-09-10T01:49:53Zcom_10033_620968col_10033_620970
Letter by Cochain et al Regarding Article, "Transcriptome Analysis Reveals Nonfoamy Rather Than Foamy Plaque Macrophages Are Proinflammatory in Atherosclerotic Murine Models".
Cochain, Clément
Saliba, Antoine-Emmanuel
Zernecke, Alma
HIRI, Helmholtz-Institut für RNA-basierte Infektionsforschung, Josef-Shneider Strasse 2, 97080 Würzburg, Germany.
2020-09-09T12:05:25Z
2020-09-09T12:05:25Z
Article
Other
Circ Res. 2018;123(11):e48-e49. doi:10.1161/CIRCRESAHA.118.314120.
30571470
10.1161/CIRCRESAHA.118.314120
http://hdl.handle.net/10033/622431
1524-4571
Circulation research
en
Attribution-NonCommercial-ShareAlike 4.0 International
http://creativecommons.org/licenses/by-nc-sa/4.0/
Lippincott, Williams & Wilkins
123
11
e48
e49
Circulation research
United States
oai:repository.helmholtz-hzi.de:10033/6224572020-09-25T03:25:00Zcom_10033_620968col_10033_620970col_10033_620969
LifeTime and improving European healthcare through cell-based interceptive medicine.
Rajewsky, Nikolaus
Almouzni, Geneviève
Gorski, Stanislaw A
Aerts, Stein
Amit, Ido
Bertero, Michela G
Bock, Christoph
Bredenoord, Annelien L
Cavalli, Giacomo
Chiocca, Susanna
Clevers, Hans
De Strooper, Bart
Eggert, Angelika
Ellenberg, Jan
Fernández, Xosé M
Figlerowicz, Marek
Gasser, Susan M
Hubner, Norbert
Kjems, Jørgen
Knoblich, Jürgen A
Krabbe, Grietje
Lichter, Peter
Linnarsson, Sten
Marine, Jean-Christophe
Marioni, John
Marti-Renom, Marc A
Netea, Mihai G
Nickel, Dörthe
Nollmann, Marcelo
Novak, Halina R
Parkinson, Helen
Piccolo, Stefano
Pinheiro, Inês
Pombo, Ana
Popp, Christian
Reik, Wolf
Roman-Roman, Sergio
Rosenstiel, Philip
Schultze, Joachim L
Stegle, Oliver
Tanay, Amos
Testa, Giuseppe
Thanos, Dimitris
Theis, Fabian J
Torres-Padilla, Maria-Elena
Valencia, Alfonso
Vallot, Céline
van Oudenaarden, Alexander
Vidal, Marie
Voet, Thierry
TWINCORE, Zentrum für experimentelle und klinische Infektionsforschung GmbH,Feodor-Lynen Str. 7, 30625 Hannover, Germany.
LifeTime aims to track, understand and target human cells during the onset and progression of complex diseases and their response to therapy at single-cell resolution. This mission will be implemented through the development and integration of single-cell multi-omics and imaging, artificial intelligence and patient-derived experimental disease models during progression from health to disease. Analysis of such large molecular and clinical datasets will discover molecular mechanisms, create predictive computational models of disease progression, and reveal new drug targets and therapies. Timely detection and interception of disease embedded in an ethical and patient-centered vision will be achieved through interactions across academia, hospitals, patient-associations, health data management systems and industry. Applying this strategy to key medical challenges in cancer, neurological, infectious, chronic inflammatory and cardiovascular diseases at the single-cell level will usher in cell-based interceptive medicine in Europe over the next decade.
2020-09-24T13:10:04Z
2020-09-24T13:10:04Z
2020-09-07
Article
Other
Nature. 2020 Sep 7. doi: 10.1038/s41586-020-2715-9. Epub ahead of print.
