1
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Tao W, Yu Z, Han JDJ. Single-cell senescence identification reveals senescence heterogeneity, trajectory, and modulators. Cell Metab 2024; 36:1126-1143.e5. [PMID: 38604170 DOI: 10.1016/j.cmet.2024.03.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/18/2023] [Revised: 12/15/2023] [Accepted: 03/13/2024] [Indexed: 04/13/2024]
Abstract
Cellular senescence underlies many aging-related pathologies, but its heterogeneity poses challenges for studying and targeting senescent cells. We present here a machine learning program senescent cell identification (SenCID), which accurately identifies senescent cells in both bulk and single-cell transcriptome. Trained on 602 samples from 52 senescence transcriptome datasets spanning 30 cell types, SenCID identifies six major senescence identities (SIDs). Different SIDs exhibit different senescence baselines, stemness, gene functions, and responses to senolytics. SenCID enables the reconstruction of senescent trajectories under normal aging, chronic diseases, and COVID-19. Additionally, when applied to single-cell Perturb-seq data, SenCID helps reveal a hierarchy of senescence modulators. Overall, SenCID is an essential tool for precise single-cell analysis of cellular senescence, enabling targeted interventions against senescent cells.
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Affiliation(s)
- Wanyu Tao
- Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Center for Quantitative Biology (CQB), Peking University, Beijing, China
| | - Zhengqing Yu
- Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Center for Quantitative Biology (CQB), Peking University, Beijing, China
| | - Jing-Dong J Han
- Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Center for Quantitative Biology (CQB), Peking University, Beijing, China; Peking University Chengdu Academy for Advanced Interdisciplinary Biotechnologies, Chengdu, China.
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2
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Lee M, Guo Q, Kim M, Choi J, Segura A, Genceroglu A, LeBlanc L, Ramirez N, Jang YJ, Jang Y, Lee BK, Marcotte EM, Kim J. Systematic mapping of TF-mediated cell fate changes by a pooled induction coupled with scRNA-seq and multi-omics approaches. Genome Res 2024; 34:484-497. [PMID: 38580401 PMCID: PMC11067882 DOI: 10.1101/gr.277926.123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2023] [Accepted: 02/21/2024] [Indexed: 04/07/2024]
Abstract
Transcriptional regulation controls cellular functions through interactions between transcription factors (TFs) and their chromosomal targets. However, understanding the fate conversion potential of multiple TFs in an inducible manner remains limited. Here, we introduce iTF-seq as a method for identifying individual TFs that can alter cell fate toward specific lineages at a single-cell level. iTF-seq enables time course monitoring of transcriptome changes, and with biotinylated individual TFs, it provides a multi-omics approach to understanding the mechanisms behind TF-mediated cell fate changes. Our iTF-seq study in mouse embryonic stem cells identified multiple TFs that trigger rapid transcriptome changes indicative of differentiation within a day of induction. Moreover, cells expressing these potent TFs often show a slower cell cycle and increased cell death. Further analysis using bioChIP-seq revealed that GCM1 and OTX2 act as pioneer factors and activators by increasing gene accessibility and activating the expression of lineage specification genes during cell fate conversion. iTF-seq has utility in both mapping cell fate conversion and understanding cell fate conversion mechanisms.
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Affiliation(s)
- Muyoung Lee
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, Texas 78712, USA
| | - Qingqing Guo
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, Texas 78712, USA
| | - Mijeong Kim
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, Texas 78712, USA
| | - Joonhyuk Choi
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, Texas 78712, USA
| | - Alia Segura
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, Texas 78712, USA
| | - Alper Genceroglu
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, Texas 78712, USA
| | - Lucy LeBlanc
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, Texas 78712, USA
| | - Nereida Ramirez
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, Texas 78712, USA
| | - Yu Jin Jang
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, Texas 78712, USA
| | - Yeejin Jang
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, Texas 78712, USA
| | - Bum-Kyu Lee
- Department of Biomedical Sciences, Cancer Research Center, University at Albany, State University of New York, Rensselaer, New York 12144, USA
| | - Edward M Marcotte
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, Texas 78712, USA
| | - Jonghwan Kim
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, Texas 78712, USA;
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3
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Chen Y, Li M, Wu Y. The occurrence and development of induced pluripotent stem cells. Front Genet 2024; 15:1389558. [PMID: 38699229 PMCID: PMC11063328 DOI: 10.3389/fgene.2024.1389558] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2024] [Accepted: 04/08/2024] [Indexed: 05/05/2024] Open
Abstract
The ectopic expression of four transcription factors, Oct3/4, Sox2, Klf4, and c-Myc (OSKM), known as "Yamanaka factors," can reprogram or stimulate the production of induced pluripotent stem cells (iPSCs). Although OSKM is still the gold standard, there are multiple ways to reprogram cells into iPSCs. In recent years, significant progress has been made in improving the efficiency of this technology. Ten years after the first report was published, human pluripotent stem cells have gradually been applied in clinical settings, including disease modeling, cell therapy, new drug development, and cell derivation. Here, we provide a review of the discovery of iPSCs and their applications in disease and development.
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Affiliation(s)
| | - Meng Li
- Department of Cardiology, The Second Affiliated Hospital, Jiangxi Medical College, Nanchang University, Nanchang, China
| | - Yanqing Wu
- Department of Cardiology, The Second Affiliated Hospital, Jiangxi Medical College, Nanchang University, Nanchang, China
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4
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Balmas E, Sozza F, Bottini S, Ratto ML, Savorè G, Becca S, Snijders KE, Bertero A. Manipulating and studying gene function in human pluripotent stem cell models. FEBS Lett 2023; 597:2250-2287. [PMID: 37519013 DOI: 10.1002/1873-3468.14709] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2023] [Revised: 07/04/2023] [Accepted: 07/05/2023] [Indexed: 08/01/2023]
Abstract
Human pluripotent stem cells (hPSCs) are uniquely suited to study human development and disease and promise to revolutionize regenerative medicine. These applications rely on robust methods to manipulate gene function in hPSC models. This comprehensive review aims to both empower scientists approaching the field and update experienced stem cell biologists. We begin by highlighting challenges with manipulating gene expression in hPSCs and their differentiated derivatives, and relevant solutions (transfection, transduction, transposition, and genomic safe harbor editing). We then outline how to perform robust constitutive or inducible loss-, gain-, and change-of-function experiments in hPSCs models, both using historical methods (RNA interference, transgenesis, and homologous recombination) and modern programmable nucleases (particularly CRISPR/Cas9 and its derivatives, i.e., CRISPR interference, activation, base editing, and prime editing). We further describe extension of these approaches for arrayed or pooled functional studies, including emerging single-cell genomic methods, and the related design and analytical bioinformatic tools. Finally, we suggest some directions for future advancements in all of these areas. Mastering the combination of these transformative technologies will empower unprecedented advances in human biology and medicine.
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Affiliation(s)
- Elisa Balmas
- Department of Molecular Biotechnology and Health Sciences, Molecular Biotechnology Center "Guido Tarone", University of Turin, Torino, Italy
| | - Federica Sozza
- Department of Molecular Biotechnology and Health Sciences, Molecular Biotechnology Center "Guido Tarone", University of Turin, Torino, Italy
| | - Sveva Bottini
- Department of Molecular Biotechnology and Health Sciences, Molecular Biotechnology Center "Guido Tarone", University of Turin, Torino, Italy
| | - Maria Luisa Ratto
- Department of Molecular Biotechnology and Health Sciences, Molecular Biotechnology Center "Guido Tarone", University of Turin, Torino, Italy
| | - Giulia Savorè
- Department of Molecular Biotechnology and Health Sciences, Molecular Biotechnology Center "Guido Tarone", University of Turin, Torino, Italy
| | - Silvia Becca
- Department of Molecular Biotechnology and Health Sciences, Molecular Biotechnology Center "Guido Tarone", University of Turin, Torino, Italy
| | - Kirsten Esmee Snijders
- Department of Molecular Biotechnology and Health Sciences, Molecular Biotechnology Center "Guido Tarone", University of Turin, Torino, Italy
| | - Alessandro Bertero
- Department of Molecular Biotechnology and Health Sciences, Molecular Biotechnology Center "Guido Tarone", University of Turin, Torino, Italy
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5
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Bi J, Wang D, Zhu F, Lu X, Xie Y, Liu H, Wang M, He X, Jiang Y, Liu K, Zhao M, Wang T, Li J. Epigenetic Iinsights into the Senescence of Porcine Fetal Fibroblasts induced by Passaging. Cell Cycle 2023; 22:1597-1613. [PMID: 37338871 PMCID: PMC10361148 DOI: 10.1080/15384101.2023.2222521] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Revised: 02/13/2023] [Accepted: 03/07/2023] [Indexed: 06/21/2023] Open
Abstract
Epigenetic status of fetal fibroblasts (FFs) is one of the crucial factors accounted for the success of somatic cell nuclear transfer and gene editing, which might inevitably be affected by passaging. But few systematic studies have been performed on the epigenetic status of passaged aging cells. Therefore, FFs from large white pig were in vitro passaged to the 5, 10, and 15 (F5, F10, and F15) passages in the present study to investigate the potential alteration of epigenetic status. Results indicated the senescence of FFs occurs with the passaging, as assessed by the weakened growth rate, increased β-gal expression, and so on. For the epigenetic status of FFs, the higher level both of DNA methylation and H3K4me1, H3K4me2, H3K4me3 was observed at F10, but the lowest level was observed at F15. However, the fluorescence intensity of m6A was significantly higher in F15, but lower (p < 0.05) in F10, and the related mRNA expression in F15 was significantly higher than F5. Further, RNA-Seq indicated a considerable difference in the expression pattern of F5, F10, and F15 FFs. Among differentially expressed genes, not only the genes involved in cell senescence were changed, but also the upregulated expression of Dnmt1, Dnmt3b, Tet1 and dysregulated expression of histone methyltransferases-related genes were detected in F10 FFs. In addition, most genes related to m6A such as METTL3, YTHDF2, and YTHDC1 were significantly different in F5, F10, and F15 FFs. In conclusion, the epigenetic status of FFs was affected by being passaged from F5 to F15.
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Affiliation(s)
- Jiaying Bi
- College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, China
| | - Dayu Wang
- College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, China
| | - Fuquan Zhu
- College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, China
| | - Xinyue Lu
- College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, China
| | - Yan Xie
- Taixing Animal Husbandry and Veterinary Center, Taizhou, Jiangsu Province, China
| | - Huijun Liu
- Key Laboratory of Microbial Technology and Bioinformatics of Zhejiang Province, Zhejiang Institute of Microbiology, Hangzhou, Zhejiang Province, China
| | - Meixia Wang
- Key Laboratory of Microbial Technology and Bioinformatics of Zhejiang Province, Zhejiang Institute of Microbiology, Hangzhou, Zhejiang Province, China
| | - Xu He
- College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, China
| | - Yuan Jiang
- College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, China
| | - Ke Liu
- College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, China
| | - Mingyue Zhao
- College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, China
| | - Tingzhang Wang
- Taixing Animal Husbandry and Veterinary Center, Taizhou, Jiangsu Province, China
| | - Juan Li
- College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, China
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6
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Song Q, Hou Y, Zhang Y, Liu J, Wang Y, Fu J, Zhang C, Cao M, Cui Y, Zhang X, Wang X, Zhang J, Liu C, Zhang Y, Wang P. Integrated multi-omics approach revealed cellular senescence landscape. Nucleic Acids Res 2022; 50:10947-10963. [PMID: 36243980 PMCID: PMC9638896 DOI: 10.1093/nar/gkac885] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2022] [Revised: 08/27/2022] [Accepted: 10/01/2022] [Indexed: 11/14/2022] Open
Abstract
Cellular senescence is a complex multifactorial biological phenomenon that plays essential roles in aging, and aging-related diseases. During this process, the senescent cells undergo gene expression altering and chromatin structure remodeling. However, studies on the epigenetic landscape of senescence using integrated multi-omics approaches are limited. In this research, we performed ATAC-seq, RNA-seq and ChIP-seq on different senescent types to reveal the landscape of senescence and identify the prime regulatory elements. We also obtained 34 key genes and deduced that NAT1, PBX1 and RRM2, which interacted with each other, could be the potential markers of aging and aging-related diseases. In summary, our work provides the landscape to study accessibility dynamics and transcriptional regulations in cellular senescence. The application of this technique in different types of senescence allows us to identify the regulatory elements responsible for the substantial regulation of transcription, providing the insights into molecular mechanisms of senescence.
