1
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Lee HC, Oliveira NMM, Hastings C, Baillie-Benson P, Moverley AA, Lu HC, Zheng Y, Wilby EL, Weil TT, Page KM, Fu J, Moris N, Stern CD. Regulation of long-range BMP gradients and embryonic polarity by propagation of local calcium-firing activity. Nat Commun 2024; 15:1463. [PMID: 38368410 PMCID: PMC10874436 DOI: 10.1038/s41467-024-45772-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2023] [Accepted: 02/02/2024] [Indexed: 02/19/2024] Open
Abstract
Many amniote vertebrate species including humans can form identical twins from a single embryo, but this only occurs rarely. It has been suggested that the primitive-streak-forming embryonic region emits signals that inhibit streak formation elsewhere but the signals involved, how they are transmitted and how they act has not been elucidated. Here we show that short tracks of calcium firing activity propagate through extraembryonic tissue via gap junctions and prevent ectopic primitive streak formation in chick embryos. Cross-regulation of calcium activity and an inhibitor of primitive streak formation (Bone Morphogenetic Protein, BMP) via NF-κB and NFAT establishes a long-range BMP gradient spanning the embryo. This mechanism explains how embryos of widely different sizes can maintain positional information that determines embryo polarity. We provide evidence for similar mechanisms in two different human embryo models and in Drosophila, suggesting an ancient evolutionary origin.
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Affiliation(s)
- Hyung Chul Lee
- Department of Cell and Developmental Biology, University College London, Gower Street, London, WC1E 6BT, UK.
- School of Biological Sciences and Technology, College of Natural Sciences, Chonnam National University, 77 Yongbong-ro, Gwangju, 61186, Korea.
| | - Nidia M M Oliveira
- Department of Cell and Developmental Biology, University College London, Gower Street, London, WC1E 6BT, UK
- College of Professional Services, Murdoch University, 90 South St, Murdoch, WA, 6150, Australia
| | - Cato Hastings
- Department of Cell and Developmental Biology, University College London, Gower Street, London, WC1E 6BT, UK
| | | | - Adam A Moverley
- Department of Cell and Developmental Biology, University College London, Gower Street, London, WC1E 6BT, UK
- Department of Cell and Developmental Biology, Institute for Regenerative Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Hui-Chun Lu
- Department of Cell and Developmental Biology, University College London, Gower Street, London, WC1E 6BT, UK
- Centre for Craniofacial & Regenerative Biology, Faculty of Dentistry, Oral and Craniofacial Sciences, King's College London, Guy's Tower, London, SE1 9RT, UK
| | - Yi Zheng
- Departments of Mechanical Engineering, Biomedical Engineering, and Cell & Developmental Biology, University of Michigan, Ann Arbor, MI, USA
- Department of Biomedical and Chemical Engineering, Syracuse University, Syracuse, NY, USA
- BioInspired Syracuse Institute for Materials and Living Systems, Syracuse University, Syracuse, NY, USA
| | - Elise L Wilby
- Department of Zoology, University of Cambridge, Downing Street, Cambridge, CB2 3EJ, UK
| | - Timothy T Weil
- Department of Zoology, University of Cambridge, Downing Street, Cambridge, CB2 3EJ, UK
| | - Karen M Page
- Department of Mathematics, University College London, Gower Street, London, WC1E 6BT, UK
| | - Jianping Fu
- Departments of Mechanical Engineering, Biomedical Engineering, and Cell & Developmental Biology, University of Michigan, Ann Arbor, MI, USA
| | - Naomi Moris
- The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK
| | - Claudio D Stern
- Department of Cell and Developmental Biology, University College London, Gower Street, London, WC1E 6BT, UK.
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2
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Anastasiadou K, Silva M, Booth T, Speidel L, Audsley T, Barrington C, Buckberry J, Fernandes D, Ford B, Gibson M, Gilardet A, Glocke I, Keefe K, Kelly M, Masters M, McCabe J, McIntyre L, Ponce P, Rowland S, Ruiz Ventura J, Swali P, Tait F, Walker D, Webb H, Williams M, Witkin A, Holst M, Loe L, Armit I, Schulting R, Skoglund P. Detection of chromosomal aneuploidy in ancient genomes. Commun Biol 2024; 7:14. [PMID: 38212558 PMCID: PMC10784527 DOI: 10.1038/s42003-023-05642-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2023] [Accepted: 11/28/2023] [Indexed: 01/13/2024] Open
Abstract
Ancient DNA is a valuable tool for investigating genetic and evolutionary history that can also provide detailed profiles of the lives of ancient individuals. In this study, we develop a generalised computational approach to detect aneuploidies (atypical autosomal and sex chromosome karyotypes) in the ancient genetic record and distinguish such karyotypes from contamination. We confirm that aneuploidies can be detected even in low-coverage genomes ( ~ 0.0001-fold), common in ancient DNA. We apply this method to ancient skeletal remains from Britain to document the first instance of mosaic Turner syndrome (45,X0/46,XX) in the ancient genetic record in an Iron Age individual sequenced to average 9-fold coverage, the earliest known incidence of an individual with a 47,XYY karyotype from the Early Medieval period, as well as individuals with Klinefelter (47,XXY) and Down syndrome (47,XY, + 21). Overall, our approach provides an accessible and automated framework allowing for the detection of individuals with aneuploidies, which extends previous binary approaches. This tool can facilitate the interpretation of burial context and living conditions, as well as elucidate past perceptions of biological sex and people with diverse biological traits.