32894860
10.1038/s41586-020-2715-9
http://hdl.handle.net/10033/622457
1476-4687
Nature
en
Attribution-NonCommercial-ShareAlike 4.0 International
http://creativecommons.org/licenses/by-nc-sa/4.0/
Nature publishing group(NPG)
Nature
England
oai:repository.helmholtz-hzi.de:10033/6224882020-09-29T03:08:56Zcom_10033_620968col_10033_620970col_10033_620969
Single-cell RNA-sequencing reports growth-condition-specific global transcriptomes of individual bacteria.
Imdahl, Fabian
Vafadarnejad, Ehsan
Homberger, Christina
Saliba, Antoine-Emmanuel
Vogel, Jörg
HIRI, Helmholtz-Institut für RNA-basierte Infektionsforschung, Josef-Shneider Strasse 2, 97080 Würzburg, Germany.
Bacteria respond to changes in their environment with specific transcriptional programmes, but even within genetically identical populations these programmes are not homogenously expressed1. Such transcriptional heterogeneity between individual bacteria allows genetically clonal communities to develop a complex array of phenotypes1, examples of which include persisters that resist antibiotic treatment and metabolically specialized cells that emerge under nutrient-limiting conditions2. Fluorescent reporter constructs have played a pivotal role in deciphering heterogeneous gene expression within bacterial populations3 but have been limited to recording the activity of single genes in a few genetically tractable model species, whereas the vast majority of bacteria remain difficult to engineer and/or even to cultivate. Single-cell transcriptomics is revolutionizing the analysis of phenotypic cell-to-cell variation in eukaryotes, but technical hurdles have prevented its robust application to prokaryotes. Here, using an improved poly(A)-independent single-cell RNA-sequencing protocol, we report the faithful capture of growth-dependent gene expression patterns in individual Salmonella and Pseudomonas bacteria across all RNA classes and genomic regions. These transcriptomes provide important reference points for single-cell RNA-sequencing of other bacterial species, mixed microbial communities and host-pathogen interactions.
2020-09-28T13:29:01Z
2020-09-28T13:29:01Z
2020-08-17
Article
Nat Microbiol. 2020 Oct;5(10):1202-1206. doi: 10.1038/s41564-020-0774-1. Epub 2020 Aug 17. PMID: 32807892.
32807892
10.1038/s41564-020-0774-1
http://hdl.handle.net/10033/622488
2058-5276
Nature microbiology
en
Attribution-NonCommercial-ShareAlike 4.0 International
http://creativecommons.org/licenses/by-nc-sa/4.0/
Nature research
5
10
1202
1206
Nature microbiology
England
oai:repository.helmholtz-hzi.de:10033/6225032020-10-09T01:34:23Zcom_10033_620597com_10033_621852com_10033_620968com_10033_620636col_10033_621853col_10033_620970col_10033_620969col_10033_620598col_10033_620638
Severe COVID-19 Is Marked by a Dysregulated Myeloid Cell Compartment.
Schulte-Schrepping, Jonas
Reusch, Nico
Paclik, Daniela
Baßler, Kevin
Schlickeiser, Stephan
Zhang, Bowen
Krämer, Benjamin
Krammer, Tobias
Brumhard, Sophia
Bonaguro, Lorenzo
De Domenico, Elena
Wendisch, Daniel
Grasshoff, Martin
Kapellos, Theodore S
Beckstette, Michael
Pecht, Tal
Saglam, Adem
Dietrich, Oliver
Mei, Henrik E
Schulz, Axel R
Conrad, Claudia
Kunkel, Désirée
Vafadarnejad, Ehsan
Xu, Cheng-Jian
Horne, Arik
Herbert, Miriam
Drews, Anna
Thibeault, Charlotte
Pfeiffer, Moritz
Hippenstiel, Stefan
Hocke, Andreas