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Affiliation(s)
- Qiao Song
- Department of Clinical laboratory, Xuanwu Hospital, National Clinical Research Center for Geriatric Diseases, Capital Medical University, Beijing 100053, PR China
| | - Yuli Hou
- Department of Clinical laboratory, Xuanwu Hospital, National Clinical Research Center for Geriatric Diseases, Capital Medical University, Beijing 100053, PR China
| | - Yiyin Zhang
- Shanghai Jiayin Biotechnology, Shanghai 200092, PR China
| | - Jing Liu
- Department of Clinical laboratory, Xuanwu Hospital, National Clinical Research Center for Geriatric Diseases, Capital Medical University, Beijing 100053, PR China
| | - Yaqi Wang
- Department of Clinical laboratory, Xuanwu Hospital, National Clinical Research Center for Geriatric Diseases, Capital Medical University, Beijing 100053, PR China
| | - Jingxuan Fu
- Department of Clinical laboratory, Xuanwu Hospital, National Clinical Research Center for Geriatric Diseases, Capital Medical University, Beijing 100053, PR China
| | - Chi Zhang
- Department of Clinical laboratory, Xuanwu Hospital, National Clinical Research Center for Geriatric Diseases, Capital Medical University, Beijing 100053, PR China
| | - Min Cao
- Department of Clinical Laboratory, Beijing Huairou Hospital, Beijing 101400, PR China
| | - Yuting Cui
- Department of Clinical laboratory, Xuanwu Hospital, National Clinical Research Center for Geriatric Diseases, Capital Medical University, Beijing 100053, PR China
| | - Xiaomin Zhang
- Department of Clinical laboratory, Xuanwu Hospital, National Clinical Research Center for Geriatric Diseases, Capital Medical University, Beijing 100053, PR China
| | - Xiaoling Wang
- Department of Clinical laboratory, Xuanwu Hospital, National Clinical Research Center for Geriatric Diseases, Capital Medical University, Beijing 100053, PR China
| | - Jingjing Zhang
- Department of Clinical laboratory, Xuanwu Hospital, National Clinical Research Center for Geriatric Diseases, Capital Medical University, Beijing 100053, PR China
| | - Congcong Liu
- Department of Clinical laboratory, Xuanwu Hospital, National Clinical Research Center for Geriatric Diseases, Capital Medical University, Beijing 100053, PR China
| | - Yingzhen Zhang
- Department of Clinical laboratory, Xuanwu Hospital, National Clinical Research Center for Geriatric Diseases, Capital Medical University, Beijing 100053, PR China
| | - Peichang Wang
- Department of Clinical laboratory, Xuanwu Hospital, National Clinical Research Center for Geriatric Diseases, Capital Medical University, Beijing 100053, PR China
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7
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Guerrero A, Innes AJ, Roux PF, Buisman SC, Jung J, Ortet L, Moiseeva V, Wagner V, Robinson L, Ausema A, Potapova A, Perdiguero E, Weersing E, Aarts M, Martin N, Wuestefeld T, Muñoz-Cánoves P, de Haan G, Bischof O, Gil J. 3-deazaadenosine (3DA) alleviates senescence to promote cellular fitness and cell therapy efficiency in mice. NATURE AGING 2022; 2:851-866. [PMID: 36438588 PMCID: PMC7613850 DOI: 10.1038/s43587-022-00279-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/25/2020] [Accepted: 08/04/2022] [Indexed: 11/09/2022]
Abstract
Cellular senescence is a stable type of cell cycle arrest triggered by different stresses. As such, senescence drives age-related diseases and curbs cellular replicative potential. Here, we show that 3-deazaadenosine (3DA), an S-adenosyl homocysteinase (AHCY) inhibitor, alleviates replicative and oncogene-induced senescence. 3DA-treated senescent cells showed reduced global Histone H3 Lysine 36 trimethylation (H3K36me3), an epigenetic modification that marks the bodies of actively transcribed genes. By integrating transcriptome and epigenome data, we demonstrate that 3DA treatment affects key factors of the senescence transcriptional program. Remarkably, 3DA treatment alleviated senescence and increased the proliferative and regenerative potential of muscle stem cells from very old mice in vitro and in vivo. Moreover, ex vivo 3DA treatment was sufficient to enhance the engraftment of human umbilical cord blood (UCB) cells in immunocompromised mice. Together, our results identify 3DA as a promising drug enhancing the efficiency of cellular therapies by restraining senescence.
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Affiliation(s)
- Ana Guerrero
- MRC London Institute of Medical Sciences (LMS), Du Cane Road, London, W12 0NN, UK
- Institute of Clinical Sciences (ICS), Faculty of Medicine, Imperial College London, Du Cane Road, London W12 0NN, UK
| | - Andrew J. Innes
- MRC London Institute of Medical Sciences (LMS), Du Cane Road, London, W12 0NN, UK
- Institute of Clinical Sciences (ICS), Faculty of Medicine, Imperial College London, Du Cane Road, London W12 0NN, UK
- Centre for Haematology, Department of Immunology and Inflammation, Faculty of Medicine, Imperial College London, Du Cane Road, London W12 0NN, UK
| | - Pierre-François Roux
- Institut Pasteur, Department of Cell Biology and Infection, 75015 Paris, France
- INSERM, U993, 75015 Paris, France
- IRCM, Institut de Recherche en Cancérologie de Montpellier, INSERM U1194, Université de Montpellier, Institut régional du Cancer de Montpellier, Montpellier, France
| | - Sonja C. Buisman
- European Research Institute for the Biology of Ageing, University Medical Center Groningen, University of Groningen, 9700 Groningen, The Netherlands
| | - Johannes Jung
- European Research Institute for the Biology of Ageing, University Medical Center Groningen, University of Groningen, 9700 Groningen, The Netherlands
- Department of Medicine, Hematology and Oncology, Faculty of Medicine, Medical Center University of Freiburg, Hugstetter Str. 55, 79106 Freiburg, Germany
| | - Laura Ortet
- Department of Experimental and Health Sciences, Pompeu Fabra University (UPF), CIBER on Neurodegenerative diseases (CIBERNED), E-08003 Barcelona, Spain
| | - Victoria Moiseeva
- Department of Experimental and Health Sciences, Pompeu Fabra University (UPF), CIBER on Neurodegenerative diseases (CIBERNED), E-08003 Barcelona, Spain
| | - Verena Wagner
- MRC London Institute of Medical Sciences (LMS), Du Cane Road, London, W12 0NN, UK
- Institute of Clinical Sciences (ICS), Faculty of Medicine, Imperial College London, Du Cane Road, London W12 0NN, UK
| | - Lucas Robinson
- Institut Pasteur, Department of Cell Biology and Infection, 75015 Paris, France
- INSERM, U993, 75015 Paris, France
- Université de Paris, Sorbonne Paris Cité, Paris, France
| | - Albertina Ausema
- European Research Institute for the Biology of Ageing, University Medical Center Groningen, University of Groningen, 9700 Groningen, The Netherlands
| | - Anna Potapova
- Laboratory of In Vivo Genetics & Gene Therapy, Genome Institute of Singapore, Singapore
| | - Eusebio Perdiguero
- Department of Experimental and Health Sciences, Pompeu Fabra University (UPF), CIBER on Neurodegenerative diseases (CIBERNED), E-08003 Barcelona, Spain
| | - Ellen Weersing
- European Research Institute for the Biology of Ageing, University Medical Center Groningen, University of Groningen, 9700 Groningen, The Netherlands
| | - Marieke Aarts
- MRC London Institute of Medical Sciences (LMS), Du Cane Road, London, W12 0NN, UK
- Institute of Clinical Sciences (ICS), Faculty of Medicine, Imperial College London, Du Cane Road, London W12 0NN, UK
| | - Nadine Martin
- MRC London Institute of Medical Sciences (LMS), Du Cane Road, London, W12 0NN, UK
- Institute of Clinical Sciences (ICS), Faculty of Medicine, Imperial College London, Du Cane Road, London W12 0NN, UK
| | - Torsten Wuestefeld
- Laboratory of In Vivo Genetics & Gene Therapy, Genome Institute of Singapore, Singapore
- National Cancer Centre, Singapore
- School of Biological Sciences, Nanyang Technological University, Singapore
| | - Pura Muñoz-Cánoves
- Department of Experimental and Health Sciences, Pompeu Fabra University (UPF), CIBER on Neurodegenerative diseases (CIBERNED), E-08003 Barcelona, Spain
- ICREA, E-08010 Barcelona, Spain
- Spanish National Center on Cardiovascular Research (CNIC), E-28029 Madrid, Spain
| | - Gerald de Haan
- European Research Institute for the Biology of Ageing, University Medical Center Groningen, University of Groningen, 9700 Groningen, The Netherlands
- Sanquin Research, and Landsteiner Laboratory,Amsterdam University Medical Center, University of Amsterdam, The Netherlands
| | - Oliver Bischof
- Institut Pasteur, Department of Cell Biology and Infection, 75015 Paris, France
- INSERM, U993, 75015 Paris, France
- INSERM U955, Université Paris-Est Créteil (UPEC), FHU SENEC, 51 Av de Lattre de Tassigny, 94100 Créteil, France
| | - Jesús Gil
- MRC London Institute of Medical Sciences (LMS), Du Cane Road, London, W12 0NN, UK
- Institute of Clinical Sciences (ICS), Faculty of Medicine, Imperial College London, Du Cane Road, London W12 0NN, UK
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8
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Zhang Y, Xu S, Wen Z, Gao J, Li S, Weissman SM, Pan X. Sample-multiplexing approaches for single-cell sequencing. Cell Mol Life Sci 2022; 79:466. [PMID: 35927335 PMCID: PMC11073057 DOI: 10.1007/s00018-022-04482-0] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2022] [Revised: 06/25/2022] [Accepted: 07/11/2022] [Indexed: 12/12/2022]
Abstract
Single-cell sequencing is widely used in biological and medical studies. However, its application with multiple samples is hindered by inefficient sample processing, high experimental costs, ambiguous identification of true single cells, and technical batch effects. Here, we introduce sample-multiplexing approaches for single-cell sequencing in transcriptomics, epigenomics, genomics, and multiomics. In single-cell transcriptomics, sample multiplexing uses variants of native or artificial features as sample markers, enabling sample pooling and decoding. Such features include: (1) natural genetic variation, (2) nucleotide-barcode anchoring on cellular or nuclear membranes, (3) nucleotide-barcode internalization to the cytoplasm or nucleus, (4) vector-based barcode expression in cells, and (5) nucleotide-barcode incorporation during library construction. Other single-cell omics methods are based on similar concepts, particularly single-cell combinatorial indexing. These methods overcome current challenges, while enabling super-loading of single cells. Finally, selection guidelines are presented that can accelerate technological application.
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Affiliation(s)
- Yulong Zhang
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Southern Medical University, Guangzhou, Guangdong, 510515, China
- Guangdong Provincial Key Laboratory of Single Cell Technology and Application, Southern Medical University, Guangzhou, Guangdong, 510515, China
- Shenzhen Bay Laboratory, Shenzhen, Guangdong, China
| | - Siwen Xu
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Southern Medical University, Guangzhou, Guangdong, 510515, China
- Guangdong Provincial Key Laboratory of Single Cell Technology and Application, Southern Medical University, Guangzhou, Guangdong, 510515, China
- SequMed BioTechnology, Inc., Guangzhou, Guangdong, China
| | - Zebin Wen
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Southern Medical University, Guangzhou, Guangdong, 510515, China
- Guangdong Provincial Key Laboratory of Single Cell Technology and Application, Southern Medical University, Guangzhou, Guangdong, 510515, China
| | - Jinyu Gao
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Southern Medical University, Guangzhou, Guangdong, 510515, China
- Guangdong Provincial Key Laboratory of Single Cell Technology and Application, Southern Medical University, Guangzhou, Guangdong, 510515, China
| | - Shuang Li
- Shenzhen Bay Laboratory, Shenzhen, Guangdong, China
| | - Sherman M Weissman
- Department of Genetics, Yale University School of Medicine, New Haven, CT, 06520-8005, USA
| | - Xinghua Pan
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Southern Medical University, Guangzhou, Guangdong, 510515, China.
- Guangdong Provincial Key Laboratory of Single Cell Technology and Application, Southern Medical University, Guangzhou, Guangdong, 510515, China.
- Shenzhen Bay Laboratory, Shenzhen, Guangdong, China.