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Affiliation(s)
- Kyriaki Anastasiadou
- Ancient genomics laboratory, The Francis Crick Institute, London, United Kingdom.
| | - Marina Silva
- Ancient genomics laboratory, The Francis Crick Institute, London, United Kingdom
| | - Thomas Booth
- Ancient genomics laboratory, The Francis Crick Institute, London, United Kingdom
| | - Leo Speidel
- Ancient genomics laboratory, The Francis Crick Institute, London, United Kingdom
- Genetics Institute, University College London, London, United Kingdom
| | | | - Christopher Barrington
- Bioinformatics and Biostatistics Science Technology Platform, The Francis Crick Institute, London, United Kingdom
| | - Jo Buckberry
- School of Archaeological and Forensic Sciences, University of Bradford, Bradford, United Kingdom
| | | | - Ben Ford
- Oxford Archaeology, Oxford, United Kingdom
| | | | - Alexandre Gilardet
- Ancient genomics laboratory, The Francis Crick Institute, London, United Kingdom
| | - Isabelle Glocke
- Ancient genomics laboratory, The Francis Crick Institute, London, United Kingdom
| | - Katie Keefe
- York Osteoarchaeology, York, United Kingdom
- On-Site Archaeology, York, United Kingdom
| | - Monica Kelly
- Ancient genomics laboratory, The Francis Crick Institute, London, United Kingdom
| | - Mackenzie Masters
- York Osteoarchaeology, York, United Kingdom
- Department of Archaeology, University of York, York, United Kingdom
| | - Jesse McCabe
- Ancient genomics laboratory, The Francis Crick Institute, London, United Kingdom
| | | | - Paola Ponce
- York Osteoarchaeology, York, United Kingdom
- Department of Archaeology, University of York, York, United Kingdom
| | | | - Jordi Ruiz Ventura
- York Osteoarchaeology, York, United Kingdom
- Department of Archaeology, University of York, York, United Kingdom
| | - Pooja Swali
- Ancient genomics laboratory, The Francis Crick Institute, London, United Kingdom
| | - Frankie Tait
- Ancient genomics laboratory, The Francis Crick Institute, London, United Kingdom
| | | | - Helen Webb
- Oxford Archaeology, Oxford, United Kingdom
| | - Mia Williams
- Ancient genomics laboratory, The Francis Crick Institute, London, United Kingdom
| | | | - Malin Holst
- York Osteoarchaeology, York, United Kingdom
- Department of Archaeology, University of York, York, United Kingdom
| | - Louise Loe
- Oxford Archaeology, Oxford, United Kingdom
| | - Ian Armit
- Department of Archaeology, University of York, York, United Kingdom
| | - Rick Schulting
- School of Archaeology, University of Oxford, Oxford, United Kingdom
| | - Pontus Skoglund
- Ancient genomics laboratory, The Francis Crick Institute, London, United Kingdom.
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3
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Raguseo F, Wang Y, Li J, Petrić Howe M, Balendra R, Huyghebaert A, Vadukul DM, Tanase DA, Maher TE, Malouf L, Rubio-Sánchez R, Aprile FA, Elani Y, Patani R, Di Michele L, Di Antonio M. The ALS/FTD-related C9orf72 hexanucleotide repeat expansion forms RNA condensates through multimolecular G-quadruplexes. Nat Commun 2023; 14:8272. [PMID: 38092738 PMCID: PMC10719400 DOI: 10.1038/s41467-023-43872-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Accepted: 11/21/2023] [Indexed: 12/17/2023] Open
Abstract
Amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD) are neurodegenerative diseases that exist on a clinico-pathogenetic spectrum, designated ALS/FTD. The most common genetic cause of ALS/FTD is expansion of the intronic hexanucleotide repeat (GGGGCC)n in C9orf72. Here, we investigate the formation of nucleic acid secondary structures in these expansion repeats, and their role in generating condensates characteristic of ALS/FTD. We observe significant aggregation of the hexanucleotide sequence (GGGGCC)n, which we associate to the formation of multimolecular G-quadruplexes (mG4s) by using a range of biophysical techniques. Exposing the condensates to G4-unfolding conditions leads to prompt disassembly, highlighting the key role of mG4-formation in the condensation process. We further validate the biological relevance of our findings by detecting an increased prevalence of G4-structures in C9orf72 mutant human motor neurons when compared to healthy motor neurons by staining with a G4-selective fluorescent probe, revealing signal in putative condensates. Our findings strongly suggest that RNA G-rich repetitive sequences can form protein-free condensates sustained by multimolecular G-quadruplexes, highlighting their potential relevance as therapeutic targets for C9orf72 mutation-related ALS/FTD.