Müller-Redetzky, Holger
Heim, Katrin-Moira
Machleidt, Felix
Uhrig, Alexander
Bosquillon de Jarcy, Laure
Jürgens, Linda
Stegemann, Miriam
Glösenkamp, Christoph R
Volk, Hans-Dieter
Goffinet, Christine
Landthaler, Markus
Wyler, Emanuel
Georg, Philipp
Schneider, Maria
Dang-Heine, Chantip
Neuwinger, Nick
Kappert, Kai
Tauber, Rudolf
Corman, Victor
Raabe, Jan
Kaiser, Kim Melanie
Vinh, Michael To
Rieke, Gereon
Meisel, Christian
Ulas, Thomas
Becker, Matthias
Geffers, Robert
Witzenrath, Martin
Drosten, Christian
Suttorp, Norbert
von Kalle, Christof
Kurth, Florian
Händler, Kristian
Schultze, Joachim L
Aschenbrenner, Anna C
Li, Yang
Nattermann, Jacob
Sawitzki, Birgit
Saliba, Antoine-Emmanuel
Sander, Leif Erik
BRICS, Braunschweiger Zentrum für Systembiologie, Rebenring 56,38106 Braunschweig, Germany.; HIRI, Helmholtz-Institut für RNA-basierte Infektionsforschung, Josef-Shneider Strasse 2, 97080 Würzburg, Germany.; CiiM, Zentrum für individualisierte Infektionsmedizin, Feodor-Lynen-Str.7, 30625 Hannover.; HZI,Helmholtz-Zentrum für Infektionsforschung GmbH, Inhoffenstr. 7,38124 Braunschweig, Germany.
COVID-19
SARS-CoV-2
dysfunctional neutrophils
emergency myelopoiesis
immune profiling
mass cytometry
monocytes
neutrophils
scRNA-seq
Coronavirus disease 2019 (COVID-19) is a mild to moderate respiratory tract infection, however, a subset of patients progress to severe disease and respiratory failure. The mechanism of protective immunity in mild forms and the pathogenesis of severe COVID-19 associated with increased neutrophil counts and dysregulated immune responses remain unclear. In a dual-center, two-cohort study, we combined single-cell RNA-sequencing and single-cell proteomics of whole-blood and peripheral-blood mononuclear cells to determine changes in immune cell composition and activation in mild versus severe COVID-19 (242 samples from 109 individuals) over time. HLA-DRhiCD11chi inflammatory monocytes with an interferon-stimulated gene signature were elevated in mild COVID-19. Severe COVID-19 was marked by occurrence of neutrophil precursors, as evidence of emergency myelopoiesis, dysfunctional mature neutrophils, and HLA-DRlo monocytes. Our study provides detailed insights into the systemic immune response to SARS-CoV-2 infection and reveals profound alterations in the myeloid cell compartment associated with severe COVID-19.
2020-10-08T14:17:42Z
2020-10-08T14:17:42Z
2020-08-05
Article
Other
Cell. 2020 Sep 17;182(6):1419-1440.e23. doi: 10.1016/j.cell.2020.08.001.
32810438
10.1016/j.cell.2020.08.001
http://hdl.handle.net/10033/622503
1097-4172
Cell
en
info:eu-repo/grantAgreement/EC/H2020/733100
openAccess
Attribution-NonCommercial-ShareAlike 4.0 International
http://creativecommons.org/licenses/by-nc-sa/4.0/
Elsevier /Cell Press)
182
6
1419
1440.e23
Cell
United States
oai:repository.helmholtz-hzi.de:10033/6227232021-02-09T04:33:31Zcom_10033_620968col_10033_620970col_10033_620969
A genome-wide transcriptomic analysis of embryos fathered by obese males in a murine model of diet-induced obesity.
Bernhardt, Laura
Dittrich, Marcus
El-Merahbi, Rabih
Saliba, Antoine-Emmanuel
Müller, Tobias
Sumara, Grzegorz
Vogel, Jörg
Nichols-Burns, Stefanie
Mitchell, Megan
Haaf, Thomas
El Hajj, Nady
HIRI, Helmholtz-Institut für RNA-basierte Infektionsforschung, Josef-Shneider Strasse 2, 97080 Würzburg, Germany.