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9
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von Joest M, Chen C, Douché T, Chantrel J, Chiche A, Gianetto QG, Matondo M, Li H. Amphiregulin mediates non-cell-autonomous effect of senescence on reprogramming. Cell Rep 2022; 40:111074. [PMID: 35830812 DOI: 10.1016/j.celrep.2022.111074] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2021] [Revised: 05/05/2022] [Accepted: 06/19/2022] [Indexed: 01/10/2023] Open
Abstract
Cellular senescence is an irreversible growth arrest with a dynamic secretome, termed the senescence-associated secretory phenotype (SASP). Senescence is a cell-intrinsic barrier for reprogramming, whereas the SASP facilitates cell fate conversion in non-senescent cells. However, the mechanisms by which reprogramming-induced senescence regulates cell plasticity are not well understood. Here, we investigate how the heterogeneity of paracrine senescence impacts reprogramming. We show that senescence promotes in vitro reprogramming in a stress-dependent manner. Unbiased proteomics identifies a catalog of SASP factors involved in the cell fate conversion. Amphiregulin (AREG), frequently secreted by senescent cells, promotes in vitro reprogramming by accelerating proliferation and the mesenchymal-epithelial transition via EGFR signaling. AREG treatment diminishes the negative effect of donor age on reprogramming. Finally, AREG enhances in vivo reprogramming in skeletal muscle. Hence, various SASP factors can facilitate cellular plasticity to promote reprogramming and tissue repair.
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Affiliation(s)
- Mathieu von Joest
- Cellular Plasticity & Disease Modelling, Department of Developmental & Stem Cell Biology, CNRS UMR 3738, Institut Pasteur, 25 rue du Dr Roux, 75015 Paris, France
| | - Cheng Chen
- Cellular Plasticity & Disease Modelling, Department of Developmental & Stem Cell Biology, CNRS UMR 3738, Institut Pasteur, 25 rue du Dr Roux, 75015 Paris, France
| | - Thibaut Douché
- Proteomics Platform, Mass Spectrometry for Biology Unit (MSBio), CNRS USR 2000, Institut Pasteur, 28 rue du Dr Roux, 75015 Paris, France
| | - Jeremy Chantrel
- Cellular Plasticity & Disease Modelling, Department of Developmental & Stem Cell Biology, CNRS UMR 3738, Institut Pasteur, 25 rue du Dr Roux, 75015 Paris, France; Sorbonne Université, Collège Doctoral, 75005 Paris, France
| | - Aurélie Chiche
- Cellular Plasticity & Disease Modelling, Department of Developmental & Stem Cell Biology, CNRS UMR 3738, Institut Pasteur, 25 rue du Dr Roux, 75015 Paris, France
| | - Quentin Giai Gianetto
- Proteomics Platform, Mass Spectrometry for Biology Unit (MSBio), CNRS USR 2000, Institut Pasteur, 28 rue du Dr Roux, 75015 Paris, France; Bioinformatics and Biostatistics Hub, Computational Biology Department, CNRS USR 3756, Institut Pasteur, 25 rue du Dr Roux, 75015 Paris, France
| | - Mariette Matondo
- Proteomics Platform, Mass Spectrometry for Biology Unit (MSBio), CNRS USR 2000, Institut Pasteur, 28 rue du Dr Roux, 75015 Paris, France
| | - Han Li
- Cellular Plasticity & Disease Modelling, Department of Developmental & Stem Cell Biology, CNRS UMR 3738, Institut Pasteur, 25 rue du Dr Roux, 75015 Paris, France.
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10
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Combined Analysis of Transcriptome and T-Cell Receptor Alpha and Beta (TRA /TRB ) Repertoire in Paucicellular Samples at the Single-Cell Level. METHODS IN MOLECULAR BIOLOGY (CLIFTON, N.J.) 2022; 2453:231-259. [PMID: 35622330 DOI: 10.1007/978-1-0716-2115-8_14] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
With the advent of next-generation sequencing (NGS) methodologies, the total repertoires of B and T cells can be disclosed in much more detail than ever before. Even though many of these strategies do provide in-depth and high-resolution information of the immunoglobulin (IG) and/or T-cell receptor (TR) repertoire, one clear disadvantage is that the IG/TR profiles cannot be connected to individual cells. Single-cell technologies do allow to study the IG/TR repertoire at the individual cell level. This is especially relevant in cell samples in which much heterogeneity of the cell population is expected. By combining the IG/TR repertoire with transcriptome data, the reactivity of the B or T cell can be associated with activation or maturation stages. An additional advantage of such single-cell technologies is that the combination of both IG and both TR chains can be studied on a per cell basis, which better reflects the antigen receptor reactivity of cells. Here we present the ICELL8 single-cell method for the parallel analysis of the TR repertoire and transcriptome, which is especially useful in samples that contain relatively few cells.
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11
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Kilmister EJ, Tan ST. Insights Into Vascular Anomalies, Cancer, and Fibroproliferative Conditions: The Role of Stem Cells and the Renin-Angiotensin System. Front Surg 2022; 9:868187. [PMID: 35574555 PMCID: PMC9091963 DOI: 10.3389/fsurg.2022.868187] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2022] [Accepted: 03/22/2022] [Indexed: 12/15/2022] Open
Abstract
Cells exhibiting embryonic stem cell (ESC) characteristics have been demonstrated in vascular anomalies (VAs), cancer, and fibroproliferative conditions, which are commonly managed by plastic surgeons and remain largely unsolved. The efficacy of the mTOR inhibitor sirolimus, and targeted therapies that block the Ras/BRAF/MEK/ERK1/2 and PI3KCA/AKT/mTOR pathways in many types of cancer and VAs, further supports the critical role of ESC-like cells in the pathogenesis of these conditions. ESC-like cells in VAs, cancer, and fibroproliferative conditions express components of the renin-angiotensin system (RAS) – a homeostatic endocrine signaling cascade that regulates cells with ESC characteristics. ESC-like cells are influenced by the Ras/BRAF/MEK/ERK1/2 and PI3KCA/AKT/mTOR pathways, which directly regulate cellular proliferation and stemness, and interact with the RAS at multiple points. Gain-of-function mutations affecting these pathways have been identified in many types of cancer and VAs, that have been treated with targeted therapies with some success. In cancer, the RAS promotes tumor progression, treatment resistance, recurrence, and metastasis. The RAS modulates cellular invasion, migration, proliferation, and angiogenesis. It also indirectly regulates ESC-like cells via its direct influence on the tissue microenvironment and by its interaction with the immune system. In vitro studies show that RAS inhibition suppresses the hallmarks of cancer in different experimental models. Numerous epidemiological studies show a reduced incidence of cancer and improved survival outcomes in patients taking RAS inhibitors, although some studies have shown no such effect. The discovery of ESC-like cells that express RAS components in infantile hemangioma (IH) underscores the paradigm shift in the understanding of its programmed biologic behavior and accelerated involution induced by β-blockers and angiotensin-converting enzyme inhibitors. The findings of SOX18 inhibition by R-propranolol suggests the possibility of targeting ESC-like cells in IH without β-adrenergic blockade, and its associated side effects. This article provides an overview of the current knowledge of ESC-like cells and the RAS in VAs, cancer, and fibroproliferative conditions. It also highlights new lines of research and potential novel therapeutic approaches for these unsolved problems in plastic surgery, by targeting the ESC-like cells through manipulation of the RAS, its bypass loops and converging signaling pathways using existing low-cost, commonly available, and safe oral medications.
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Affiliation(s)
| | - Swee T. Tan
- Gillies McIndoe Research Institute, Wellington, New Zealand
- Wellington Regional Plastic, Maxillofacial & Burns Unit, Hutt Hospital, Lower Hutt, New Zealand
- Department of Surgery, The Royal Melbourne Hospital, The University of Melbourne, Parkville, VIC, Australia
- *Correspondence: Swee T. Tan
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12
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Hansen L, Brasch HD, Paterson E, Patel J, Bockett N, Davis PF, Tan ST. Expression of Cathepsins B, D, and G in Extracranial Arterio-Venous Malformation. Front Surg 2021; 8:676871. [PMID: 34409065 PMCID: PMC8367294 DOI: 10.3389/fsurg.2021.676871] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2021] [Accepted: 06/30/2021] [Indexed: 12/16/2022] Open
Abstract
Objectives: We have previously identified a population of cells that expressed stemness-associated markers in extracranial arterio-venous malformation (AVM) and demonstrated expression of cathepsins B, D, and G on embryonic stem cell (ESC)-like populations in other vascular anomalies. This study investigated the expression of cathepsins B, D, and G, and their localization in relation to this primitive population in extracranial AVM. Methods: Immunohistochemical staining was performed on AVM tissue samples from 13 patients to demonstrate expression of cathepsins B, D, and G. Western blotting was performed on four AVM tissue samples and three AVM-derived primary cell lines to confirm protein expression of cathepsins B and D proteins. RT-qPCR was performed on three AVM-derived primary cell lines to demonstrate transcript expression of cathepsins B, D, and G. Enzymatic activity assays were performed on three AVM-derived primary cell lines to investigate if cathepsins B and D were active. Localization of the cathepsins was investigated using immunofluorescence dual-staining of the cathepsins with the ESC markers OCT4 and SOX2, and mast cells marker chymase on two of the 13 AVM tissue samples. Results: Immunohistochemical staining demonstrated expression of cathepsins B, D, and G in all 13 AVM tissue samples. Western blotting showed expression of cathepsins B and D proteins in all four AVM tissue samples and all three AVM-derived primary cell lines. RT-qPCR demonstrated transcripts of cathepsins B, D, and G in all three AVM-derived primary cell lines. Enzymatic activity assays showed that cathepsins B and D were active. Immunofluorescence staining showed expression of cathepsins B and D on the OCT4+/SOX2+ endothelium and media of the lesional vessels and cells within the stroma in AVM nidus. Cathepsin G was expressed on the chymase+ phenotypic mast cells. Conclusions: This study demonstrated the novel finding of the expression of cathepsins B, D, and G in AVM. Cathepsins B and D were expressed by the primitive population, and cathepsin G was localized to mast cells, within the AVM nidus.
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Affiliation(s)
- Lauren Hansen
- Gillies McIndoe Research Institute, Wellington, New Zealand
| | - Helen D Brasch
- Gillies McIndoe Research Institute, Wellington, New Zealand
| | - Erin Paterson
- Gillies McIndoe Research Institute, Wellington, New Zealand
| | - Josie Patel
- Gillies McIndoe Research Institute, Wellington, New Zealand
| | | | - Paul F Davis
- Gillies McIndoe Research Institute, Wellington, New Zealand
| | - Swee T Tan
- Gillies McIndoe Research Institute, Wellington, New Zealand.,Centre for the Study and Treatment of Vascular Birthmarks, Wellington Regional Plastic, Maxillofacial and Burns Unit, Hutt Hospital, Lower Hutt, New Zealand.,Department of Surgery, The Royal Melbourne Hospital, The University of Melbourne, Melbourne, VIC, Australia
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13
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Functional annotation of lncRNA in high-throughput screening. Essays Biochem 2021; 65:761-773. [PMID: 33835127 PMCID: PMC8564734 DOI: 10.1042/ebc20200061] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2021] [Revised: 02/25/2021] [Accepted: 03/15/2021] [Indexed: 12/17/2022]
Abstract
Recent efforts on the characterization of long non-coding RNAs (lncRNAs) revealed their functional roles in modulating diverse cellular processes. These include pluripotency maintenance, lineage commitment, carcinogenesis, and pathogenesis of various diseases. By interacting with DNA, RNA and protein, lncRNAs mediate multifaceted mechanisms to regulate transcription, RNA processing, RNA interference and translation. Of more than 173000 discovered lncRNAs, the majority remain functionally unknown. The cell type-specific expression and localization of the lncRNA also suggest potential distinct functions of lncRNAs across different cell types. This highlights the niche of identifying functional lncRNAs in different biological processes and diseases through high-throughput (HTP) screening. This review summarizes the current work performed and perspectives on HTP screening of functional lncRNAs where different technologies, platforms, cellular responses and the downstream analyses are discussed. We hope to provide a better picture in applying different technologies to facilitate functional annotation of lncRNA efficiently.