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Affiliation(s)
- Federica Raguseo
- Imperial College London, Department of Chemistry, Molecular Sciences Research Hub, 82 Wood Lane, London, W12 0BZ, UK
- University of Cambridge, Department of Chemical Engineering and Biotechnology, Philippa Fawcett Drive, Cambridge, CB3 0AS, UK
- Imperial College London, Institute of Chemical Biology, Molecular Sciences Research Hub, 82 Wood Lane, London, W12 0BZ, UK
| | - Yiran Wang
- The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK
- Department of Neuromuscular Diseases, Queen Square Institute of Neurology, University College London, London, WC1N 3BG, UK
| | - Jessica Li
- The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK
- Department of Neuromuscular Diseases, Queen Square Institute of Neurology, University College London, London, WC1N 3BG, UK
| | - Marija Petrić Howe
- The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK
- Department of Neuromuscular Diseases, Queen Square Institute of Neurology, University College London, London, WC1N 3BG, UK
| | - Rubika Balendra
- The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK
- Department of Neuromuscular Diseases, Queen Square Institute of Neurology, University College London, London, WC1N 3BG, UK
| | - Anouk Huyghebaert
- Imperial College London, Department of Chemistry, Molecular Sciences Research Hub, 82 Wood Lane, London, W12 0BZ, UK
- Imperial College London, Institute of Chemical Biology, Molecular Sciences Research Hub, 82 Wood Lane, London, W12 0BZ, UK
| | - Devkee M Vadukul
- Imperial College London, Department of Chemistry, Molecular Sciences Research Hub, 82 Wood Lane, London, W12 0BZ, UK
| | - Diana A Tanase
- Imperial College London, Department of Chemistry, Molecular Sciences Research Hub, 82 Wood Lane, London, W12 0BZ, UK
- University of Cambridge, Department of Chemical Engineering and Biotechnology, Philippa Fawcett Drive, Cambridge, CB3 0AS, UK
| | - Thomas E Maher
- Imperial College London, Department of Chemistry, Molecular Sciences Research Hub, 82 Wood Lane, London, W12 0BZ, UK
- Imperial College London, Institute of Chemical Biology, Molecular Sciences Research Hub, 82 Wood Lane, London, W12 0BZ, UK
| | - Layla Malouf
- Imperial College London, Department of Chemistry, Molecular Sciences Research Hub, 82 Wood Lane, London, W12 0BZ, UK
- University of Cambridge, Department of Chemical Engineering and Biotechnology, Philippa Fawcett Drive, Cambridge, CB3 0AS, UK
| | - Roger Rubio-Sánchez
- University of Cambridge, Department of Chemical Engineering and Biotechnology, Philippa Fawcett Drive, Cambridge, CB3 0AS, UK
| | - Francesco A Aprile
- Imperial College London, Department of Chemistry, Molecular Sciences Research Hub, 82 Wood Lane, London, W12 0BZ, UK
- Imperial College London, Institute of Chemical Biology, Molecular Sciences Research Hub, 82 Wood Lane, London, W12 0BZ, UK
| | - Yuval Elani
- Imperial College London, Department of Chemical Engineering, South Kensington, London, SW7 2AZ, UK
| | - Rickie Patani
- The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK.
- Department of Neuromuscular Diseases, Queen Square Institute of Neurology, University College London, London, WC1N 3BG, UK.
| | - Lorenzo Di Michele
- Imperial College London, Department of Chemistry, Molecular Sciences Research Hub, 82 Wood Lane, London, W12 0BZ, UK.
- University of Cambridge, Department of Chemical Engineering and Biotechnology, Philippa Fawcett Drive, Cambridge, CB3 0AS, UK.
| | - Marco Di Antonio
- Imperial College London, Department of Chemistry, Molecular Sciences Research Hub, 82 Wood Lane, London, W12 0BZ, UK.