Paternal obesity is known to have a negative impact on the male's reproductive health as well as the health of his offspring. Although epigenetic mechanisms have been implicated in the non-genetic transmission of acquired traits, the effect of paternal obesity on gene expression in the preimplantation embryo has not been fully studied. To this end, we investigated whether paternal obesity is associated with gene expression changes in eight-cell stage embryos fathered by males on a high-fat diet. We used single embryo RNA-seq to compare the gene expression profile of embryos generated by males on a high fat (HFD) versus control (CD) diet. This analysis revealed significant upregulation of the Samd4b and Gata6 gene in embryos in response to a paternal HFD. Furthermore, we could show a significant increase in expression of both Gata6 and Samd4b during differentiation of stromal vascular cells into mature adipocytes. These findings suggest that paternal obesity may induce changes in the male germ cells which are associated with the gene expression changes in the resulting preimplantation embryos.
2021-02-08T14:19:16Z
2021-02-08T14:19:16Z
2021-01-21
Article
Sci Rep. 2021 Jan 21;11(1):1979. doi: 10.1038/s41598-021-81226-3.
33479343
10.1038/s41598-021-81226-3
http://hdl.handle.net/10033/622723
2045-2322
Scientific reports
en
Attribution 4.0 International
http://creativecommons.org/licenses/by/4.0/
Nature Pulishing Group
11
1
1979
Scientific reports
England
oai:repository.helmholtz-hzi.de:10033/6227462021-02-17T04:32:35Zcom_10033_620968col_10033_620970col_10033_620969
Opposing Wnt signals regulate cervical squamocolumnar homeostasis and emergence of metaplasia.
Chumduri, Cindrilla
Gurumurthy, Rajendra Kumar
Berger, Hilmar
Dietrich, Oliver
Kumar, Naveen
Koster, Stefanie
Brinkmann, Volker
Hoffmann, Kirstin
Drabkina, Marina
Arampatzi, Panagiota
Son, Dajung
Klemm, Uwe
Mollenkopf, Hans-Joachim
Herbst, Hermann
Mangler, Mandy
Vogel, Jörg
Saliba, Antoine-Emmanuel
Meyer, Thomas F
HIRI, Helmholtz-Institut für RNA-basierte Infektionsforschung, Josef-Shneider Strasse 2, 97080 Würzburg, Germany.
The transition zones of the squamous and columnar epithelia constitute hotspots for the emergence of cancer, often preceded by metaplasia, in which one epithelial type is replaced by another. It remains unclear how the epithelial spatial organization is maintained and how the transition zone niche is remodelled during metaplasia. Here we used single-cell RNA sequencing to characterize epithelial subpopulations and the underlying stromal compartment of endo- and ectocervix, encompassing the transition zone. Mouse lineage tracing, organoid culture and single-molecule RNA in situ hybridizations revealed that the two epithelia derive from separate cervix-resident lineage-specific stem cell populations regulated by opposing Wnt signals from the stroma. Using a mouse model of cervical metaplasia, we further show that the endocervical stroma undergoes remodelling and increases expression of the Wnt inhibitor Dickkopf-2 (DKK2), promoting the outgrowth of ectocervical stem cells. Our data indicate that homeostasis at the transition zone results from divergent stromal signals, driving the differential proliferation of resident epithelial lineages.
2021-02-16T13:51:59Z
2021-02-16T13:51:59Z
2021-01-18
Article
Nat Cell Biol. 2021 Feb;23(2):184-197. doi: 10.1038/s41556-020-00619-0. Epub 2021 Jan 18.
33462395
10.1038/s41556-020-00619-0
http://hdl.handle.net/10033/622746
1476-4679
Nature cell biology
en
Attribution 4.0 International
http://creativecommons.org/licenses/by/4.0/
Nature research
23
2
184
197
Nature cell biology
England
oai:repository.helmholtz-hzi.de:10033/6228272021-04-10T01:34:11Zcom_10033_620968col_10033_620970
Time-Resolved scRNA-Seq Tracks the Adaptation of a Sensitive MCL Cell Line to Ibrutinib Treatment.
