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Jakab M, Lee KH, Uvarovskii A, Ovchinnikova S, Kulkarni SR, Jakab S, Rostalski T, Spegg C, Anders S, Augustin HG. Lung endothelium exploits susceptible tumor cell states to instruct metastatic latency. Nat Cancer 2024:10.1038/s43018-023-00716-7. [PMID: 38308117 DOI: 10.1038/s43018-023-00716-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/22/2022] [Accepted: 12/15/2023] [Indexed: 02/04/2024]
Abstract
In metastasis, cancer cells travel around the circulation to colonize distant sites. Due to the rarity of these events, the immediate fates of metastasizing tumor cells (mTCs) are poorly understood while the role of the endothelium as a dissemination interface remains elusive. Using a newly developed combinatorial mTC enrichment approach, we provide a transcriptional blueprint of the early colonization process. Following their arrest at the metastatic site, mTCs were found to either proliferate intravascularly or extravasate, thereby establishing metastatic latency. Endothelial-derived angiocrine Wnt factors drive this bifurcation, instructing mTCs to follow the extravasation-latency route. Surprisingly, mTC responsiveness towards niche-derived Wnt was established at the epigenetic level, which predetermined tumor cell behavior. Whereas hypomethylation enabled high Wnt activity leading to metastatic latency, methylated mTCs exhibited low activity and proliferated intravascularly. Collectively the data identify the predetermined methylation status of disseminated tumor cells as a key regulator of mTC behavior in the metastatic niche.
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Affiliation(s)
- Moritz Jakab
- European Center for Angioscience, Medical Faculty Mannheim, Heidelberg University, Heidelberg, Germany.
- Division of Vascular Oncology and Metastasis, German Cancer Research Center Heidelberg (DKFZ-ZMBH Alliance), Heidelberg, Germany.
- Faculty of Biosciences, Heidelberg University, Heidelberg, Germany.
| | - Ki Hong Lee
- European Center for Angioscience, Medical Faculty Mannheim, Heidelberg University, Heidelberg, Germany
- Division of Vascular Oncology and Metastasis, German Cancer Research Center Heidelberg (DKFZ-ZMBH Alliance), Heidelberg, Germany
- Faculty of Biosciences, Heidelberg University, Heidelberg, Germany
| | - Alexey Uvarovskii
- Center for Molecular Biology, Heidelberg University, Heidelberg, Germany
- Evotec SE, Göttingen, Germany
| | - Svetlana Ovchinnikova
- Center for Molecular Biology, Heidelberg University, Heidelberg, Germany
- Bioquant Center, Heidelberg University, Heidelberg, Germany
| | - Shubhada R Kulkarni
- European Center for Angioscience, Medical Faculty Mannheim, Heidelberg University, Heidelberg, Germany
- Division of Vascular Oncology and Metastasis, German Cancer Research Center Heidelberg (DKFZ-ZMBH Alliance), Heidelberg, Germany
| | - Sevinç Jakab
- Faculty of Biosciences, Heidelberg University, Heidelberg, Germany
| | - Till Rostalski
- European Center for Angioscience, Medical Faculty Mannheim, Heidelberg University, Heidelberg, Germany
- Division of Vascular Oncology and Metastasis, German Cancer Research Center Heidelberg (DKFZ-ZMBH Alliance), Heidelberg, Germany
| | - Carleen Spegg
- Division of Vascular Oncology and Metastasis, German Cancer Research Center Heidelberg (DKFZ-ZMBH Alliance), Heidelberg, Germany
| | - Simon Anders
- Center for Molecular Biology, Heidelberg University, Heidelberg, Germany
- Bioquant Center, Heidelberg University, Heidelberg, Germany
| | - Hellmut G Augustin
- European Center for Angioscience, Medical Faculty Mannheim, Heidelberg University, Heidelberg, Germany.
- Division of Vascular Oncology and Metastasis, German Cancer Research Center Heidelberg (DKFZ-ZMBH Alliance), Heidelberg, Germany.