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14
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Lee S, Kim J, Park JE. Single-Cell Toolkits Opening a New Era for Cell Engineering. Mol Cells 2021; 44:127-135. [PMID: 33795531 PMCID: PMC8019599 DOI: 10.14348/molcells.2021.0002] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2020] [Revised: 03/04/2021] [Accepted: 03/11/2021] [Indexed: 02/07/2023] Open
Abstract
Since the introduction of RNA sequencing (RNA-seq) as a high-throughput mRNA expression analysis tool, this procedure has been increasingly implemented to identify cell-level transcriptome changes in a myriad of model systems. However, early methods processed cell samples in bulk, and therefore the unique transcriptomic patterns of individual cells would be lost due to data averaging. Nonetheless, the recent and continuous development of new single-cell RNA sequencing (scRNA-seq) toolkits has enabled researchers to compare transcriptomes at a single-cell resolution, thus facilitating the analysis of individual cellular features and a deeper understanding of cellular functions. Nonetheless, the rapid evolution of high throughput single-cell "omics" tools has created the need for effective hypothesis verification strategies. Particularly, this issue could be addressed by coupling cell engineering techniques with single-cell sequencing. This approach has been successfully employed to gain further insights into disease pathogenesis and the dynamics of differentiation trajectories. Therefore, this review will discuss the current status of cell engineering toolkits and their contributions to single-cell and genome-wide data collection and analyses.
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Affiliation(s)
- Sean Lee
- Graduate School of Medical Science and Engineering, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Korea
| | - Jireh Kim
- Graduate School of Medical Science and Engineering, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Korea
| | - Jong-Eun Park
- Graduate School of Medical Science and Engineering, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Korea
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15
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Kilmister EJ, Hansen L, Davis PF, Hall SRR, Tan ST. Cell Populations Expressing Stemness-Associated Markers in Vascular Anomalies. Front Surg 2021; 7:610758. [PMID: 33634164 PMCID: PMC7900499 DOI: 10.3389/fsurg.2020.610758] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2020] [Accepted: 12/31/2020] [Indexed: 12/31/2022] Open
Abstract
Treatment of vascular anomalies (VAs) is mostly empirical and, in many instances unsatisfactory, as the pathogeneses of these heterogeneous conditions remain largely unknown. There is emerging evidence of the presence of cell populations expressing stemness-associated markers within many types of vascular tumors and vascular malformations. The presence of these populations in VAs is supported, in part, by the observed clinical effect of the mTOR inhibitor, sirolimus, that regulates differentiation of embryonic stem cells (ESCs). The discovery of the central role of the renin-angiotensin system (RAS) in regulating stem cells in infantile hemangioma (IH) provides a plausible explanation for its spontaneous and accelerated involution induced by β-blockers and ACE inhibitors. Recent work on targeting IH stem cells by inhibiting the transcription factor SOX18 using the stereoisomer R(+) propranolol, independent of β-adrenergic blockade, opens up exciting opportunities for novel treatment of IH without the β-adrenergic blockade-related side effects. Gene mutations have been identified in several VAs, involving mainly the PI3K/AKT/mTOR and/or the Ras/RAF/MEK/ERK pathways. Existing cancer therapies that target these pathways engenders the exciting possibility of repurposing these agents for challenging VAs, with early results demonstrating clinical efficacy. However, there are several shortcomings with this approach, including the treatment cost, side effects, emergence of treatment resistance and unknown long-term effects in young patients. The presence of populations expressing stemness-associated markers, including transcription factors involved in the generation of induced pluripotent stem cells (iPSCs), in different types of VAs, suggests the possible role of stem cell pathways in their pathogenesis. Components of the RAS are expressed by cell populations expressing stemness-associated markers in different types of VAs. The gene mutations affecting the PI3K/AKT/mTOR and/or the Ras/RAF/MEK/ERK pathways interact with different components of the RAS, which may influence cell populations expressing stemness-associated markers within VAs. The potential of targeting these populations by manipulating the RAS using repurposed, low-cost and commonly available oral medications, warrants further investigation. This review presents the accumulating evidence demonstrating the presence of stemness-associated markers in VAs, their expression of the RAS, and their interaction with gene mutations affecting the PI3K/AKT/mTOR and/or the Ras/RAF/MEK/ERK pathways, in the pathogenesis of VAs.
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Affiliation(s)
| | - Lauren Hansen
- Gillies McIndoe Research Institute, Wellington, New Zealand
| | - Paul F. Davis
- Gillies McIndoe Research Institute, Wellington, New Zealand
| | | | - Swee T. Tan
- Gillies McIndoe Research Institute, Wellington, New Zealand
- Wellington Regional Plastic, Maxillofacial and Burns Unit, Hutt Hospital, Wellington, New Zealand
- Department of Surgery, The Royal Melbourne Hospital, The University of Melbourne, Melbourne, VIC, Australia
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16
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Abstract
Senescence is a state of long-term cell cycle arrest that arises in cells that have incurred sublethal damage. While senescent cells no longer replicate, they remain metabolically active and further develop unique and stable phenotypes that are not present in proliferating cells. On one hand, senescent cells increase in size, maintain an active mTORC1 complex, and produce and secrete a substantial amount of inflammatory proteins as part of the senescence-associated secretory phenotype (SASP). On the other hand, these progrowth phenotypes contrast with the p53-mediated growth arrest typical of senescent cells that is associated with nucleolar stress and an inhibition of rRNA processing and ribosome biogenesis. In sum, translation in senescent cells paradoxically comprises both a global repression of translation triggered by DNA damage and a select increase in the translation of specific proteins, including SASP factors.
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17
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An Introduction to Single-Cell RNA-Seq Analysis and its Applications. SYSTEMS MEDICINE 2021. [DOI: 10.1016/b978-0-12-801238-3.11592-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
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18
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Uyar B, Palmer D, Kowald A, Murua Escobar H, Barrantes I, Möller S, Akalin A, Fuellen G. Single-cell analyses of aging, inflammation and senescence. Ageing Res Rev 2020; 64:101156. [PMID: 32949770 PMCID: PMC7493798 DOI: 10.1016/j.arr.2020.101156] [Citation(s) in RCA: 82] [Impact Index Per Article: 20.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2020] [Revised: 08/23/2020] [Accepted: 08/25/2020] [Indexed: 02/09/2023]
Abstract
Single-cell gene expression (transcriptomics) data are becoming robust and abundant, and are increasingly used to track organisms along their life-course. This allows investigation into how aging affects cellular transcriptomes, and how changes in transcriptomes may underlie aging, including chronic inflammation (inflammaging), immunosenescence and cellular senescence. We compiled and tabulated aging-related single-cell datasets published to date, collected and discussed relevant findings, and inspected some of these datasets ourselves. We specifically note insights that cannot (or not easily) be based on bulk data. For example, in some datasets, the fraction of cells expressing p16 (CDKN2A), one of the most prominent markers of cellular senescence, was reported to increase, in addition to its upregulated mean expression over all cells. Moreover, we found evidence for inflammatory processes in most datasets, some of these driven by specific cells of the immune system. Further, single-cell data are specifically useful to investigate whether transcriptional heterogeneity (also called noise or variability) increases with age, and many (but not all) studies in our review report an increase in such heterogeneity. Finally, we demonstrate some stability of marker gene expression patterns across closely similar studies and suggest that single-cell experiments may hold the key to provide detailed insights whenever interventions (countering aging, inflammation, senescence, disease, etc.) are affecting cells depending on cell type.
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Affiliation(s)
- Bora Uyar
- Bioinformatics and Omics Data Science Platform, Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine, Berlin, Germany
| | - Daniel Palmer
- Rostock University Medical Center, Institute for Biostatistics and Informatics in Medicine and Aging Research, Rostock, Germany
| | - Axel Kowald
- Rostock University Medical Center, Institute for Biostatistics and Informatics in Medicine and Aging Research, Rostock, Germany
| | - Hugo Murua Escobar
- Rostock University Medical Center, Department of Hematology, Oncology and Palliative Medicine, Department of Medicine III, Rostock, Germany
| | - Israel Barrantes
- Rostock University Medical Center, Institute for Biostatistics and Informatics in Medicine and Aging Research, Rostock, Germany
| | - Steffen Möller
- Rostock University Medical Center, Institute for Biostatistics and Informatics in Medicine and Aging Research, Rostock, Germany
| | - Altuna Akalin
- Bioinformatics and Omics Data Science Platform, Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine, Berlin, Germany
| | - Georg Fuellen
- Rostock University Medical Center, Institute for Biostatistics and Informatics in Medicine and Aging Research, Rostock, Germany.
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19
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Huidobro C, Martín-Vicente P, López-Martínez C, Alonso-López I, Amado-Rodríguez L, Crespo I, M Albaiceta G. Cellular and molecular features of senescence in acute lung injury. Mech Ageing Dev 2020; 193:111410. [PMID: 33249191 DOI: 10.1016/j.mad.2020.111410] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2020] [Accepted: 11/20/2020] [Indexed: 12/14/2022]
Abstract
A wide range of insults can trigger acute injury in the lungs, which eventually may lead to respiratory failure and death of patients. Current treatment relies mainly on supportive measures and mechanical ventilation. Even so, survivors frequently develop important sequels that compromise quality of life. In the search for new approaches to prevent and treat acute lung injury, many investigations have focused on molecular and cellular pathways which could exert a pathogenic role in this disease. Herein, we review recent findings in the literature suggesting that cellular senescence could be involved in lung injury and discuss the potential use of senotherapies to prevent disease progression.
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Affiliation(s)
- Covadonga Huidobro
- Instituto de Investigación Sanitaria del Principado de Asturias, Avenida de Roma s/n, 33011, Oviedo, Spain.
| | - Paula Martín-Vicente
- Instituto de Investigación Sanitaria del Principado de Asturias, Avenida de Roma s/n, 33011, Oviedo, Spain; Centro de Investigación Biomédica en Red (CIBER)-Enfermedades Respiratorias, Calle de Melchor Fernández Almagro, 3, 28029, Madrid, Spain; Instituto Universitario de Oncología del Principado de Asturias, Calle Fernando Bongera s/n, 33006, Oviedo, Spain
| | - Cecilia López-Martínez
- Instituto de Investigación Sanitaria del Principado de Asturias, Avenida de Roma s/n, 33011, Oviedo, Spain; Centro de Investigación Biomédica en Red (CIBER)-Enfermedades Respiratorias, Calle de Melchor Fernández Almagro, 3, 28029, Madrid, Spain; Instituto Universitario de Oncología del Principado de Asturias, Calle Fernando Bongera s/n, 33006, Oviedo, Spain
| | - Inés Alonso-López
- Instituto de Investigación Sanitaria del Principado de Asturias, Avenida de Roma s/n, 33011, Oviedo, Spain; Centro de Investigación Biomédica en Red (CIBER)-Enfermedades Respiratorias, Calle de Melchor Fernández Almagro, 3, 28029, Madrid, Spain; Instituto Universitario de Oncología del Principado de Asturias, Calle Fernando Bongera s/n, 33006, Oviedo, Spain
| | - Laura Amado-Rodríguez
- Instituto de Investigación Sanitaria del Principado de Asturias, Avenida de Roma s/n, 33011, Oviedo, Spain; Unidad de Cuidados Intensivos Cardiológicos, Hospital Universitario Central de Asturias, Oviedo, Avenida de Roma s/n, 33011, Oviedo, Spain
| | - Irene Crespo
- Departamento de Biología Funcional. Universidad de Oviedo, C/ Julián Clavería s/n, 33006, Oviedo, Spain
| | - Guillermo M Albaiceta
- Instituto de Investigación Sanitaria del Principado de Asturias, Avenida de Roma s/n, 33011, Oviedo, Spain; Centro de Investigación Biomédica en Red (CIBER)-Enfermedades Respiratorias, Calle de Melchor Fernández Almagro, 3, 28029, Madrid, Spain; Instituto Universitario de Oncología del Principado de Asturias, Calle Fernando Bongera s/n, 33006, Oviedo, Spain; Unidad de Cuidados Intensivos Cardiológicos, Hospital Universitario Central de Asturias, Oviedo, Avenida de Roma s/n, 33011, Oviedo, Spain; Departamento de Biología Funcional. Universidad de Oviedo, C/ Julián Clavería s/n, 33006, Oviedo, Spain
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20
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Litjens NHR, Langerak AW, van der List ACJ, Klepper M, de Bie M, Azmani Z, den Dekker AT, Brouwer RWW, Betjes MGH, Van IJcken WFJ. Validation of a Combined Transcriptome and T Cell Receptor Alpha/Beta (TRA/TRB) Repertoire Assay at the Single Cell Level for Paucicellular Samples. Front Immunol 2020; 11:1999. [PMID: 33013853 PMCID: PMC7500136 DOI: 10.3389/fimmu.2020.01999] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2020] [Accepted: 07/23/2020] [Indexed: 11/13/2022] Open
Abstract
Transcriptomics can be combined with TRA and TRB clonotype analysis at the single cell level. The aim of this study was to validate this approach on the ICELL8 Single-Cell system and to evaluate its usefulness to analyse clinical paucicellular samples. For this purpose, we carefully selected T cell lines with defined TRA/TRB clonotypes as well as clinical samples enriched for CD3+ T cells that possess a complex TCR repertoire. Low cell numbers of the different samples were dispensed in a chip on the ICELL8 Single-Cell System. Two sequencing libraries were generated from each single cell cDNA preparation, one for the TRA/TRB repertoire and one for the 5' ends of transcripts, and subsequently sequenced. Transcriptome analysis revealed that the cell lines on average express 2,268 unique genes/cell and T cells of clinical samples 770 unique genes/cell. The expected combined TRA/TRB clonotype was determined for on average 71% of the cells of the cell lines. In the clinical samples the TRA/TRB repertoire was more complex than those of the cell lines. Furthermore, the TRB clonotype distribution of the clinical samples was positively correlated to frequencies of TCRVβ families in CD3+ T cells obtained by a flow cytometry-based approach (Spearman's Rho correlation coefficient 0.81, P = 6.49 * 10-7). Combined analyses showed that transcriptome-based cell type-specific clusters in clinical samples corresponded to clinical features such as CMV status. In conclusion, we showed that the ICELL8 Single-Cell System enabled combined interrogation of both TRA/TRB repertoire and transcriptome of paucicellular clinical samples. This opens the way to study the response of single T cells within heterogeneous samples for both their transcriptome and TRA/TRB clonotypes in disease or upon treatment.