Fuhr, Viktoria
Vafadarnejad, Ehsan
Dietrich, Oliver
Arampatzi, Panagiota
Riedel, Angela
Saliba, Antoine-Emmanuel
Rosenwald, Andreas
Rauert-Wunderlich, Hilka
HIRI, Helmholtz-Institut für RNA-basierte Infektionsforschung, Josef-Shneider Strasse 2, 97080 Würzburg, Germany.
drug resistance
ibrutinib
mantle cell lymphoma
scRNA-seq
Since the approval of ibrutinib for relapsed/refractory mantle cell lymphoma (MCL), the treatment of this rare mature B-cell neoplasm has taken a great leap forward. Despite promising efficacy of the Bruton tyrosine kinase inhibitor, resistance arises inevitably and the underlying mechanisms remain to be elucidated. Here, we aimed to decipher the response of a sensitive MCL cell line treated with ibrutinib using time-resolved single-cell RNA sequencing. The analysis uncovered five subpopulations and their individual responses to the treatment. The effects on the B cell receptor pathway, cell cycle, surface antigen expression, and metabolism were revealed by the computational analysis and were validated by molecular biological methods. The observed upregulation of B cell receptor signaling, crosstalk with the microenvironment, upregulation of CD52, and metabolic reprogramming towards dependence on oxidative phosphorylation favor resistance to ibrutinib treatment. Targeting these cellular responses provide new therapy options in MCL.
2021-04-09T10:36:49Z
2021-04-09T10:36:49Z
2021-02-25
Article
Int J Mol Sci. 2021 Feb 25;22(5):2276. doi: 10.3390/ijms22052276.
33668876
10.3390/ijms22052276
http://hdl.handle.net/10033/622827
1422-0067
International journal of molecular sciences
en
Attribution 4.0 International
http://creativecommons.org/licenses/by/4.0/
MDPI
22
5
International journal of molecular sciences
Switzerland
oai:repository.helmholtz-hzi.de:10033/6228542021-05-06T01:46:08Zcom_10033_620597com_10033_620968col_10033_620970col_10033_620969col_10033_620598
Longitudinal Multi-omics Analyses Identify Responses of Megakaryocytes, Erythroid Cells, and Plasmablasts as Hallmarks of Severe COVID-19.
Bernardes, Joana P
Mishra, Neha
Tran, Florian
Bahmer, Thomas
Best, Lena
Blase, Johanna I
Bordoni, Dora
Franzenburg, Jeanette
Geisen, Ulf
Josephs-Spaulding, Jonathan
Köhler, Philipp
Künstner, Axel
Rosati, Elisa
Aschenbrenner, Anna C
Bacher, Petra
Baran, Nathan
Boysen, Teide
Brandt, Burkhard
Bruse, Niklas
Dörr, Jonathan
Dräger, Andreas
Elke, Gunnar
Ellinghaus, David
Fischer, Julia
Forster, Michael
Franke, Andre
Franzenburg, Sören
Frey, Norbert
Friedrichs, Anette
Fuß, Janina
Glück, Andreas
Hamm, Jacob
Hinrichsen, Finn
Hoeppner, Marc P
Imm, Simon
Junker, Ralf
Kaiser, Sina
Kan, Ying H
Knoll, Rainer
Lange, Christoph
Laue, Georg
Lier, Clemens
Lindner, Matthias
Marinos, Georgios
Markewitz, Robert
Nattermann, Jacob
Noth, Rainer
Pickkers, Peter
Rabe, Klaus F
Renz, Alina
Röcken, Christoph
Rupp, Jan
Schaffarzyk, Annika
Scheffold, Alexander
Schulte-Schrepping, Jonas
Schunk, Domagoj
Skowasch, Dirk
Ulas, Thomas
Wandinger, Klaus-Peter
Wittig, Michael
Zimmermann, Johannes
Busch, Hauke
Hoyer, Bimba F
Kaleta, Christoph
Heyckendorf, Jan
Kox, Matthijs
Rybniker, Jan
Schreiber, Stefan
Schultze, Joachim L
Rosenstiel, Philip
Deutsche COVID-19 Omics Initiative (DeCOI)
HIRI, Helmholtz-Institut für RNA-basierte Infektionsforschung, Josef-Shneider Strasse 2, 97080 Würzburg, Germany.; BRICS, Braunschweiger Zentrum für Systembiologie, Rebenring 56,38106 Braunschweig, Germany.
