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Ren S, Bai F, Schnell V, Stanko C, Ritsch M, Schenk T, Barth E, Marz M, Wang B, Pei XH, Bierhoff H. PAPAS promotes differentiation of mammary epithelial cells and suppresses breast carcinogenesis. Cell Rep 2024; 43:113644. [PMID: 38180837 DOI: 10.1016/j.celrep.2023.113644] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Revised: 10/18/2023] [Accepted: 12/19/2023] [Indexed: 01/07/2024] Open
Abstract
Extensive remodeling of the female mammary epithelium during development and pregnancy has been linked to cancer susceptibility. The faithful response of mammary epithelial cells (MECs) to hormone signaling is key to avoiding breast cancer development. Here, we show that lactogenic differentiation of murine MECs requires silencing of genes encoding ribosomal RNA (rRNA) by the antisense transcript PAPAS. Accordingly, knockdown of PAPAS derepresses rRNA genes, attenuates the response to lactogenic hormones, and induces malignant transformation. Restoring PAPAS levels in breast cancer cells reduces tumorigenicity and lung invasion and activates many interferon-regulated genes previously linked to metastasis suppression. Mechanistically, PAPAS transcription depends on R-loop formation at the 3' end of rRNA genes, which is repressed by RNase H1 and replication protein A (RPA) overexpression in breast cancer cells. Depletion of PAPAS and upregulation of RNase H1 and RPA in human breast cancer underpin the clinical relevance of our findings.
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Affiliation(s)
- Sijia Ren
- Institute of Biochemistry and Biophysics, Center for Molecular Biomedicine (CMB), Friedrich Schiller University Jena, Hans-Knöll-Str. 2, 07745 Jena, Germany; Guangdong Provincial Key Laboratory of Regional Immunity and Diseases, International Cancer Center, Marshall Laboratory of Biomedical Engineering, Department of Anatomy and Histology, Shenzhen University Medical School, Shenzhen 518060, China; Leibniz-Institute on Aging-Fritz Lipmann Institute (FLI), Beutenbergstr. 11, 07745 Jena, Germany
| | - Feng Bai
- Department of Pathology, Shenzhen University Medical School, Shenzhen 518060, China
| | - Viviane Schnell
- Institute of Biochemistry and Biophysics, Center for Molecular Biomedicine (CMB), Friedrich Schiller University Jena, Hans-Knöll-Str. 2, 07745 Jena, Germany; Leibniz-Institute on Aging-Fritz Lipmann Institute (FLI), Beutenbergstr. 11, 07745 Jena, Germany
| | - Clara Stanko
- Department of Hematology and Medical Oncology, Jena University Hospital, Am Klinikum 1, 07747 Jena, Germany; Institute of Molecular Cell Biology, Center for Molecular Biomedicine (CMB), Jena University Hospital, Jena, Hans-Knöll-Str. 2, 07745 Jena, Germany
| | - Muriel Ritsch
- Bioinformatics Core Facility Jena, Friedrich Schiller University Jena, Leutragraben 1, 07743 Jena, Germany; RNA Bioinformatics/High Throughput Analysis, Faculty of Mathematics and Computer Science, Leutragraben 1, 07743 Jena, Germany
| | - Tino Schenk
- Department of Hematology and Medical Oncology, Jena University Hospital, Am Klinikum 1, 07747 Jena, Germany; Institute of Molecular Cell Biology, Center for Molecular Biomedicine (CMB), Jena University Hospital, Jena, Hans-Knöll-Str. 2, 07745 Jena, Germany
| | - Emanuel Barth
- Bioinformatics Core Facility Jena, Friedrich Schiller University Jena, Leutragraben 1, 07743 Jena, Germany; RNA Bioinformatics/High Throughput Analysis, Faculty of Mathematics and Computer Science, Leutragraben 1, 07743 Jena, Germany
| | - Manja Marz
- Bioinformatics Core Facility Jena, Friedrich Schiller University Jena, Leutragraben 1, 07743 Jena, Germany; RNA Bioinformatics/High Throughput Analysis, Faculty of Mathematics and Computer Science, Leutragraben 1, 07743 Jena, Germany
| | - Bin Wang
- Department of General Surgery, Shenzhen Children's Hospital, Shenzhen 518060, China
| | - Xin-Hai Pei
- Guangdong Provincial Key Laboratory of Regional Immunity and Diseases, International Cancer Center, Marshall Laboratory of Biomedical Engineering, Department of Anatomy and Histology, Shenzhen University Medical School, Shenzhen 518060, China.
| | - Holger Bierhoff
- Institute of Biochemistry and Biophysics, Center for Molecular Biomedicine (CMB), Friedrich Schiller University Jena, Hans-Knöll-Str. 2, 07745 Jena, Germany; Leibniz-Institute on Aging-Fritz Lipmann Institute (FLI), Beutenbergstr. 11, 07745 Jena, Germany.