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Jakobi T, Uvarovskii A, Dieterich C. circtools-a one-stop software solution for circular RNA research. Bioinformatics 2020; 35:2326-2328. [PMID: 30462173 PMCID: PMC6596886 DOI: 10.1093/bioinformatics/bty948] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2018] [Revised: 10/02/2018] [Accepted: 11/20/2018] [Indexed: 12/25/2022] Open
Abstract
MOTIVATION Circular RNAs (circRNAs) originate through back-splicing events from linear primary transcripts, are resistant to exonucleases, are not polyadenylated and have been shown to be highly specific for cell type and developmental stage. CircRNA detection starts from high-throughput sequencing data and is a multi-stage bioinformatics process yielding sets of potential circRNA candidates that require further analyses. While a number of tools for the prediction process already exist, publicly available analysis tools for further characterization are rare. Our work provides researchers with a harmonized workflow that covers different stages of in silico circRNA analyses, from prediction to first functional insights. RESULTS Here, we present circtools, a modular, Python-based framework for computational circRNA analyses. The software includes modules for circRNA detection, internal sequence reconstruction, quality checking, statistical testing, screening for enrichment of RBP binding sites, differential exon RNase R resistance and circRNA-specific primer design. circtools supports researchers with visualization options and data export into commonly used formats. AVAILABILITY AND IMPLEMENTATION circtools is available via https://github.com/dieterich-lab/circtools and http://circ.tools under GPLv3.0. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Tobias Jakobi
- Department of Cardiology, Angiology, and Pneumology, University Hospital Heidelberg.,DZHK (German Centre for Cardiovascular Research), Partner Site Heidelberg/Mannheim, Heidelberg, Germany
| | - Alexey Uvarovskii
- Department of Cardiology, Angiology, and Pneumology, University Hospital Heidelberg.,DZHK (German Centre for Cardiovascular Research), Partner Site Heidelberg/Mannheim, Heidelberg, Germany
| | - Christoph Dieterich
- Department of Cardiology, Angiology, and Pneumology, University Hospital Heidelberg.,DZHK (German Centre for Cardiovascular Research), Partner Site Heidelberg/Mannheim, Heidelberg, Germany
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Uvarovskii A, Dieterich C. pulseR: Versatile computational analysis of RNA turnover from metabolic labeling experiments. Bioinformatics 2017; 33:3305-3307. [DOI: 10.1093/bioinformatics/btx368] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2017] [Accepted: 06/19/2017] [Indexed: 11/13/2022] Open
Affiliation(s)
- Alexey Uvarovskii
- Section of Bioinformatics and Systems Cardiology, Department of Internal Medicine III, Klaus Tschira Institute for Integrative Computational Cardiology, University Hospital Heidelberg, Heidelberg, Germany
- German Center for Cardiovascular Research (DZHK) - Partner site Heidelberg/Mannheim, Heidelberg, Germany
| | - Christoph Dieterich
- Section of Bioinformatics and Systems Cardiology, Department of Internal Medicine III, Klaus Tschira Institute for Integrative Computational Cardiology, University Hospital Heidelberg, Heidelberg, Germany
- German Center for Cardiovascular Research (DZHK) - Partner site Heidelberg/Mannheim, Heidelberg, Germany
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Halle S, Keyser KA, Stahl FR, Busche A, Marquardt A, Zheng X, Galla M, Heissmeyer V, Heller K, Boelter J, Wagner K, Bischoff Y, Martens R, Braun A, Werth K, Uvarovskii A, Kempf H, Meyer-Hermann M, Arens R, Kremer M, Sutter G, Messerle M, Förster R. In Vivo Killing Capacity of Cytotoxic T Cells Is Limited and Involves Dynamic Interactions and T Cell Cooperativity. Immunity 2016; 44:233-45. [PMID: 26872694 PMCID: PMC4846978 DOI: 10.1016/j.immuni.2016.01.010] [Citation(s) in RCA: 155] [Impact Index Per Article: 19.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2015] [Revised: 10/08/2015] [Accepted: 11/18/2015] [Indexed: 01/11/2023]
Abstract
According to in vitro assays, T cells are thought to kill rapidly and efficiently, but the efficacy and dynamics of cytotoxic T lymphocyte (CTL)-mediated killing of virus-infected cells in vivo remains elusive. We used two-photon microscopy to quantify CTL-mediated killing in mice infected with herpesviruses or poxviruses. On average, one CTL killed 2–16 virus-infected cells per day as determined by real-time imaging and by mathematical modeling. In contrast, upon virus-induced MHC class I downmodulation, CTLs failed to destroy their targets. During killing, CTLs remained migratory and formed motile kinapses rather than static synapses with targets. Viruses encoding the calcium sensor GCaMP6s revealed strong heterogeneity in individual CTL functional capacity. Furthermore, the probability of death of infected cells increased for those contacted by more than two CTLs, indicative of CTL cooperation. Thus, direct visualization of CTLs during killing of virus-infected cells reveals crucial parameters of CD8+ T cell immunity. Two-photon imaging indicates that CTLs kill 2–16 virus-infected cells per day CTLs form kinapses rather than stable synapses when killing virus-infected cells Some CTL contacts trigger long-lasting calcium fluxes in virus-infected cells CTLs can cooperate during killing of virus-infected cells
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Affiliation(s)
- Stephan Halle
- Institute of Immunology, Hannover Medical School, 30625 Hannover, Germany.