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Affiliation(s)
- Nicolle H R Litjens
- Department of Internal Medicine Section Nephrology and Transplantation, Erasmus MC, University Medical Center, Rotterdam, Netherlands
| | - Anton W Langerak
- Laboratory Medical Immunology, Department of Immunology, Erasmus MC, University Medical Center, Rotterdam, Netherlands
| | - Amy C J van der List
- Department of Internal Medicine Section Nephrology and Transplantation, Erasmus MC, University Medical Center, Rotterdam, Netherlands
| | - Mariska Klepper
- Department of Internal Medicine Section Nephrology and Transplantation, Erasmus MC, University Medical Center, Rotterdam, Netherlands
| | - Maaike de Bie
- Laboratory Medical Immunology, Department of Immunology, Erasmus MC, University Medical Center, Rotterdam, Netherlands
| | - Zakia Azmani
- Center for Biomics, Erasmus MC, University Medical Center, Rotterdam, Netherlands.,Department of Cell Biology, Erasmus MC, University Medical Center, Rotterdam, Netherlands
| | - Alexander T den Dekker
- Center for Biomics, Erasmus MC, University Medical Center, Rotterdam, Netherlands.,Department of Cell Biology, Erasmus MC, University Medical Center, Rotterdam, Netherlands
| | - Rutger W W Brouwer
- Center for Biomics, Erasmus MC, University Medical Center, Rotterdam, Netherlands.,Department of Cell Biology, Erasmus MC, University Medical Center, Rotterdam, Netherlands
| | - Michiel G H Betjes
- Department of Internal Medicine Section Nephrology and Transplantation, Erasmus MC, University Medical Center, Rotterdam, Netherlands
| | - Wilfred F J Van IJcken
- Center for Biomics, Erasmus MC, University Medical Center, Rotterdam, Netherlands.,Department of Cell Biology, Erasmus MC, University Medical Center, Rotterdam, Netherlands
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21
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Walters HE, Yun MH. Rising from the ashes: cellular senescence in regeneration. Curr Opin Genet Dev 2020; 64:94-100. [PMID: 32721584 DOI: 10.1016/j.gde.2020.06.002] [Citation(s) in RCA: 83] [Impact Index Per Article: 20.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2020] [Revised: 05/14/2020] [Accepted: 06/03/2020] [Indexed: 11/29/2022]
Abstract
Cellular senescence has recently become causally implicated in pathological ageing. Hence, a great deal of research is currently dedicated towards developing senolytic agents to selectively kill senescent cells. However, senescence also plays important roles in a range of physiological processes including during organismal development, providing a barrier to tumorigenesis and in limiting fibrosis. Recent evidence also suggests a role for senescence in coordinating tissue remodelling and in the regeneration of complex structures. Through its non-cell-autonomous effects, a transient induction of senescence may create a permissive environment for remodelling or regeneration through promoting local proliferation, cell plasticity, tissue patterning, balancing growth, or indirectly through finely tuned interactions with infiltrating immune mediators. A careful analysis of the beneficial roles of cellular senescence may provide insights into important physiological processes as well as informing strategies to counteract its detrimental consequences in ageing and disease.
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Affiliation(s)
- Hannah E Walters
- CRTD/DFG-Center for Regenerative Therapies Dresden (Cluster of Excellence), TU Dresden, Germany
| | - Maximina H Yun
- CRTD/DFG-Center for Regenerative Therapies Dresden (Cluster of Excellence), TU Dresden, Germany; Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany.
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22
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Chiche A, Chen C, Li H. The crosstalk between cellular reprogramming and senescence in aging and regeneration. Exp Gerontol 2020; 138:111005. [PMID: 32561400 DOI: 10.1016/j.exger.2020.111005] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2019] [Revised: 05/17/2020] [Accepted: 06/10/2020] [Indexed: 02/09/2023]
Abstract
Aging is associated with diminished regenerative capacity and increased risk of chronic diseases. There is now compelling evidence suggests that aging process is reversible. Besides metabolic modification and systematic factors, both senescence elimination and cellular reprogramming showed beneficial effects on tissue regeneration and rejuvenation. Here we review recent studies on the interplay between cellular senescence and reprogramming. We discuss how both strategies could impact aging process and the possibility of combine them for more efficient regeneration and rejuvenation.
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Affiliation(s)
- Aurélie Chiche
- Cellular Plasticity and Disease Modelling, Department of Developmental and Stem Cell Biology, CNRS UMR 3738, Institut Pasteur, 25 Rue du Dr Roux, Paris 75015, France
| | - Cheng Chen
- Cellular Plasticity and Disease Modelling, Department of Developmental and Stem Cell Biology, CNRS UMR 3738, Institut Pasteur, 25 Rue du Dr Roux, Paris 75015, France
| | - Han Li
- Cellular Plasticity and Disease Modelling, Department of Developmental and Stem Cell Biology, CNRS UMR 3738, Institut Pasteur, 25 Rue du Dr Roux, Paris 75015, France.
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23
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Jiang Q, Huang X, Hu X, Shan Z, Wu Y, Wu G, Lei L. Histone demethylase KDM6A promotes somatic cell reprogramming by epigenetically regulating the PTEN and IL-6 signal pathways. Stem Cells 2020; 38:960-972. [PMID: 32346926 DOI: 10.1002/stem.3188] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2019] [Revised: 03/18/2020] [Accepted: 03/29/2020] [Indexed: 12/13/2022]
Abstract
Aberrant epigenetic reprogramming is one of the major barriers for somatic cell reprogramming. Although our previous study has indicated that H3K27me3 demethylase KDM6A can improve the nuclear reprogramming efficiency, the mechanism remains unclear. In this study, we demonstrate that the overexpression of Kdm6a may improve induced pluripotent stem cell (iPSC) reprogramming efficiency in a demethylase enzymatic activity-dependent manner. KDM6A erased H3K27me3 on pluripotency- and metabolism-related genes, and consequently facilitated changing the gene expression profile and metabolic pattern to an intermediate state. Furthermore, KDM6A may promote IL-6 expression, and the secreted IL-6 may further improve iPSC reprogramming efficiency. In addition, KDM6A may promote PTEN expression to decrease p-AKT and p-mTOR levels, which in turn facilitates reprogramming. Overall, our results reveal that KDM6A may promote iPSC reprogramming efficiency by accelerating changes in the gene expression profile and the metabolic pattern in a demethylation-activity-dependent manner. These results may provide an insight into the relationship between epigenomics, transcriptomics, metabolomics, and reprogramming.
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Affiliation(s)
- Qi Jiang
- Department of Histology and Embryology, Basic Medical Science College, Harbin Medical University, Harbin, People's Republic of China
| | - Xingwei Huang
- Department of Histology and Embryology, Basic Medical Science College, Harbin Medical University, Harbin, People's Republic of China
| | - Xinglin Hu
- Department of Histology and Embryology, Basic Medical Science College, Harbin Medical University, Harbin, People's Republic of China
| | - Zhiyan Shan
- Department of Histology and Embryology, Basic Medical Science College, Harbin Medical University, Harbin, People's Republic of China
| | - Yanshuang Wu
- Department of Histology and Embryology, Basic Medical Science College, Harbin Medical University, Harbin, People's Republic of China
| | - Guangming Wu
- Guangzhou Regenerative Medicine and Health Guangdong Laboratory, Guangzhou, People's Republic of China
| | - Lei Lei
- Department of Histology and Embryology, Basic Medical Science College, Harbin Medical University, Harbin, People's Republic of China.,Key laboratory of preservation of human genetic resources and disease control in China(Harbin Medical University), Harbin Medical University, Harbin, People's Republic of China
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24
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Anerillas C, Abdelmohsen K, Gorospe M. Regulation of senescence traits by MAPKs. GeroScience 2020; 42:397-408. [PMID: 32300964 PMCID: PMC7205942 DOI: 10.1007/s11357-020-00183-3] [Citation(s) in RCA: 78] [Impact Index Per Article: 19.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2020] [Accepted: 03/10/2020] [Indexed: 01/10/2023] Open
Abstract
A phenotype of indefinite growth arrest acquired in response to sublethal damage, cellular senescence affects normal aging and age-related disease. Mitogen-activated protein kinases (MAPKs) are capable of sensing changes in cellular conditions, and in turn elicit adaptive responses including cell senescence. MAPKs modulate the levels and function of many proteins, including proinflammatory factors and factors in the p21/p53 and p16/RB pathways, the main senescence-regulatory axes. Through these actions, MAPKs implement key traits of senescence-growth arrest, cell survival, and the senescence-associated secretory phenotype (SASP). In this review, we summarize and discuss our current knowledge of the impact of MAPKs in senescence. In addition, given that eliminating or suppressing senescent cells can improve health span, we discuss the function and possible exploitation of MAPKs in the elimination (senolysis) or suppression (senostasis) of senescent cells.
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Affiliation(s)
- Carlos Anerillas
- Laboratory of Genetics and Genomics, National Institute on Aging Intramural Research Program, National Institutes of Health, 251 Bayview Blvd., Baltimore, MD, 21224, USA
| | - Kotb Abdelmohsen
- Laboratory of Genetics and Genomics, National Institute on Aging Intramural Research Program, National Institutes of Health, 251 Bayview Blvd., Baltimore, MD, 21224, USA
| | - Myriam Gorospe
- Laboratory of Genetics and Genomics, National Institute on Aging Intramural Research Program, National Institutes of Health, 251 Bayview Blvd., Baltimore, MD, 21224, USA.
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25
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Guerrero A, Guiho R, Herranz N, Uren A, Withers DJ, Martínez‐Barbera JP, Tietze LF, Gil J. Galactose-modified duocarmycin prodrugs as senolytics. Aging Cell 2020; 19:e13133. [PMID: 32175667 PMCID: PMC7189988 DOI: 10.1111/acel.13133] [Citation(s) in RCA: 76] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2019] [Revised: 02/09/2020] [Accepted: 02/23/2020] [Indexed: 12/22/2022] Open
Abstract
Senescence is a stable growth arrest that impairs the replication of damaged, old or preneoplastic cells, therefore contributing to tissue homeostasis. Senescent cells accumulate during ageing and are associated with cancer, fibrosis and many age-related pathologies. Recent evidence suggests that the selective elimination of senescent cells can be effective on the treatment of many of these senescence-associated diseases. A universal characteristic of senescent cells is that they display elevated activity of the lysosomal β-galactosidase, and this has been exploited as a marker for senescence (senescence-associated β-galactosidase activity). Consequently, we hypothesized that galactose-modified cytotoxic prodrugs will be preferentially processed by senescent cells, resulting in their selective killing. Here, we show that different galactose-modified duocarmycin (GMD) derivatives preferentially kill senescent cells. GMD prodrugs induce selective apoptosis of senescent cells in a lysosomal β-galactosidase (GLB1)-dependent manner. GMD prodrugs can eliminate a broad range of senescent cells in culture, and treatment with a GMD prodrug enhances the elimination of bystander senescent cells that accumulate upon whole-body irradiation treatment of mice. Moreover, taking advantage of a mouse model of adamantinomatous craniopharyngioma (ACP), we show that treatment with a GMD prodrug selectively reduced the number of β-catenin-positive preneoplastic senescent cells. In summary, the above results make a case for testing the potential of galactose-modified duocarmycin prodrugs to treat senescence-related pathologies.