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Ritsch M, Cassman NA, Saghaei S, Marz M. Navigating the Landscape: A Comprehensive Review of Current Virus Databases. Viruses 2023; 15:1834. [PMID: 37766241 PMCID: PMC10537806 DOI: 10.3390/v15091834] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2023] [Revised: 08/18/2023] [Accepted: 08/21/2023] [Indexed: 09/29/2023] Open
Abstract
Viruses are abundant and diverse entities that have important roles in public health, ecology, and agriculture. The identification and surveillance of viruses rely on an understanding of their genome organization, sequences, and replication strategy. Despite technological advancements in sequencing methods, our current understanding of virus diversity remains incomplete, highlighting the need to explore undiscovered viruses. Virus databases play a crucial role in providing access to sequences, annotations and other metadata, and analysis tools for studying viruses. However, there has not been a comprehensive review of virus databases in the last five years. This study aimed to fill this gap by identifying 24 active virus databases and included an extensive evaluation of their content, functionality and compliance with the FAIR principles. In this study, we thoroughly assessed the search capabilities of five database catalogs, which serve as comprehensive repositories housing a diverse array of databases and offering essential metadata. Moreover, we conducted a comprehensive review of different types of errors, encompassing taxonomy, names, missing information, sequences, sequence orientation, and chimeric sequences, with the intention of empowering users to effectively tackle these challenges. We expect this review to aid users in selecting suitable virus databases and other resources, and to help databases in error management and improve their adherence to the FAIR principles. The databases listed here represent the current knowledge of viruses and will help aid users find databases of interest based on content, functionality, and scope. The use of virus databases is integral to gaining new insights into the biology, evolution, and transmission of viruses, and developing new strategies to manage virus outbreaks and preserve global health.
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Affiliation(s)
- Muriel Ritsch
- RNA Bioinformatics and High-Throughput Analysis, Friedrich Schiller University Jena, 07743 Jena, Germany;
- European Virus Bioinformatics Center, 07743 Jena, Germany
| | - Noriko A. Cassman
- RNA Bioinformatics and High-Throughput Analysis, Friedrich Schiller University Jena, 07743 Jena, Germany;
- European Virus Bioinformatics Center, 07743 Jena, Germany
| | - Shahram Saghaei
- RNA Bioinformatics and High-Throughput Analysis, Friedrich Schiller University Jena, 07743 Jena, Germany;
- European Virus Bioinformatics Center, 07743 Jena, Germany
| | - Manja Marz
- RNA Bioinformatics and High-Throughput Analysis, Friedrich Schiller University Jena, 07743 Jena, Germany;
- European Virus Bioinformatics Center, 07743 Jena, Germany
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, 04103 Leipzig, Germany
- FLI Leibniz Institute for Age Research, 07745 Jena, Germany
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Hufsky F, Beslic D, Boeckaerts D, Duchene S, González-Tortuero E, Gruber AJ, Guo J, Jansen D, Juma J, Kongkitimanon K, Luque A, Ritsch M, Lencioni Lovate G, Nishimura L, Pas C, Domingo E, Hodcroft E, Lemey P, Sullivan MB, Weber F, González-Candelas F, Krautwurst S, Pérez-Cataluña A, Randazzo W, Sánchez G, Marz M. The International Virus Bioinformatics Meeting 2022. Viruses 2022; 14:973. [PMID: 35632715 PMCID: PMC9144528 DOI: 10.3390/v14050973] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2022] [Accepted: 04/28/2022] [Indexed: 12/22/2022] Open
Abstract
The International Virus Bioinformatics Meeting 2022 took place online, on 23-25 March 2022, and has attracted about 380 participants from all over the world. The goal of the meeting was to provide a meaningful and interactive scientific environment to promote discussion and collaboration and to inspire and suggest new research directions and questions. The participants created a highly interactive scientific environment even without physical face-to-face interactions. This meeting is a focal point to gain an insight into the state-of-the-art of the virus bioinformatics research landscape and to interact with researchers in the forefront as well as aspiring young scientists. The meeting featured eight invited and 18 contributed talks in eight sessions on three days, as well as 52 posters, which were presented during three virtual poster sessions. The main topics were: SARS-CoV-2, viral emergence and surveillance, virus-host interactions, viral sequence analysis, virus identification and annotation, phages, and viral diversity. This report summarizes the main research findings and highlights presented at the meeting.