- Imperial College London, Institute of Chemical Biology, Molecular Sciences Research Hub, 82 Wood Lane, London, W12 0BZ, UK.
- The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK.
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4
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Sampedro-Castañeda M, Baltussen LL, Lopes AT, Qiu Y, Sirvio L, Mihaylov SR, Claxton S, Richardson JC, Lignani G, Ultanir SK. Epilepsy-linked kinase CDKL5 phosphorylates voltage-gated calcium channel Cav2.3, altering inactivation kinetics and neuronal excitability. Nat Commun 2023; 14:7830. [PMID: 38081835 PMCID: PMC10713615 DOI: 10.1038/s41467-023-43475-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2023] [Accepted: 11/09/2023] [Indexed: 12/18/2023] Open
Abstract
Developmental and epileptic encephalopathies (DEEs) are a group of rare childhood disorders characterized by severe epilepsy and cognitive deficits. Numerous DEE genes have been discovered thanks to advances in genomic diagnosis, yet putative molecular links between these disorders are unknown. CDKL5 deficiency disorder (CDD, DEE2), one of the most common genetic epilepsies, is caused by loss-of-function mutations in the brain-enriched kinase CDKL5. To elucidate CDKL5 function, we looked for CDKL5 substrates using a SILAC-based phosphoproteomic screen. We identified the voltage-gated Ca2+ channel Cav2.3 (encoded by CACNA1E) as a physiological target of CDKL5 in mice and humans. Recombinant channel electrophysiology and interdisciplinary characterization of Cav2.3 phosphomutant mice revealed that loss of Cav2.3 phosphorylation leads to channel gain-of-function via slower inactivation and enhanced cholinergic stimulation, resulting in increased neuronal excitability. Our results thus show that CDD is partly a channelopathy. The properties of unphosphorylated Cav2.3 closely resemble those described for CACNA1E gain-of-function mutations causing DEE69, a disorder sharing clinical features with CDD. We show that these two single-gene diseases are mechanistically related and could be ameliorated with Cav2.3 inhibitors.
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Affiliation(s)
| | - Lucas L Baltussen
- Kinases and Brain Development Lab, The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK
- Laboratory for the Research of Neurodegenerative Diseases (VIB-KU Leuven), Department of Neurosciences, ON5 Herestraat 49, 3000, Leuven, Belgium
| | - André T Lopes
- Kinases and Brain Development Lab, The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK
| | - Yichen Qiu
- Department of Clinical and Experimental Epilepsy, UCL Queen Square Institute of Neurology, Queen Square House, London, WC1N 3BG, UK
| | - Liina Sirvio
- Kinases and Brain Development Lab, The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK
| | - Simeon R Mihaylov
- Kinases and Brain Development Lab, The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK
| | - Suzanne Claxton
- Kinases and Brain Development Lab, The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK
| | - Jill C Richardson
- Neuroscience, MSD Research Laboratories, 120 Moorgate, London, EC2M 6UR, UK
| | - Gabriele Lignani
- Department of Clinical and Experimental Epilepsy, UCL Queen Square Institute of Neurology, Queen Square House, London, WC1N 3BG, UK
| | - Sila K Ultanir
- Kinases and Brain Development Lab, The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK.
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5
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de Boer LL, Vanes L, Melgrati S, Biggs O'May J, Hayward D, Driscoll PC, Day J, Griffiths A, Magueta R, Morrell A, MacRae JI, Köchl R, Tybulewicz VLJ. T cell migration requires ion and water influx to regulate actin polymerization. Nat Commun 2023; 14:7844. [PMID: 38057317 PMCID: PMC10700356 DOI: 10.1038/s41467-023-43423-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2022] [Accepted: 11/08/2023] [Indexed: 12/08/2023] Open
Abstract
Migration of T cells is essential for their ability to mount immune responses. Chemokine-induced T cell migration requires WNK1, a kinase that regulates ion influx into the cell. However, it is not known why ion entry is necessary for T cell movement. Here we show that signaling from the chemokine receptor CCR7 leads to activation of WNK1 and its downstream pathway at the leading edge of migrating CD4+ T cells, resulting in ion influx and water entry by osmosis. We propose that WNK1-induced water entry is required to swell the membrane at the leading edge, generating space into which actin filaments can polymerize, thereby facilitating forward movement of the cell. Given the broad expression of WNK1 pathway proteins, our study suggests that ion and water influx are likely to be essential for migration in many cell types, including leukocytes and metastatic tumor cells.