COVID-19
RNA-seq
acute respiratory distress
blood
disease trajectory
immune response
infectious disease
methylation
scRNA-seq
virus
Temporal resolution of cellular features associated with a severe COVID-19 disease trajectory is needed for understanding skewed immune responses and defining predictors of outcome. Here, we performed a longitudinal multi-omics study using a two-center cohort of 14 patients. We analyzed the bulk transcriptome, bulk DNA methylome, and single-cell transcriptome (>358,000 cells, including BCR profiles) of peripheral blood samples harvested from up to 5 time points. Validation was performed in two independent cohorts of COVID-19 patients. Severe COVID-19 was characterized by an increase of proliferating, metabolically hyperactive plasmablasts. Coinciding with critical illness, we also identified an expansion of interferon-activated circulating megakaryocytes and increased erythropoiesis with features of hypoxic signaling. Megakaryocyte- and erythroid-cell-derived co-expression modules were predictive of fatal disease outcome. The study demonstrates broad cellular effects of SARS-CoV-2 infection beyond adaptive immune cells and provides an entry point toward developing biomarkers and targeted treatments of patients with COVID-19.
2021-05-05T11:04:51Z
2021-05-05T11:04:51Z
2020-11-26
Article
mmunity. 2020 Dec 15;53(6):1296-1314.e9. doi: 10.1016/j.immuni.2020.11.017. Epub 2020 Nov 26.
33296687
10.1016/j.immuni.2020.11.017
http://hdl.handle.net/10033/622854
1097-4180
Immunity
en
Attribution 4.0 International
http://creativecommons.org/licenses/by/4.0/
Elsevier (Cell Press)
53
6
1296
1314.e9
Immunity
United States
oai:repository.helmholtz-hzi.de:10033/6228912021-06-03T04:38:50Zcom_10033_620589com_10033_620968col_10033_620970col_10033_620590
Initial HCV infection of adult hepatocytes triggers a temporally structured transcriptional program containing diverse pro- and anti-viral elements.
Tegtmeyer, Birthe
Vieyres, Gabrielle
Todt, Daniel
Lauber, Chris
Ginkel, Corinne
Engelmann, Michael
Herrmann, Maike
Pfaller, Christian K
Vondran, Florian W R
Broering, Ruth
Vafadarnejad, Ehsan
Saliba, Antoine-Emmanuel
Puff, Christina
Baumgärtner, Wolfgang
Miskey, Csaba
Ivics, Zoltán
Steinmann, Eike
Pietschmann, Thomas
Brown, Richard J P
TWINCORE, Zentrum für Experimentelle und Klinische Infektionsforschung GmbH, Feodor-Lynen-Str. 7, 30625 Hannover.; HIRI, Helmholtz-Institut für RNA-basierte Infektionsforschung, Josef-Schneider-Straße 2, 97080 Würzburg, Germany.