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Affiliation(s)
- Franziska Hufsky
- European Virus Bioinformatics Center, 07743 Jena, Germany; (E.G.-T.); (A.J.G.); (J.G.); (D.J.); (K.K.); (A.L.); (M.R.); (G.L.L.); (L.N.); (E.D.); (E.H.); (P.L.); (M.B.S.); (F.W.); (F.G.-C.); (A.P.-C.); (W.R.); (G.S.)
- RNA Bioinformatics and High-Throughput Analysis, Friedrich Schiller University Jena, 07743 Jena, Germany;
| | - Denis Beslic
- Methodology and Research Infrastructure, MF1 Bioinformatics, Robert Koch Institute, 13353 Berlin, Germany;
| | - Dimitri Boeckaerts
- Laboratory of Applied Biotechnology, Department of Biotechnology, Ghent University, 9000 Ghent, Belgium; (D.B.); (C.P.)
- KERMIT, Department of Data Analysis and Mathematical Modelling, Ghent University, 9000 Ghent, Belgium
| | - Sebastian Duchene
- Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne 3000, Australia;
| | - Enrique González-Tortuero
- European Virus Bioinformatics Center, 07743 Jena, Germany; (E.G.-T.); (A.J.G.); (J.G.); (D.J.); (K.K.); (A.L.); (M.R.); (G.L.L.); (L.N.); (E.D.); (E.H.); (P.L.); (M.B.S.); (F.W.); (F.G.-C.); (A.P.-C.); (W.R.); (G.S.)
- School of Science, Engineering and Environment (SEE), University of Salford, Salford M5 4WT, UK
| | - Andreas J. Gruber
- European Virus Bioinformatics Center, 07743 Jena, Germany; (E.G.-T.); (A.J.G.); (J.G.); (D.J.); (K.K.); (A.L.); (M.R.); (G.L.L.); (L.N.); (E.D.); (E.H.); (P.L.); (M.B.S.); (F.W.); (F.G.-C.); (A.P.-C.); (W.R.); (G.S.)
- Department of Biology, University of Konstanz, 78464 Konstanz, Germany
| | - Jiarong Guo
- European Virus Bioinformatics Center, 07743 Jena, Germany; (E.G.-T.); (A.J.G.); (J.G.); (D.J.); (K.K.); (A.L.); (M.R.); (G.L.L.); (L.N.); (E.D.); (E.H.); (P.L.); (M.B.S.); (F.W.); (F.G.-C.); (A.P.-C.); (W.R.); (G.S.)
- Departments of Microbiology, and Civil, Environmental, and Geodetic Engineering, Ohio State University, Columbus, OH 43210, USA
| | - Daan Jansen
- European Virus Bioinformatics Center, 07743 Jena, Germany; (E.G.-T.); (A.J.G.); (J.G.); (D.J.); (K.K.); (A.L.); (M.R.); (G.L.L.); (L.N.); (E.D.); (E.H.); (P.L.); (M.B.S.); (F.W.); (F.G.-C.); (A.P.-C.); (W.R.); (G.S.)
- Department of Microbiology, Immunology and Transplantation, Rega Institute, Laboratory of Viral Metagenomics, KU Leuven, 3000 Leuven, Belgium
| | - John Juma
- International Livestock Research Institute (ILRI), Nairobi 00100, Kenya;
- South African National Bioinformatics Institute, South African MRC Bioinformatics Unit, Cape Town 7530, South Africa
| | - Kunaphas Kongkitimanon
- European Virus Bioinformatics Center, 07743 Jena, Germany; (E.G.-T.); (A.J.G.); (J.G.); (D.J.); (K.K.); (A.L.); (M.R.); (G.L.L.); (L.N.); (E.D.); (E.H.); (P.L.); (M.B.S.); (F.W.); (F.G.-C.); (A.P.-C.); (W.R.); (G.S.)