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Affiliation(s)
- Leonard L de Boer
- The Francis Crick Institute, London, NW1 1AT, UK
- Department of Immunology and Inflammation, Imperial College London, London, W12 0NN, UK
- Science for Life Laboratory, Department of Women's and Children's Health, Karolinska Institutet, 171 65, Stockholm, Sweden
| | - Lesley Vanes
- The Francis Crick Institute, London, NW1 1AT, UK
| | - Serena Melgrati
- The Francis Crick Institute, London, NW1 1AT, UK
- Department of Immunology and Inflammation, Imperial College London, London, W12 0NN, UK
- Institute for Research in Biomedicine, Università della Svizzera Italiana, Bellinzona, Switzerland
| | | | - Darryl Hayward
- The Francis Crick Institute, London, NW1 1AT, UK
- GSK, Stevenage, SG1 2NY, UK
| | | | - Jason Day
- Department of Earth Sciences, University of Cambridge, Cambridge, CB2 3EQ, UK
| | - Alexander Griffiths
- London Metallomics Facility, Research Management & Innovation Directorate, King's College London, London, SE1 1UL, UK
| | - Renata Magueta
- London Metallomics Facility, Research Management & Innovation Directorate, King's College London, London, SE1 1UL, UK
| | - Alexander Morrell
- London Metallomics Facility, Research Management & Innovation Directorate, King's College London, London, SE1 1UL, UK
| | | | - Robert Köchl
- The Francis Crick Institute, London, NW1 1AT, UK
- Kings College London, London, SE1 9RT, UK
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6
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Houghton FM, Adams SE, Ríos AS, Masino L, Purkiss AG, Briggs DC, Ledda F, McDonald NQ. Architecture and regulation of a GDNF-GFRα1 synaptic adhesion assembly. Nat Commun 2023; 14:7551. [PMID: 37985758 PMCID: PMC10661694 DOI: 10.1038/s41467-023-43148-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2023] [Accepted: 11/01/2023] [Indexed: 11/22/2023] Open
Abstract
Glial-cell line derived neurotrophic factor (GDNF) bound to its co-receptor GFRα1 stimulates the RET receptor tyrosine kinase, promoting neuronal survival and neuroprotection. The GDNF-GFRα1 complex also supports synaptic cell adhesion independently of RET. Here, we describe the structure of a decameric GDNF-GFRα1 assembly determined by crystallography and electron microscopy, revealing two GFRα1 pentamers bridged by five GDNF dimers. We reconsitituted the assembly between adhering liposomes and used cryo-electron tomography to visualize how the complex fulfils its membrane adhesion function. The GFRα1:GFRα1 pentameric interface was further validated both in vitro by native PAGE and in cellulo by cell-clustering and dendritic spine assays. Finally, we provide biochemical and cell-based evidence that RET and heparan sulfate cooperate to prevent assembly of the adhesion complex by competing for the adhesion interface. Our results provide a mechanistic framework to understand GDNF-driven cell adhesion, its relationship to trophic signalling, and the central role played by GFRα1.
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Affiliation(s)
- F M Houghton
- Signalling and Structural Biology laboratory, The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK
| | - S E Adams
- Signalling and Structural Biology laboratory, The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK
- Vertex Pharmaceuticals, 86-88 Jubilee Avenue, Milton Park, Abingdon, Oxfordshire, OX14 4RW, UK
| | - A S Ríos
- Fundación Instituto Leloir, Instituto de Investigaciones Bioquímicas de Buenos Aires, Av. Patricias Argentinas 435, C1405BWE, Buenos Aires, Argentina
| | - L Masino
- Structural Biology Science and Technology Platform, The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK
| | - A G Purkiss
- Structural Biology Science and Technology Platform, The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK
| | - D C Briggs
- Signalling and Structural Biology laboratory, The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK
| | - F Ledda
- Fundación Instituto Leloir, Instituto de Investigaciones Bioquímicas de Buenos Aires, Av. Patricias Argentinas 435, C1405BWE, Buenos Aires, Argentina
| | - N Q McDonald
- Signalling and Structural Biology laboratory, The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK.
- Institute of Structural and Molecular Biology, Department of Biological Sciences, Birkbeck College, Malet Street, London, WC1E 7HX, UK.