Transcriptional profiling provides global snapshots of virus-mediated cellular reprogramming, which can simultaneously encompass pro- and antiviral components. To determine early transcriptional signatures associated with HCV infection of authentic target cells, we performed ex vivo infections of adult primary human hepatocytes (PHHs) from seven donors. Longitudinal sampling identified minimal gene dysregulation at six hours post infection (hpi). In contrast, at 72 hpi, massive increases in the breadth and magnitude of HCV-induced gene dysregulation were apparent, affecting gene classes associated with diverse biological processes. Comparison with HCV-induced transcriptional dysregulation in Huh-7.5 cells identified limited overlap between the two systems. Of note, in PHHs, HCV infection initiated broad upregulation of canonical interferon (IFN)-mediated defense programs, limiting viral RNA replication and abrogating virion release. We further find that constitutive expression of IRF1 in PHHs maintains a steady-state antiviral program in the absence of infection, which can additionally reduce HCV RNA translation and replication. We also detected infection-induced downregulation of ∼90 genes encoding components of the EIF2 translation initiation complex and ribosomal subunits in PHHs, consistent with a signature of translational shutoff. As HCV polyprotein translation occurs independently of the EIF2 complex, this process is likely pro-viral: only translation initiation of host transcripts is arrested. The combination of antiviral intrinsic and inducible immunity, balanced against pro-viral programs, including translational arrest, maintains HCV replication at a low-level in PHHs. This may ultimately keep HCV under the radar of extra-hepatocyte immune surveillance while initial infection is established, promoting tolerance, preventing clearance and facilitating progression to chronicity.IMPORTANCEAcute HCV infections are often asymptomatic and therefore frequently undiagnosed. We endeavored to recreate this understudied phase of HCV infection using explanted PHHs and monitored host responses to initial infection. We detected temporally distinct virus-induced perturbations in the transcriptional landscape, which were initially narrow but massively amplified in breadth and magnitude over time. At 72 hpi, we detected dysregulation of diverse gene programs, concurrently promoting both virus clearance and virus persistence. On the one hand, baseline expression of IRF1 combined with infection-induced upregulation of IFN-mediated effector genes suppresses virus propagation. On the other, we detect transcriptional signatures of host translational inhibition, which likely reduces processing of IFN-regulated gene transcripts and facilitates virus survival. Together, our data provide important insights into constitutive and virus-induced transcriptional programs in PHHs, and identifies simultaneous antagonistic dysregulation of pro-and anti-viral programs which may facilitate host tolerance and promote viral persistence.
2021-06-02T11:34:59Z
2021-06-02T11:34:59Z
2021-03-03
Article
J Virol. 2021 Mar 3:JVI.00245-21. doi: 10.1128/JVI.00245-21. Epub ahead of print.
33658347
10.1128/JVI.00245-21
http://hdl.handle.net/10033/622891
1098-5514
Journal of virology
en
Attribution 4.0 International
http://creativecommons.org/licenses/by/4.0/
ASM
Journal of virology
United States
oai:repository.helmholtz-hzi.de:10033/6231302022-01-08T01:49:20Zcom_10033_620618com_10033_620636com_10033_620968col_10033_620970col_10033_620638col_10033_620621
Dysregulated Immunometabolism Is Associated with the Generation of Myeloid-Derived Suppressor Cells in Staphylococcus aureus Chronic Infection.
Dietrich, Oliver
Heinz, Alexander
Goldmann, Oliver
Geffers, Robert
Beineke, Andreas
Hiller, Karsten
Saliba, Antoine-Emmanuel
Medina, Eva
HZI,Helmholtz-Zentrum für Infektionsforschung GmbH, Inhoffenstr. 7,38124 Braunschweig, Germany.
Immunometabolism
Myeloid-derived suppressor cells
Single-cell RNA sequencing
Staphylococcus aureus
Myeloid-derived suppressor cells (MDSCs) are a compendium of immature myeloid cells that exhibit potent T-cell suppressive capacity and expand during pathological conditions such as cancer and chronic infections. Although well-characterized in cancer, the physiology of MDSCs in the infection setting remains enigmatic. Here, we integrated single-cell RNA sequencing (scRNA-seq) and functional metabolic profiling to gain deeper insights into the factors governing the generation and maintenance of MDSCs in chronic Staphylococcus aureus infection. We found that MDSCs originate not only in the bone marrow but also at extramedullary sites in S. aureus-infected mice. scRNA-seq showed that infection-driven MDSCs encompass a spectrum of myeloid precursors in different stages of differentiation, ranging from promyelocytes to mature neutrophils. Furthermore, the scRNA-seq analysis has also uncovered valuable phenotypic markers to distinguish mature myeloid cells from immature MDSCs. Metabolic profiling indicates that MDSCs exhibit high glycolytic activity and high glucose consumption rates, which are required for undergoing terminal maturation. However, rapid glucose consumption by MDSCs added to infection-induced perturbations in the glucose supplies in infected mice hinders the terminal maturation of MDSCs and promotes their accumulation in an immature stage. In a proof-of-concept in vivo experiment, we demonstrate the beneficial effect of increasing glucose availability in promoting MDSC terminal differentiation in infected mice. Our results provide valuable information of how metabolic alterations induced by infection influence reprogramming and differentiation of MDSCs.