- Methodology and Research Infrastructure, MF1 Bioinformatics, Robert Koch Institute, 13353 Berlin, Germany;
| | - Antoni Luque
- European Virus Bioinformatics Center, 07743 Jena, Germany; (E.G.-T.); (A.J.G.); (J.G.); (D.J.); (K.K.); (A.L.); (M.R.); (G.L.L.); (L.N.); (E.D.); (E.H.); (P.L.); (M.B.S.); (F.W.); (F.G.-C.); (A.P.-C.); (W.R.); (G.S.)
- Viral Information Institute, San Diego State University, San Diego, CA 92116, USA
- Computational Science Research Center, San Diego State University, San Diego, CA 92116, USA
- Department of Mathematics and Statistics, San Diego State University, San Diego, CA 92116, USA
| | - Muriel Ritsch
- European Virus Bioinformatics Center, 07743 Jena, Germany; (E.G.-T.); (A.J.G.); (J.G.); (D.J.); (K.K.); (A.L.); (M.R.); (G.L.L.); (L.N.); (E.D.); (E.H.); (P.L.); (M.B.S.); (F.W.); (F.G.-C.); (A.P.-C.); (W.R.); (G.S.)
- RNA Bioinformatics and High-Throughput Analysis, Friedrich Schiller University Jena, 07743 Jena, Germany;
| | - Gabriel Lencioni Lovate
- European Virus Bioinformatics Center, 07743 Jena, Germany; (E.G.-T.); (A.J.G.); (J.G.); (D.J.); (K.K.); (A.L.); (M.R.); (G.L.L.); (L.N.); (E.D.); (E.H.); (P.L.); (M.B.S.); (F.W.); (F.G.-C.); (A.P.-C.); (W.R.); (G.S.)
- RNA Bioinformatics and High-Throughput Analysis, Friedrich Schiller University Jena, 07743 Jena, Germany;
- JRG Analytical MicroBioinformatics, Friedrich Schiller University Jena, 07743 Jena, Germany
| | - Luca Nishimura
- European Virus Bioinformatics Center, 07743 Jena, Germany; (E.G.-T.); (A.J.G.); (J.G.); (D.J.); (K.K.); (A.L.); (M.R.); (G.L.L.); (L.N.); (E.D.); (E.H.); (P.L.); (M.B.S.); (F.W.); (F.G.-C.); (A.P.-C.); (W.R.); (G.S.)
- Department of Genetics, School of Life Science, The Graduate University for Advanced Studies (SOKENDAI), Mishima 411-8540, Japan
- Human Genetics Laboratory, National Institute of Genetics, Mishima 411-8540, Japan
| | - Célia Pas
- Laboratory of Applied Biotechnology, Department of Biotechnology, Ghent University, 9000 Ghent, Belgium; (D.B.); (C.P.)
| | - Esteban Domingo
- European Virus Bioinformatics Center, 07743 Jena, Germany; (E.G.-T.); (A.J.G.); (J.G.); (D.J.); (K.K.); (A.L.); (M.R.); (G.L.L.); (L.N.); (E.D.); (E.H.); (P.L.); (M.B.S.); (F.W.); (F.G.-C.); (A.P.-C.); (W.R.); (G.S.)
- Centro de Biología Molecular “Severo Ochoa” (CSIC-UAM), 28049 Madrid, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd) del Instituto de Salud Carlos III, 28029 Madrid, Spain
| | - Emma Hodcroft
- European Virus Bioinformatics Center, 07743 Jena, Germany; (E.G.-T.); (A.J.G.); (J.G.); (D.J.); (K.K.); (A.L.); (M.R.); (G.L.L.); (L.N.); (E.D.); (E.H.); (P.L.); (M.B.S.); (F.W.); (F.G.-C.); (A.P.-C.); (W.R.); (G.S.)
- Institute of Social and Preventive Medicine, University of Bern, 3012 Bern, Switzerland
- Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland
| | - Philippe Lemey
- European Virus Bioinformatics Center, 07743 Jena, Germany; (E.G.-T.); (A.J.G.); (J.G.); (D.J.); (K.K.); (A.L.); (M.R.); (G.L.L.); (L.N.); (E.D.); (E.H.); (P.L.); (M.B.S.); (F.W.); (F.G.-C.); (A.P.-C.); (W.R.); (G.S.)