| | | | - Felix Rolf Stahl
- Institute of Immunology, Hannover Medical School, 30625 Hannover, Germany
| | - Andreas Busche
- Institute of Virology, Hannover Medical School, 30625 Hannover, Germany
| | - Anja Marquardt
- Institute of Virology, Hannover Medical School, 30625 Hannover, Germany
| | - Xiang Zheng
- Institute of Immunology, Hannover Medical School, 30625 Hannover, Germany
| | - Melanie Galla
- Institute of Experimental Hematology, Hannover Medical School, 30625 Hannover, Germany
| | - Vigo Heissmeyer
- Institute for Immunology, Ludwig-Maximilians-Universität München, 80336 München, Germany; Institute of Molecular Immunology, Helmholtz Zentrum München, 81377 München, Germany
| | - Katrin Heller
- Institute of Immunology, Hannover Medical School, 30625 Hannover, Germany
| | - Jasmin Boelter
- Institute of Immunology, Hannover Medical School, 30625 Hannover, Germany
| | - Karen Wagner
- Institute of Virology, Hannover Medical School, 30625 Hannover, Germany
| | - Yvonne Bischoff
- Institute of Immunology, Hannover Medical School, 30625 Hannover, Germany
| | - Rieke Martens
- Institute of Immunology, Hannover Medical School, 30625 Hannover, Germany
| | - Asolina Braun
- Institute of Immunology, Hannover Medical School, 30625 Hannover, Germany
| | - Kathrin Werth
- Institute of Immunology, Hannover Medical School, 30625 Hannover, Germany
| | - Alexey Uvarovskii
- Department of Systems Immunology and Braunschweig Integrated Centre of Systems Biology, Helmholtz Centre for Infection Research, 38124 Braunschweig, Germany
| | - Harald Kempf
- Department of Systems Immunology and Braunschweig Integrated Centre of Systems Biology, Helmholtz Centre for Infection Research, 38124 Braunschweig, Germany
| | - Michael Meyer-Hermann
- Department of Systems Immunology and Braunschweig Integrated Centre of Systems Biology, Helmholtz Centre for Infection Research, 38124 Braunschweig, Germany; Institute for Biochemistry, Biotechnology, and Bioinformatics, Technische Universität Braunschweig, 38124 Braunschweig, Germany
| | - Ramon Arens
- Department of Immunohematology and Blood Transfusion, Leiden University Medical Center, 2333 ZA Leiden, the Netherlands
| | - Melanie Kremer
- Institute for Infectious Diseases and Zoonoses, Ludwig-Maximilians-Universität München, 80539 München, Germany
| | - Gerd Sutter
- Institute for Infectious Diseases and Zoonoses, Ludwig-Maximilians-Universität München, 80539 München, Germany
| | - Martin Messerle
- Institute of Virology, Hannover Medical School, 30625 Hannover, Germany
| | - Reinhold Förster
- Institute of Immunology, Hannover Medical School, 30625 Hannover, Germany.
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