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Affiliation(s)
- Ana Guerrero
- MRC London Institute of Medical Sciences (LMS)LondonUK
- Faculty of MedicineInstitute of Clinical Sciences (ICS)Imperial College LondonLondonUK
| | - Romain Guiho
- Developmental Biology and Cancer ProgrammeBirth Defects Research CentreGreat Ormond Street Institute of Child HealthUniversity College LondonLondonUK
| | - Nicolás Herranz
- MRC London Institute of Medical Sciences (LMS)LondonUK
- Faculty of MedicineInstitute of Clinical Sciences (ICS)Imperial College LondonLondonUK
| | - Anthony Uren
- MRC London Institute of Medical Sciences (LMS)LondonUK
- Faculty of MedicineInstitute of Clinical Sciences (ICS)Imperial College LondonLondonUK
| | - Dominic J. Withers
- MRC London Institute of Medical Sciences (LMS)LondonUK
- Faculty of MedicineInstitute of Clinical Sciences (ICS)Imperial College LondonLondonUK
| | - Juan Pedro Martínez‐Barbera
- Developmental Biology and Cancer ProgrammeBirth Defects Research CentreGreat Ormond Street Institute of Child HealthUniversity College LondonLondonUK
| | - Lutz F. Tietze
- Institute of Organic and Biomolecular ChemistryGeorg‐August UniversityGöttingenGermany
| | - Jesús Gil
- MRC London Institute of Medical Sciences (LMS)LondonUK
- Faculty of MedicineInstitute of Clinical Sciences (ICS)Imperial College LondonLondonUK
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26
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Jiang Y, An XL, Yu H, Cai NN, Zhai YH, Li Q, Cheng H, Zhang S, Tang B, Li ZY, Zhang XM. Transcriptome profile of bovine iPSCs derived from Sertoli Cells. Theriogenology 2020; 146:120-132. [DOI: 10.1016/j.theriogenology.2019.11.022] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2019] [Revised: 11/16/2019] [Accepted: 11/17/2019] [Indexed: 12/18/2022]
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27
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Lee SJ, Kang KW, Kim JH, Lee BH, Jung JH, Park Y, Hong SC, Kim BS. CXCR2 Ligands and mTOR Activation Enhance Reprogramming of Human Somatic Cells to Pluripotent Stem Cells. Stem Cells Dev 2020; 29:119-132. [DOI: 10.1089/scd.2019.0188] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023] Open
Affiliation(s)
- Seung-Jin Lee
- Institute of Stem Cell Research, Korea University College of Medicine, Seoul, Korea
- Department of Biomedical and Science, Graduate School of Medicine, Korea University, Seoul, Korea
| | - Ka-Won Kang
- Department of Internal Medicine, Korea University Medical Center, Seoul, Korea
| | - Ji-Hea Kim
- Institute of Stem Cell Research, Korea University College of Medicine, Seoul, Korea
- Department of Biomedical and Science, Graduate School of Medicine, Korea University, Seoul, Korea
| | - Byung-Hyun Lee
- Department of Internal Medicine, Korea University Medical Center, Seoul, Korea
| | - Ji-Hye Jung
- Institute of Stem Cell Research, Korea University College of Medicine, Seoul, Korea
| | - Yong Park
- Department of Internal Medicine, Korea University Medical Center, Seoul, Korea
| | - Soon-Cheol Hong
- Department of Obstetrics and Gynecology, Korea University Medical Center, Seoul, Korea
| | - Byung-Soo Kim
- Institute of Stem Cell Research, Korea University College of Medicine, Seoul, Korea
- Department of Biomedical and Science, Graduate School of Medicine, Korea University, Seoul, Korea
- Department of Internal Medicine, Korea University Medical Center, Seoul, Korea
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28
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Tolios A, De Las Rivas J, Hovig E, Trouillas P, Scorilas A, Mohr T. Computational approaches in cancer multidrug resistance research: Identification of potential biomarkers, drug targets and drug-target interactions. Drug Resist Updat 2019; 48:100662. [PMID: 31927437 DOI: 10.1016/j.drup.2019.100662] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2019] [Revised: 10/15/2019] [Accepted: 10/17/2019] [Indexed: 02/07/2023]
Abstract
Like physics in the 19th century, biology and molecular biology in particular, has been fertilized and enhanced like few other scientific fields, by the incorporation of mathematical methods. In the last decades, a whole new scientific field, bioinformatics, has developed with an output of over 30,000 papers a year (Pubmed search using the keyword "bioinformatics"). Huge databases of mass throughput data have been established, with ArrayExpress alone containing more than 2.7 million assays (October 2019). Computational methods have become indispensable tools in molecular biology, particularly in one of the most challenging areas of cancer research, multidrug resistance (MDR). However, confronted with a plethora of different algorithms, approaches, and methods, the average researcher faces key questions: Which methods do exist? Which methods can be used to tackle the aims of a given study? Or, more generally, how do I use computational biology/bioinformatics to bolster my research? The current review is aimed at providing guidance to existing methods with relevance to MDR research. In particular, we provide an overview on: a) the identification of potential biomarkers using expression data; b) the prediction of treatment response by machine learning methods; c) the employment of network approaches to identify gene/protein regulatory networks and potential key players; d) the identification of drug-target interactions; e) the use of bipartite networks to identify multidrug targets; f) the identification of cellular subpopulations with the MDR phenotype; and, finally, g) the use of molecular modeling methods to guide and enhance drug discovery. This review shall serve as a guide through some of the basic concepts useful in MDR research. It shall give the reader some ideas about the possibilities in MDR research by using computational tools, and, finally, it shall provide a short overview of relevant literature.
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Affiliation(s)
- A Tolios
- Department of Blood Group Serology and Transfusion Medicine, Medical University of Vienna, Vienna, Austria; Department of Laboratory Medicine, Medical University of Vienna, Vienna, Austria; Institute of Clinical Chemistry and Laboratory Medicine, Heinrich Heine University, Duesseldorf, Germany.
| | - J De Las Rivas
- Bioinformatics and Functional Genomics Group, Cancer Research Center (CiC-IMBCC, CSIC/USAL/IBSAL), Consejo Superior de Investigaciones Científicas (CSIC) and University of Salamanca (USAL), Campus Miguel de Unamuno s/n, Salamanca, Spain.
| | - E Hovig
- Department of Tumor Biology, Institute for Cancer Research, Oslo University Hospital and Center for Bioinformatics, Department of Informatics, University of Oslo, Oslo, Norway.
| | - P Trouillas
- UMR 1248 INSERM, Univ. Limoges, 2 rue du Dr Marland, 87052, Limoges, France; RCPTM, University Palacký of Olomouc, tr. 17. listopadu 12, 771 46, Olomouc, Czech Republic.
| | - A Scorilas
- Department of Biochemistry & Molecular Biology, Faculty of Biology, National and Kapodistrian University of Athens, Athens, Greece.
| | - T Mohr
- Institute of Cancer Research, Department of Medicine I, Medical University of Vienna, Vienna, Austria; ScienceConsult - DI Thomas Mohr KG, Guntramsdorf, Austria.
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29
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Li QV, Rosen BP, Huangfu D. Decoding pluripotency: Genetic screens to interrogate the acquisition, maintenance, and exit of pluripotency. WILEY INTERDISCIPLINARY REVIEWS-SYSTEMS BIOLOGY AND MEDICINE 2019; 12:e1464. [PMID: 31407519 DOI: 10.1002/wsbm.1464] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/09/2018] [Revised: 05/31/2019] [Accepted: 07/17/2019] [Indexed: 01/25/2023]
Abstract
Pluripotent stem cells have the ability to unlimitedly self-renew and differentiate to any somatic cell lineage. A number of systems biology approaches have been used to define this pluripotent state. Complementary to systems level characterization, genetic screens offer a unique avenue to functionally interrogate the pluripotent state and identify the key players in pluripotency acquisition and maintenance, exit of pluripotency, and lineage differentiation. Here we review how genetic screens have helped us decode pluripotency regulation. We will summarize results from RNA interference (RNAi) based screens, discuss recent advances in CRISPR/Cas-based genetic perturbation methods, and how these advances have made it possible to more comprehensively interrogate pluripotency and differentiation through genetic screens. Such investigations will not only provide a better understanding of this unique developmental state, but may enhance our ability to use pluripotent stem cells as an experimental model to study human development and disease progression. Functional interrogation of pluripotency also provides a valuable roadmap for utilizing genetic perturbation to gain systems level understanding of additional cellular states, from later stages of development to pathological disease states. This article is categorized under: Developmental Biology > Stem Cell Biology and Regeneration Developmental Biology > Developmental Processes in Health and Disease Biological Mechanisms > Cell Fates.
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Affiliation(s)
- Qing V Li
- Sloan Kettering Institute, New York, New York.,Louis V. Gerstner Jr. Graduate School of Biomedical Sciences, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Bess P Rosen
- Sloan Kettering Institute, New York, New York.,Weill Graduate School of Medical Sciences at Cornell University, New York, New York
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30
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McGinnis CS, Patterson DM, Winkler J, Conrad DN, Hein MY, Srivastava V, Hu JL, Murrow LM, Weissman JS, Werb Z, Chow ED, Gartner ZJ. MULTI-seq: sample multiplexing for single-cell RNA sequencing using lipid-tagged indices. Nat Methods 2019. [PMID: 31209384 DOI: 10.1101/387241] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
Sample multiplexing facilitates scRNA-seq by reducing costs and identifying artifacts such as cell doublets. However, universal and scalable sample barcoding strategies have not been described. We therefore developed MULTI-seq: multiplexing using lipid-tagged indices for single-cell and single-nucleus RNA sequencing. MULTI-seq reagents can barcode any cell type or nucleus from any species with an accessible plasma membrane. The method involves minimal sample processing, thereby preserving cell viability and endogenous gene expression patterns. When cells are classified into sample groups using MULTI-seq barcode abundances, data quality is improved through doublet identification and recovery of cells with low RNA content that would otherwise be discarded by standard quality-control workflows. We use MULTI-seq to track the dynamics of T-cell activation, perform a 96-plex perturbation experiment with primary human mammary epithelial cells and multiplex cryopreserved tumors and metastatic sites isolated from a patient-derived xenograft mouse model of triple-negative breast cancer.
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Affiliation(s)
- Christopher S McGinnis
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, CA, USA
| | - David M Patterson
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, CA, USA
| | - Juliane Winkler
- Department of Anatomy, University of California San Francisco, San Francisco, CA, USA
| | - Daniel N Conrad
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, CA, USA
| | - Marco Y Hein
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA
- Howard Hughes Medical Institute, Chevy Chase, MD, USA
| | - Vasudha Srivastava
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, CA, USA
| | - Jennifer L Hu
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, CA, USA
| | - Lyndsay M Murrow
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, CA, USA
| | - Jonathan S Weissman
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA
- Howard Hughes Medical Institute, Chevy Chase, MD, USA
| | - Zena Werb
- Department of Anatomy, University of California San Francisco, San Francisco, CA, USA
- Helen Diller Family Comprehensive Cancer Center, San Francisco, CA, USA
| | - Eric D Chow
- Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, CA, USA.
- Center for Advanced Technology, University of California San Francisco, San Francisco, CA, USA.
| | - Zev J Gartner
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, CA, USA.
- Helen Diller Family Comprehensive Cancer Center, San Francisco, CA, USA.
- Chan Zuckerberg BioHub, University of California San Francisco, San Francisco, CA, USA.
- Center for Cellular Construction, University of California San Francisco, San Francisco, CA, USA.
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31
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McGinnis CS, Patterson DM, Winkler J, Conrad DN, Hein MY, Srivastava V, Hu JL, Murrow LM, Weissman JS, Werb Z, Chow ED, Gartner ZJ. MULTI-seq: sample multiplexing for single-cell RNA sequencing using lipid-tagged indices. Nat Methods 2019; 16:619-626. [PMID: 31209384 PMCID: PMC6837808 DOI: 10.1038/s41592-019-0433-8] [Citation(s) in RCA: 314] [Impact Index Per Article: 62.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2018] [Accepted: 04/29/2019] [Indexed: 12/12/2022]
Abstract
Sample multiplexing facilitates scRNA-seq by reducing costs and identifying artifacts such as cell doublets. However, universal and scalable sample barcoding strategies have not been described. We therefore developed MULTI-seq: multiplexing using lipid-tagged indices for single-cell and single-nucleus RNA sequencing. MULTI-seq reagents can barcode any cell type or nucleus from any species with an accessible plasma membrane. The method involves minimal sample processing, thereby preserving cell viability and endogenous gene expression patterns. When cells are classified into sample groups using MULTI-seq barcode abundances, data quality is improved through doublet identification and recovery of cells with low RNA content that would otherwise be discarded by standard quality-control workflows. We use MULTI-seq to track the dynamics of T-cell activation, perform a 96-plex perturbation experiment with primary human mammary epithelial cells and multiplex cryopreserved tumors and metastatic sites isolated from a patient-derived xenograft mouse model of triple-negative breast cancer.