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7
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Rzechorzek NJ, Kunzelmann S, Purkiss AG, Silva Dos Santos M, MacRae JI, Taylor IA, Fugger K, West SC. Mechanism of substrate hydrolysis by the human nucleotide pool sanitiser DNPH1. Nat Commun 2023; 14:6809. [PMID: 37884503 PMCID: PMC10603095 DOI: 10.1038/s41467-023-42544-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2023] [Accepted: 10/13/2023] [Indexed: 10/28/2023] Open
Abstract
Poly(ADP-ribose) polymerase (PARP) inhibitors are used in the clinic to treat BRCA-deficient breast, ovarian and prostate cancers. As their efficacy is potentiated by loss of the nucleotide salvage factor DNPH1 there is considerable interest in the development of highly specific small molecule DNPH1 inhibitors. Here, we present X-ray crystal structures of dimeric DNPH1 bound to its substrate hydroxymethyl deoxyuridine monophosphate (hmdUMP). Direct interaction with the hydroxymethyl group is important for substrate positioning, while conserved residues surrounding the base facilitate target discrimination. Glycosidic bond cleavage is driven by a conserved catalytic triad and proceeds via a two-step mechanism involving formation and subsequent disruption of a covalent glycosyl-enzyme intermediate. Mutation of a previously uncharacterised yet conserved glutamate traps the intermediate in the active site, demonstrating its role in the hydrolytic step. These observations define the enzyme's catalytic site and mechanism of hydrolysis, and provide important insights for inhibitor discovery.
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Affiliation(s)
- Neil J Rzechorzek
- DNA Recombination and Repair Laboratory, The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK
| | - Simone Kunzelmann
- Structural Biology Science Technology Platform, The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK
| | - Andrew G Purkiss
- Structural Biology Science Technology Platform, The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK
| | - Mariana Silva Dos Santos
- Metabolomics Science Technology Platform, The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK
| | - James I MacRae
- Metabolomics Science Technology Platform, The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK
| | - Ian A Taylor
- Macromolecular Structure Laboratory, The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK
| | - Kasper Fugger
- DNA Recombination and Repair Laboratory, The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK
- University College London Cancer Institute, 72 Huntley Street, London, WC1E 6DD, UK
| | - Stephen C West
- DNA Recombination and Repair Laboratory, The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK.
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8
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Sammon D, Krueger A, Busse-Wicher M, Morgan RM, Haslam SM, Schumann B, Briggs DC, Hohenester E. Molecular mechanism of decision-making in glycosaminoglycan biosynthesis. Nat Commun 2023; 14:6425. [PMID: 37828045 PMCID: PMC10570366 DOI: 10.1038/s41467-023-42236-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2023] [Accepted: 09/27/2023] [Indexed: 10/14/2023] Open
Abstract
Two major glycosaminoglycan types, heparan sulfate (HS) and chondroitin sulfate (CS), control many aspects of development and physiology in a type-specific manner. HS and CS are attached to core proteins via a common linker tetrasaccharide, but differ in their polymer backbones. How core proteins are specifically modified with HS or CS has been an enduring mystery. By reconstituting glycosaminoglycan biosynthesis in vitro, we establish that the CS-initiating N-acetylgalactosaminyltransferase CSGALNACT2 modifies all glycopeptide substrates equally, whereas the HS-initiating N-acetylglucosaminyltransferase EXTL3 is selective. Structure-function analysis reveals that acidic residues in the glycopeptide substrate and a basic exosite in EXTL3 are critical for specifying HS biosynthesis. Linker phosphorylation by the xylose kinase FAM20B accelerates linker synthesis and initiation of both HS and CS, but has no effect on the subsequent polymerisation of the backbone. Our results demonstrate that modification with CS occurs by default and must be overridden by EXTL3 to produce HS.
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Affiliation(s)
- Douglas Sammon
- Department of Life Sciences, Imperial College London, London, SW7 2AZ, UK
| | - Anja Krueger
- Department of Life Sciences, Imperial College London, London, SW7 2AZ, UK
| | - Marta Busse-Wicher
- Department of Life Sciences, Imperial College London, London, SW7 2AZ, UK
- Abzena, Babraham Research Campus, Cambridge, CB22 3AT, UK
| | - Rhodri Marc Morgan
- Department of Life Sciences, Imperial College London, London, SW7 2AZ, UK
- ZoBio, 2333 CH, Leiden, Netherlands
| | - Stuart M Haslam
- Department of Life Sciences, Imperial College London, London, SW7 2AZ, UK
| | - Benjamin Schumann
- Department of Chemistry, Imperial College London, London, W12 0BZ, UK
- Chemical Glycobiology Laboratory, The Francis Crick Institute, London, NW1 1AT, UK
| | - David C Briggs
- Department of Life Sciences, Imperial College London, London, SW7 2AZ, UK.
- Signalling and Structural Biology Laboratory, The Francis Crick Institute, London, NW1 1AT, UK.
| | - Erhard Hohenester
- Department of Life Sciences, Imperial College London, London, SW7 2AZ, UK.