2022-01-07T10:16:18Z
2022-01-07T10:16:18Z
2021-11-11
Article
J Innate Immun. 2021 Nov 11:1-18. doi: 10.1159/000519306. Epub ahead of print.
34763332
10.1159/000519306
http://hdl.handle.net/10033/623130
1662-8128
Journal of innate immunity
en
Attribution 4.0 International
http://creativecommons.org/licenses/by/4.0/
Karger
1
18
Journal of innate immunity
Switzerland
oai:repository.helmholtz-hzi.de:10033/6232172022-06-14T01:55:30Zcom_10033_620968col_10033_620970
Dynamics of Cardiac Neutrophil Diversity in Murine Myocardial Infarction.
Vafadarnejad, Ehsan
Rizzo, Giuseppe
Krampert, Laura
Arampatzi, Panagiota
Arias-Loza, Anahi-Paula
Nazzal, Yara
Rizakou, Anna
Knochenhauer, Tim
Bandi, Sourish Reddy
Nugroho, Vallery Audy
Schulz, Dirk J J
Roesch, Melanie
Alayrac, Paul
Vilar, Jose
Silvestre, Jean-Sébastien
Zernecke, Alma
Saliba, Antoine-Emmanuel
Cochain, Clément
inflammation
myocardial infarction
neutrophils
We employed single-cell transcriptomics combined with cell surface epitope detection by sequencing to investigate temporal neutrophil diversity in the blood and heart after murine myocardial infarction. At day 1, 3, and 5 after infarction, cardiac Ly6G+ (lymphocyte antigen 6G) neutrophils could be delineated into 6 distinct clusters with specific time-dependent patterning and proportions. At day 1, neutrophils were characterized by a gene expression profile proximal to bone marrow neutrophils (Cd177, Lcn2, Fpr1), and putative activity of transcriptional regulators involved in hypoxic response (Hif1a) and emergency granulopoiesis (Cebpb). At 3 and 5 days, 2 major subsets of Siglecfhi (enriched for eg, Icam1 and Tnf) and Siglecflow (Slpi, Ifitm1) neutrophils were found. Cellular indexing of transcriptomes and epitopes by sequencing (CITE-seq) analysis in blood and heart revealed that while circulating neutrophils undergo a process of aging characterized by loss of surface CD62L and upregulation of Cxcr4, heart infiltrating neutrophils acquired a unique SiglecFhi signature. SiglecFhi neutrophils were absent from the bone marrow and spleen, indicating local acquisition of the SiglecFhi signature. Reducing the influx of blood neutrophils by anti-Ly6G treatment increased proportions of cardiac SiglecFhi neutrophils, suggesting accumulation of locally aged neutrophils. Computational analysis of ligand/receptor interactions revealed putative pathways mediating neutrophil to macrophage communication in the myocardium. Finally, SiglecFhi neutrophils were also found in atherosclerotic vessels, revealing that they arise across distinct contexts of cardiovascular inflammation.
2022-06-13T11:31:22Z
2022-06-13T11:31:22Z
2020-08-19
2020-04-20
Article
32811295
10.1161/CIRCRESAHA.120.317200
http://hdl.handle.net/10033/623217
1524-4571
Circulation research
en
Attribution 4.0 International
http://creativecommons.org/licenses/by/4.0/
127
9
e232
e249
Circulation research
United States