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Affiliation(s)
- Christopher S McGinnis
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, CA, USA
| | - David M Patterson
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, CA, USA
| | - Juliane Winkler
- Department of Anatomy, University of California San Francisco, San Francisco, CA, USA
| | - Daniel N Conrad
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, CA, USA
| | - Marco Y Hein
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA
- Howard Hughes Medical Institute, Chevy Chase, MD, USA
| | - Vasudha Srivastava
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, CA, USA
| | - Jennifer L Hu
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, CA, USA
| | - Lyndsay M Murrow
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, CA, USA
| | - Jonathan S Weissman
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA
- Howard Hughes Medical Institute, Chevy Chase, MD, USA
| | - Zena Werb
- Department of Anatomy, University of California San Francisco, San Francisco, CA, USA
- Helen Diller Family Comprehensive Cancer Center, San Francisco, CA, USA
| | - Eric D Chow
- Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, CA, USA.
- Center for Advanced Technology, University of California San Francisco, San Francisco, CA, USA.
| | - Zev J Gartner
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, CA, USA.
- Helen Diller Family Comprehensive Cancer Center, San Francisco, CA, USA.
- Chan Zuckerberg BioHub, University of California San Francisco, San Francisco, CA, USA.
- Center for Cellular Construction, University of California San Francisco, San Francisco, CA, USA.
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32
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Lujambio A, Banito A. Functional screening to identify senescence regulators in cancer. Curr Opin Genet Dev 2019; 54:17-24. [PMID: 30877988 DOI: 10.1016/j.gde.2019.02.001] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2018] [Accepted: 02/01/2019] [Indexed: 12/12/2022]
Abstract
Cellular senescence is implicated in numerous biological processes, and can play pleiotropic, sometimes opposing, roles in cancer. Several triggers, cell types, contexts, and senescence-associated phenotypes introduce a multitude of possibilities when studying this process and its biological consequences. Recent studies continue to characterize cellular senescence at different levels, using a combination of functional screens, in silico analysis, omics characterizations and more targeted studies. However, a comprehensive analysis of its context-dependent effects and multiple phenotypes is required. Application of state-of-the-art and emerging technologies will increase our understanding of this complex process and better guide future strategies to harness senescence to our advantage, or to target it when detrimental.
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Affiliation(s)
- Amaia Lujambio
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, USA; Liver Cancer Program, Division of Liver Diseases, Department of Medicine, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, USA; The Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, USA; Graduate School of Biomedical Sciences at Icahn School of Medicine at Mount Sinai, New York, USA
| | - Ana Banito
- Hopp Children's Cancer Center (KiTZ) and Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ), Heidelberg, Germany.
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33
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De Lope C, Martín-Alonso S, Auzmendi-Iriarte J, Escudero C, Mulet I, Larrasa-Alonso J, López-Antona I, Matheu A, Palmero I. SIX1 represses senescence and promotes SOX2-mediated cellular plasticity during tumorigenesis. Sci Rep 2019; 9:1412. [PMID: 30723235 PMCID: PMC6363751 DOI: 10.1038/s41598-018-38176-0] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2018] [Accepted: 12/21/2018] [Indexed: 12/25/2022] Open
Abstract
Six1 is a developmental transcriptional regulator frequently overexpressed in human tumors. Recent results show that SIX1 also acts as a repressor of cell senescence, an antiproliferative response with a key role in tumor suppression, among other physiological and pathological settings. Here, we set to study the impact of SIX1 gain of function in transformation and tumorigenesis of fibroblasts, in connection with senescence. Using transcriptomic, histological, and functional analyses in murine tumors and cells of fibroblast origin, we show that SIX1 has a strong pro-tumorigenic action in this model, linked to the repression of a senescence-related gene signature and the induction of an undifferentiated phenotype mediated, at least in part, by the regulation of the stemness factor Sox2. Moreover, functional analyses with human glioma cell lines also show that SIX1 controls SOX2 expression, senescence and self-renewal in this model. Collectively, our results support a general link of SIX1 with senescence and SOX2-mediated cell plasticity in tumors.
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Affiliation(s)
- Cristina De Lope
- Instituto de Investigaciones Biomédicas "Alberto Sols" CSIC-UAM, Madrid, Spain
| | - Samara Martín-Alonso
- Instituto de Investigaciones Biomédicas "Alberto Sols" CSIC-UAM, Madrid, Spain.,Centro de Biología Molecular Severo Ochoa, CSIC-UAM, Madrid, Spain
| | | | - Carmen Escudero
- Instituto de Investigaciones Biomédicas "Alberto Sols" CSIC-UAM, Madrid, Spain
| | - Isabel Mulet
- Instituto de Investigaciones Biomédicas "Alberto Sols" CSIC-UAM, Madrid, Spain.,Instituto de Biomedicina de Valencia CSIC, Valencia, Spain
| | - Javier Larrasa-Alonso
- Instituto de Investigaciones Biomédicas "Alberto Sols" CSIC-UAM, Madrid, Spain.,Centro Nacional de Investigaciones Cardiovasculares, Madrid, Spain
| | - Irene López-Antona
- Instituto de Investigaciones Biomédicas "Alberto Sols" CSIC-UAM, Madrid, Spain
| | - Ander Matheu
- Instituto de Investigación Sanitaria Biodonostia, San Sebastián, Spain.,IKERBASQUE, Basque Foundation for Science, and CIBERfes, Madrid, Spain
| | - Ignacio Palmero
- Instituto de Investigaciones Biomédicas "Alberto Sols" CSIC-UAM, Madrid, Spain.
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34
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Heme detoxification by heme oxygenase-1 reinstates proliferative and immune balances upon genotoxic tissue injury. Cell Death Dis 2019; 10:72. [PMID: 30683864 PMCID: PMC6347604 DOI: 10.1038/s41419-019-1342-6] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2018] [Accepted: 01/02/2019] [Indexed: 12/13/2022]
Abstract
Phenotypic changes of myeloid cells are critical to the regulation of premature aging, development of cancer, and responses to infection. Heme metabolism has a fundamental role in the regulation of myeloid cell function and activity. Here, we show that deletion of heme oxygenase-1 (HO-1), an enzyme that removes heme, results in an impaired DNA damage response (DDR), reduced cell proliferation, and increased cellular senescence. We detected increased levels of p16INK4a, H2AXγ, and senescence-associated-β-galactosidase (SA-β-Gal) in cells and tissues isolated from HO-1-deficient mice. Importantly, deficiency of HO-1 in residential macrophages in chimeric mice results in elevated DNA damage and senescence upon radiation-induced injury. Mechanistically, we found that mammalian target of rapamycin (mTOR)/S6 protein signaling is critical for heme and HO-1-regulated phenotype of macrophages. Collectively, our data indicate that HO-1, by detoxifying heme, blocks p16INK4a expression in macrophages, preventing DNA damage and cellular senescence.
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35
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The dynamic nature of senescence in cancer. Nat Cell Biol 2019; 21:94-101. [PMID: 30602768 DOI: 10.1038/s41556-018-0249-2] [Citation(s) in RCA: 337] [Impact Index Per Article: 67.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2018] [Accepted: 11/07/2018] [Indexed: 12/14/2022]
Abstract
Cellular senescence is implicated in physiological and pathological processes spanning development, wound healing, age-related decline in organ functions and cancer. Here, we discuss cell-autonomous and non-cell-autonomous properties of senescence in the context of tumour formation and anticancer therapy, and characterize these properties, such as reprogramming into stemness, tissue remodelling and immune crosstalk, as far more dynamic than suggested by the common view of senescence as an irreversible, static condition.
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36
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Abstract
Rapamycin inhibits cell proliferation, yet preserves (re)-proliferative potential (RPP). RPP is a potential of quiescent cells that is lost in senescent cells. mTOR drives conversion from quiescence to senescence (geroconversion). By suppressing geroconversion, rapamycin preserves RPP. Geroconversion is characterized by proliferation-like levels of phospho-S6K/S6/4E-BP1 in nonproliferating cells arrested by p16 and/or p21. mTOR-driven geroconversion is associated with cellular hyperfunction, which in turn leads to organismal aging manifested by age-related diseases.
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37
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Abstract
The growing scale and declining cost of single-cell RNA-sequencing (RNA-seq) now permit a repetition of cell sampling that increases the power to detect rare cell states, reconstruct developmental trajectories, and measure phenotype in new terms such as cellular variance. The characterization of anatomy and developmental dynamics has not had an equivalent breakthrough since groundbreaking advances in live fluorescent microscopy. The new resolution obtained by single-cell RNA-seq is a boon to genetics because the novel description of phenotype offers the opportunity to refine gene function and dissect pleiotropy. In addition, the recent pairing of high-throughput genetic perturbation with single-cell RNA-seq has made practical a scale of genetic screening not previously possible.
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Affiliation(s)
- Kenneth D Birnbaum
- Center for Genomics and Systems Biology, New York University, New York, NY 10003, USA;
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38
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Shifrut E, Carnevale J, Tobin V, Roth TL, Woo JM, Bui CT, Li PJ, Diolaiti ME, Ashworth A, Marson A. Genome-wide CRISPR Screens in Primary Human T Cells Reveal Key Regulators of Immune Function. Cell 2018; 175:1958-1971.e15. [PMID: 30449619 DOI: 10.1016/j.cell.2018.10.024] [Citation(s) in RCA: 312] [Impact Index Per Article: 52.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2018] [Revised: 09/08/2018] [Accepted: 10/08/2018] [Indexed: 12/11/2022]
Abstract
Human T cells are central effectors of immunity and cancer immunotherapy. CRISPR-based functional studies in T cells could prioritize novel targets for drug development and improve the design of genetically reprogrammed cell-based therapies. However, large-scale CRISPR screens have been challenging in primary human cells. We developed a new method, single guide RNA (sgRNA) lentiviral infection with Cas9 protein electroporation (SLICE), to identify regulators of stimulation responses in primary human T cells. Genome-wide loss-of-function screens identified essential T cell receptor signaling components and genes that negatively tune proliferation following stimulation. Targeted ablation of individual candidate genes characterized hits and identified perturbations that enhanced cancer cell killing. SLICE coupled with single-cell RNA sequencing (RNA-seq) revealed signature stimulation-response gene programs altered by key genetic perturbations. SLICE genome-wide screening was also adaptable to identify mediators of immunosuppression, revealing genes controlling responses to adenosine signaling. The SLICE platform enables unbiased discovery and characterization of functional gene targets in primary cells.
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Affiliation(s)
- Eric Shifrut
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA 94143, USA; Diabetes Center, University of California, San Francisco, San Francisco, CA 94143, USA; Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Julia Carnevale
- UCSF Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA 94158, USA; Department of Medicine, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Victoria Tobin
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA 94143, USA; Diabetes Center, University of California, San Francisco, San Francisco, CA 94143, USA; Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Theodore L Roth
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA 94143, USA; Diabetes Center, University of California, San Francisco, San Francisco, CA 94143, USA; Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Jonathan M Woo
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA 94143, USA; Diabetes Center, University of California, San Francisco, San Francisco, CA 94143, USA; Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Christina T Bui
- UCSF Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA 94158, USA
| | - P Jonathan Li
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA 94143, USA; Diabetes Center, University of California, San Francisco, San Francisco, CA 94143, USA; Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Morgan E Diolaiti
- UCSF Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Alan Ashworth
- UCSF Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA 94158, USA; Department of Medicine, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Alexander Marson
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA 94143, USA; Diabetes Center, University of California, San Francisco, San Francisco, CA 94143, USA; Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA 94720, USA; UCSF Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA 94158, USA; Department of Medicine, University of California, San Francisco, San Francisco, CA 94143, USA; Chan Zuckerberg Biohub, San Francisco, CA 94158, USA.