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9
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Mihaylov SR, Castelli LM, Lin YH, Gül A, Soni N, Hastings C, Flynn HR, Păun O, Dickman MJ, Snijders AP, Goldstone R, Bandmann O, Shelkovnikova TA, Mortiboys H, Ultanir SK, Hautbergue GM. The master energy homeostasis regulator PGC-1α exhibits an mRNA nuclear export function. Nat Commun 2023; 14:5496. [PMID: 37679383 PMCID: PMC10485026 DOI: 10.1038/s41467-023-41304-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2022] [Accepted: 08/30/2023] [Indexed: 09/09/2023] Open
Abstract
PGC-1α plays a central role in maintaining mitochondrial and energy metabolism homeostasis, linking external stimuli to transcriptional co-activation of genes involved in adaptive and age-related pathways. The carboxyl-terminus encodes a serine/arginine-rich (RS) region and an RNA recognition motif, however the RNA-processing function(s) were poorly investigated over the past 20 years. Here, we show that the RS domain of human PGC-1α directly interacts with RNA and the nuclear RNA export receptor NXF1. Inducible depletion of PGC-1α and expression of RNAi-resistant RS-deleted PGC-1α further demonstrate that its RNA/NXF1-binding activity is required for the nuclear export of some canonical mitochondrial-related mRNAs and mitochondrial homeostasis. Genome-wide investigations reveal that the nuclear export function is not strictly linked to promoter-binding, identifying in turn novel regulatory targets of PGC-1α in non-homologous end-joining and nucleocytoplasmic transport. These findings provide new directions to further elucidate the roles of PGC-1α in gene expression, metabolic disorders, aging and neurodegeneration.
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Affiliation(s)
- Simeon R Mihaylov
- Sheffield Institute for Translational Neuroscience (SITraN), Department of Neuroscience, University of Sheffield, 385 Glossop Road, Sheffield, S10 2HQ, UK
- Kinases and Brain Development Laboratory, The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK
| | - Lydia M Castelli
- Sheffield Institute for Translational Neuroscience (SITraN), Department of Neuroscience, University of Sheffield, 385 Glossop Road, Sheffield, S10 2HQ, UK
| | - Ya-Hui Lin
- Sheffield Institute for Translational Neuroscience (SITraN), Department of Neuroscience, University of Sheffield, 385 Glossop Road, Sheffield, S10 2HQ, UK
| | - Aytac Gül
- Sheffield Institute for Translational Neuroscience (SITraN), Department of Neuroscience, University of Sheffield, 385 Glossop Road, Sheffield, S10 2HQ, UK
| | - Nikita Soni
- Sheffield Institute for Translational Neuroscience (SITraN), Department of Neuroscience, University of Sheffield, 385 Glossop Road, Sheffield, S10 2HQ, UK
| | - Christopher Hastings
- Sheffield Institute for Translational Neuroscience (SITraN), Department of Neuroscience, University of Sheffield, 385 Glossop Road, Sheffield, S10 2HQ, UK
| | - Helen R Flynn
- Proteomics Science Technology Platform, The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK
| | - Oana Păun
- Neural Stem Cell Biology Laboratory, The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK
| | - Mark J Dickman
- Department of Chemical and Biological Engineering, Sir Robert Hadfield Building, University of Sheffield, Mappin Street, Sheffield, S1 3JD, UK
- Neuroscience Institute, University of Sheffield, Western Bank, Sheffield, S10 2TN, UK
| | - Ambrosius P Snijders
- Proteomics Science Technology Platform, The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK
- Life Science Mass Spectrometry, Bruker Daltonics, Banner Lane, Coventry, CV4 9GH, UK
| | - Robert Goldstone
- Bioinformatics and Biostatistics Science and Technology Platform, The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK
| | - Oliver Bandmann
- Sheffield Institute for Translational Neuroscience (SITraN), Department of Neuroscience, University of Sheffield, 385 Glossop Road, Sheffield, S10 2HQ, UK
- Neuroscience Institute, University of Sheffield, Western Bank, Sheffield, S10 2TN, UK
- Healthy Lifespan Institute (HELSI), University of Sheffield, Western Bank, Sheffield, S10 2TN, UK
| | - Tatyana A Shelkovnikova
- Sheffield Institute for Translational Neuroscience (SITraN), Department of Neuroscience, University of Sheffield, 385 Glossop Road, Sheffield, S10 2HQ, UK
- Neuroscience Institute, University of Sheffield, Western Bank, Sheffield, S10 2TN, UK
| | - Heather Mortiboys
- Sheffield Institute for Translational Neuroscience (SITraN), Department of Neuroscience, University of Sheffield, 385 Glossop Road, Sheffield, S10 2HQ, UK
- Neuroscience Institute, University of Sheffield, Western Bank, Sheffield, S10 2TN, UK
- Healthy Lifespan Institute (HELSI), University of Sheffield, Western Bank, Sheffield, S10 2TN, UK
| | - Sila K Ultanir
- Kinases and Brain Development Laboratory, The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK
| | - Guillaume M Hautbergue
- Sheffield Institute for Translational Neuroscience (SITraN), Department of Neuroscience, University of Sheffield, 385 Glossop Road, Sheffield, S10 2HQ, UK.