- Department of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven, 3000 Leuven, Belgium
| | - Matthew B. Sullivan
- European Virus Bioinformatics Center, 07743 Jena, Germany; (E.G.-T.); (A.J.G.); (J.G.); (D.J.); (K.K.); (A.L.); (M.R.); (G.L.L.); (L.N.); (E.D.); (E.H.); (P.L.); (M.B.S.); (F.W.); (F.G.-C.); (A.P.-C.); (W.R.); (G.S.)
- Departments of Microbiology, and Civil, Environmental, and Geodetic Engineering, Ohio State University, Columbus, OH 43210, USA
| | - Friedemann Weber
- European Virus Bioinformatics Center, 07743 Jena, Germany; (E.G.-T.); (A.J.G.); (J.G.); (D.J.); (K.K.); (A.L.); (M.R.); (G.L.L.); (L.N.); (E.D.); (E.H.); (P.L.); (M.B.S.); (F.W.); (F.G.-C.); (A.P.-C.); (W.R.); (G.S.)
- Institute for Virology, Veterinary Medicine, Justus-Liebig University, 35390 Gießen, Germany
| | - Fernando González-Candelas
- European Virus Bioinformatics Center, 07743 Jena, Germany; (E.G.-T.); (A.J.G.); (J.G.); (D.J.); (K.K.); (A.L.); (M.R.); (G.L.L.); (L.N.); (E.D.); (E.H.); (P.L.); (M.B.S.); (F.W.); (F.G.-C.); (A.P.-C.); (W.R.); (G.S.)
- Joint Research Unit “Infection and Public Health” FISABIO, University of Valencia, 46010 Valencia, Spain
- Institute for Integrative Systems Biology (I2SysBio), CSIC, University of Valencia, 46010 Valencia, Spain
| | - Sarah Krautwurst
- RNA Bioinformatics and High-Throughput Analysis, Friedrich Schiller University Jena, 07743 Jena, Germany;
| | - Alba Pérez-Cataluña
- European Virus Bioinformatics Center, 07743 Jena, Germany; (E.G.-T.); (A.J.G.); (J.G.); (D.J.); (K.K.); (A.L.); (M.R.); (G.L.L.); (L.N.); (E.D.); (E.H.); (P.L.); (M.B.S.); (F.W.); (F.G.-C.); (A.P.-C.); (W.R.); (G.S.)
- VISAFELab, Department of Preservation and Food Safety Technologies, Institute of Agrochemistry and Food Technology, IATA-CSIC, 46980 Valencia, Spain
| | - Walter Randazzo
- European Virus Bioinformatics Center, 07743 Jena, Germany; (E.G.-T.); (A.J.G.); (J.G.); (D.J.); (K.K.); (A.L.); (M.R.); (G.L.L.); (L.N.); (E.D.); (E.H.); (P.L.); (M.B.S.); (F.W.); (F.G.-C.); (A.P.-C.); (W.R.); (G.S.)
- VISAFELab, Department of Preservation and Food Safety Technologies, Institute of Agrochemistry and Food Technology, IATA-CSIC, 46980 Valencia, Spain
| | - Gloria Sánchez
- European Virus Bioinformatics Center, 07743 Jena, Germany; (E.G.-T.); (A.J.G.); (J.G.); (D.J.); (K.K.); (A.L.); (M.R.); (G.L.L.); (L.N.); (E.D.); (E.H.); (P.L.); (M.B.S.); (F.W.); (F.G.-C.); (A.P.-C.); (W.R.); (G.S.)
- VISAFELab, Department of Preservation and Food Safety Technologies, Institute of Agrochemistry and Food Technology, IATA-CSIC, 46980 Valencia, Spain
| | - Manja Marz
- European Virus Bioinformatics Center, 07743 Jena, Germany; (E.G.-T.); (A.J.G.); (J.G.); (D.J.); (K.K.); (A.L.); (M.R.); (G.L.L.); (L.N.); (E.D.); (E.H.); (P.L.); (M.B.S.); (F.W.); (F.G.-C.); (A.P.-C.); (W.R.); (G.S.)
- RNA Bioinformatics and High-Throughput Analysis, Friedrich Schiller University Jena, 07743 Jena, Germany;
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