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39
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Brioschi M, Banfi C. The application of gene silencing in proteomics: from laboratory to clinic. Expert Rev Proteomics 2018; 15:717-732. [PMID: 30205712 DOI: 10.1080/14789450.2018.1521275] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
INTRODUCTION Since the completion of genome sequencing, gene silencing technologies have emerged as powerful tools to study gene functions in various biological processes, both in vivo and in vitro. Moreover, they have also been proposed as therapeutic agents to inhibit selected genes in a variety of pathological conditions, such as cancer, neurodegenerative, and cardiovascular diseases. Area covered: This review summarizes the mechanisms of action and applications of genome editing tools, from RNA interference to clustered regularly interspaced short palindromic repeats-based systems, in research and in clinics. We describe their essential role in high-throughput genetic screens and, in particular, in functional proteomics studies, to identify diagnostic markers and therapeutic targets. Indeed, gene silencing and proteomics have been extensively integrated to study global proteome changes, posttranslational modifications, and protein-protein interactions. Expert commentary: Functional proteomics approaches that leverage gene silencing tools have been successfully applied to examine the role of several genes in various contexts, leading to a deeper knowledge of biological pathways and disease mechanisms. Recent developments of gene silencing tools have improved their performance, also in terms of off-targets effects reduction, paving the way for a wider therapeutic application of these systems.
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Affiliation(s)
- Maura Brioschi
- a Unit of Proteomics , Centro Cardiologico Monzino IRCCS , Milano , Italy
| | - Cristina Banfi
- a Unit of Proteomics , Centro Cardiologico Monzino IRCCS , Milano , Italy
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Georgilis A, Klotz S, Hanley CJ, Herranz N, Weirich B, Morancho B, Leote AC, D'Artista L, Gallage S, Seehawer M, Carroll T, Dharmalingam G, Wee KB, Mellone M, Pombo J, Heide D, Guccione E, Arribas J, Barbosa-Morais NL, Heikenwalder M, Thomas GJ, Zender L, Gil J. PTBP1-Mediated Alternative Splicing Regulates the Inflammatory Secretome and the Pro-tumorigenic Effects of Senescent Cells. Cancer Cell 2018; 34:85-102.e9. [PMID: 29990503 PMCID: PMC6048363 DOI: 10.1016/j.ccell.2018.06.007] [Citation(s) in RCA: 134] [Impact Index Per Article: 22.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/22/2017] [Revised: 03/26/2018] [Accepted: 06/11/2018] [Indexed: 12/11/2022]
Abstract
Oncogene-induced senescence is a potent tumor-suppressive response. Paradoxically, senescence also induces an inflammatory secretome that promotes carcinogenesis and age-related pathologies. Consequently, the senescence-associated secretory phenotype (SASP) is a potential therapeutic target. Here, we describe an RNAi screen for SASP regulators. We identified 50 druggable targets whose knockdown suppresses the inflammatory secretome and differentially affects other SASP components. Among the screen candidates was PTBP1. PTBP1 regulates the alternative splicing of genes involved in intracellular trafficking, such as EXOC7, to control the SASP. Inhibition of PTBP1 prevents the pro-tumorigenic effects of the SASP and impairs immune surveillance without increasing the risk of tumorigenesis. In conclusion, our study identifies SASP inhibition as a powerful and safe therapy against inflammation-driven cancer.
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Affiliation(s)
- Athena Georgilis
- MRC London Institute of Medical Sciences (LMS), Du Cane Road, London W12 0NN, UK; Institute of Clinical Sciences (ICS), Faculty of Medicine, Imperial College London, Du Cane Road, London W12 0NN, UK
| | - Sabrina Klotz
- Department of Internal Medicine VIII, University Hospital Tübingen, Tübingen 72076, Germany; Department of Physiology I, Institute of Physiology, Eberhard Karls University Tübingen, Tübingen 72076, Germany
| | - Christopher J Hanley
- Cancer Sciences Unit, Cancer Research UK Centre, University of Southampton, Somers Building, Southampton SO16 6YD, UK
| | - Nicolas Herranz
- MRC London Institute of Medical Sciences (LMS), Du Cane Road, London W12 0NN, UK; Institute of Clinical Sciences (ICS), Faculty of Medicine, Imperial College London, Du Cane Road, London W12 0NN, UK
| | - Benedikt Weirich
- Division of Chronic Inflammation and Cancer, German Cancer Research Centre (DKFZ), Heidelberg 69121, Germany
| | - Beatriz Morancho
- Preclinical Research Program, Vall d'Hebron Institute of Oncology (VHIO) and CIBERONC, Barcelona 08035, Spain
| | - Ana Carolina Leote
- Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, Lisbon, Portugal
| | - Luana D'Artista
- Department of Internal Medicine VIII, University Hospital Tübingen, Tübingen 72076, Germany; Department of Physiology I, Institute of Physiology, Eberhard Karls University Tübingen, Tübingen 72076, Germany
| | - Suchira Gallage
- MRC London Institute of Medical Sciences (LMS), Du Cane Road, London W12 0NN, UK; Institute of Clinical Sciences (ICS), Faculty of Medicine, Imperial College London, Du Cane Road, London W12 0NN, UK; Division of Chronic Inflammation and Cancer, German Cancer Research Centre (DKFZ), Heidelberg 69121, Germany
| | - Marco Seehawer
- Department of Internal Medicine VIII, University Hospital Tübingen, Tübingen 72076, Germany; Department of Physiology I, Institute of Physiology, Eberhard Karls University Tübingen, Tübingen 72076, Germany
| | - Thomas Carroll
- MRC London Institute of Medical Sciences (LMS), Du Cane Road, London W12 0NN, UK; Institute of Clinical Sciences (ICS), Faculty of Medicine, Imperial College London, Du Cane Road, London W12 0NN, UK
| | - Gopuraja Dharmalingam
- MRC London Institute of Medical Sciences (LMS), Du Cane Road, London W12 0NN, UK; Institute of Clinical Sciences (ICS), Faculty of Medicine, Imperial College London, Du Cane Road, London W12 0NN, UK
| | - Keng Boon Wee
- Institute of High Performance Computing, A(∗)STAR, 1 Fusionopolis Way, #16-16 Connexis, Singapore 138632, Singapore; Bioinformatics Institute, A(∗)STAR, 30 Biopolis Street, #07-01 Matrix, Singapore 138671, Singapore
| | - Marco Mellone
- Cancer Sciences Unit, Cancer Research UK Centre, University of Southampton, Somers Building, Southampton SO16 6YD, UK
| | - Joaquim Pombo
- MRC London Institute of Medical Sciences (LMS), Du Cane Road, London W12 0NN, UK; Institute of Clinical Sciences (ICS), Faculty of Medicine, Imperial College London, Du Cane Road, London W12 0NN, UK
| | - Danijela Heide
- Division of Chronic Inflammation and Cancer, German Cancer Research Centre (DKFZ), Heidelberg 69121, Germany
| | - Ernesto Guccione
- Methyltransferases in Development and Disease Group, Institute of Molecular and Cell Biology, Agency for Science, Technology and Research (A(∗)STAR), Singapore, Singapore
| | - Joaquín Arribas
- Preclinical Research Program, Vall d'Hebron Institute of Oncology (VHIO) and CIBERONC, Barcelona 08035, Spain; Department of Biochemistry and Molecular Biology, Universitat Autónoma de Barcelona, Campus de la UAB, Bellaterra 08193, Spain; Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona 08010, Spain
| | - Nuno L Barbosa-Morais
- Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, Lisbon, Portugal
| | - Mathias Heikenwalder
- Division of Chronic Inflammation and Cancer, German Cancer Research Centre (DKFZ), Heidelberg 69121, Germany
| | - Gareth J Thomas
- Cancer Sciences Unit, Cancer Research UK Centre, University of Southampton, Somers Building, Southampton SO16 6YD, UK
| | - Lars Zender
- Department of Internal Medicine VIII, University Hospital Tübingen, Tübingen 72076, Germany; Department of Physiology I, Institute of Physiology, Eberhard Karls University Tübingen, Tübingen 72076, Germany; Translational Gastrointestinal Oncology Group, German Consortium for Translational Cancer Research (DKTK), German Cancer Research Center (DKFZ), Heidelberg 69120, Germany
| | - Jesús Gil
- MRC London Institute of Medical Sciences (LMS), Du Cane Road, London W12 0NN, UK; Institute of Clinical Sciences (ICS), Faculty of Medicine, Imperial College London, Du Cane Road, London W12 0NN, UK.
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41
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Gonzalez-Meljem JM, Apps JR, Fraser HC, Martinez-Barbera JP. Paracrine roles of cellular senescence in promoting tumourigenesis. Br J Cancer 2018; 118:1283-1288. [PMID: 29670296 PMCID: PMC5959857 DOI: 10.1038/s41416-018-0066-1] [Citation(s) in RCA: 108] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2017] [Revised: 03/02/2018] [Accepted: 03/02/2018] [Indexed: 12/26/2022] Open
Abstract
Senescent cells activate genetic programmes that irreversibly inhibit cellular proliferation, but also endow these cells with distinctive metabolic and signalling phenotypes. Although senescence has historically been considered a protective mechanism against tumourigenesis, the activities of senescent cells are increasingly being associated with age-related diseases, including cancer. An important feature of senescent cells is the secretion of a vast array of pro-inflammatory cytokines, chemokines, and growth factors collectively known as the senescence-associated secretory phenotype (SASP). Recent research has shown that SASP paracrine signalling can mediate several pro-tumourigenic effects, such as enhancing malignant phenotypes and promoting tumour initiation. In this review, we summarise the paracrine activities of senescent cells and their role in tumourigenesis through direct effects on growth and proliferation of tumour cells, tumour angiogenesis, invasion and metastasis, cellular reprogramming and emergence of tumour-initiating cells, and tumour interactions with the local immune environment. The evidence described here suggests cellular senescence acts as a double-edged sword in cancer pathogenesis, which demands further attention in order to support the use of senolytic or SASP-modulating compounds for cancer treatment.
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Affiliation(s)
- Jose Mario Gonzalez-Meljem
- Developmental Biology and Cancer Research Programme, UCL Great Ormond Street Institute of Child Health, Guilford Street, London, WC1N 1EH, UK.,Basic Research Department, Instituto Nacional de Geriatría, Anillo Periférico 2767, Magdalena Contreras, 10200, Mexico City, Mexico
| | - John Richard Apps
- Developmental Biology and Cancer Research Programme, UCL Great Ormond Street Institute of Child Health, Guilford Street, London, WC1N 1EH, UK
| | - Helen Christina Fraser
- Developmental Biology and Cancer Research Programme, UCL Great Ormond Street Institute of Child Health, Guilford Street, London, WC1N 1EH, UK
| | - Juan Pedro Martinez-Barbera
- Developmental Biology and Cancer Research Programme, UCL Great Ormond Street Institute of Child Health, Guilford Street, London, WC1N 1EH, UK.
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42
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Adams FF, Hoffmann T, Zuber J, Heckl D, Schambach A, Schwarzer A. Pooled Generation of Lentiviral Tetracycline-Regulated microRNA Embedded Short Hairpin RNA Libraries. Hum Gene Ther Methods 2018; 29:16-29. [PMID: 29325442 DOI: 10.1089/hgtb.2017.182] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Short hairpin RNA (shRNA) screens are powerful tools to probe genetic dependencies in loss-of-function studies, such as the identification of therapeutic targets in cancer research. Lentivirally delivered shRNAs embedded in endogenous microRNA contexts (shRNAmiRs) mediate efficient long-term suppression of target genes suitable for numerous experimental contexts and clinical applications. Here, an easy-to-use laboratory protocol is described, covering the design and pooled assembly of focused shRNAmiR libraries into an optimized, Tet-inducible all-in-one lentiviral vector, packaging of viral particles, followed by retrieval and quantification of hairpin sequences after cellular DNA-recovery. Starting from a gene list to the identification of hits, the protocol enables shRNA screens within 6 weeks.
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Affiliation(s)
- Felix F Adams
- 1 Institute of Experimental Hematology, Hannover Medical School, Hannover, Germany
| | - Thomas Hoffmann
- 2 Research Institute of Molecular Pathology (IMP), Vienna, Austria
| | - Johannes Zuber
- 2 Research Institute of Molecular Pathology (IMP), Vienna, Austria
| | - Dirk Heckl
- 3 Pediatric Hematology and Oncology, Hannover Medical School, Hannover, Germany
| | - Axel Schambach
- 1 Institute of Experimental Hematology, Hannover Medical School, Hannover, Germany .,4 Division of Hematology/Oncology, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Adrian Schwarzer
- 1 Institute of Experimental Hematology, Hannover Medical School, Hannover, Germany .,5 Department of Hematology, Hemostasis, Oncology, and Stem Cell Transplantation, Hannover Medical School, Hannover, Germany
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