- Neuroscience Institute, University of Sheffield, Western Bank, Sheffield, S10 2TN, UK.
- Healthy Lifespan Institute (HELSI), University of Sheffield, Western Bank, Sheffield, S10 2TN, UK.
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10
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Hart MN, Mohring F, DonVito SM, Thomas JA, Muller-Sienerth N, Wright GJ, Knuepfer E, Saibil HR, Moon RW. Sequential roles for red blood cell binding proteins enable phased commitment to invasion for malaria parasites. Nat Commun 2023; 14:4619. [PMID: 37528099 PMCID: PMC10393984 DOI: 10.1038/s41467-023-40357-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2022] [Accepted: 07/20/2023] [Indexed: 08/03/2023] Open
Abstract
Invasion of red blood cells (RBCs) by Plasmodium merozoites is critical to their continued survival within the host. Two major protein families, the Duffy binding-like proteins (DBPs/EBAs) and the reticulocyte binding like proteins (RBLs/RHs) have been studied extensively in P. falciparum and are hypothesized to have overlapping, but critical roles just prior to host cell entry. The zoonotic malaria parasite, P. knowlesi, has larger invasive merozoites and contains a smaller, less redundant, DBP and RBL repertoire than P. falciparum. One DBP (DBPα) and one RBL, normocyte binding protein Xa (NBPXa) are essential for invasion of human RBCs. Taking advantage of the unique biological features of P. knowlesi and iterative CRISPR-Cas9 genome editing, we determine the precise order of key invasion milestones and demonstrate distinct roles for each family. These distinct roles support a mechanism for phased commitment to invasion and can be targeted synergistically with invasion inhibitory antibodies.
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Affiliation(s)
- Melissa N Hart
- Department of Infection Biology, Faculty of Infectious and Tropical Disease, London School of Hygiene and Tropical Medicine, London, WC1E 7HT, UK
- Department of Pathobiology and Population Sciences, Royal Veterinary College, Hawkshead Lane, Hatfield, AL9 7TA, UK
| | - Franziska Mohring
- Department of Infection Biology, Faculty of Infectious and Tropical Disease, London School of Hygiene and Tropical Medicine, London, WC1E 7HT, UK
| | - Sophia M DonVito
- Department of Infection Biology, Faculty of Infectious and Tropical Disease, London School of Hygiene and Tropical Medicine, London, WC1E 7HT, UK
| | - James A Thomas
- Department of Infection Biology, Faculty of Infectious and Tropical Disease, London School of Hygiene and Tropical Medicine, London, WC1E 7HT, UK
| | | | - Gavin J Wright
- Wellcome Sanger Institute, Hinxton, Cambridge, CB10 1SA, UK
- Department of Biology, Hull York Medical School, York Biomedical Research Institute, University of York, Wentworth Way, York, YO10 5DD, UK
| | - Ellen Knuepfer
- Department of Pathobiology and Population Sciences, Royal Veterinary College, Hawkshead Lane, Hatfield, AL9 7TA, UK
- Malaria Parasitology Laboratory, Francis Crick Institute, London, NW1 1AT, UK
| | - Helen R Saibil
- ISMB, Biological Sciences, Birkbeck, University of London, Malet St, London, WC1E 7HX, UK
| | - Robert W Moon
- Department of Infection Biology, Faculty of Infectious and Tropical Disease, London School of Hygiene and Tropical Medicine, London, WC1E 7HT, UK.
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11
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Crotta S, Villa M, Major J, Finsterbusch K, Llorian M, Carmeliet P, Buescher J, Wack A. Repair of airway epithelia requires metabolic rewiring towards fatty acid oxidation. Nat Commun 2023; 14:721. [PMID: 36781848 PMCID: PMC9925445 DOI: 10.1038/s41467-023-36352-z] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2022] [Accepted: 01/27/2023] [Indexed: 02/15/2023] Open
Abstract
Epithelial tissues provide front-line barriers shielding the organism from invading pathogens and harmful substances. In the airway epithelium, the combined action of multiciliated and secretory cells sustains the mucociliary escalator required for clearance of microbes and particles from the airways. Defects in components of mucociliary clearance or barrier integrity are associated with recurring infections and chronic inflammation. The timely and balanced differentiation of basal cells into mature epithelial cell subsets is therefore tightly controlled. While different growth factors regulating progenitor cell proliferation have been described, little is known about the role of metabolism in these regenerative processes. Here we show that basal cell differentiation correlates with a shift in cellular metabolism from glycolysis to fatty acid oxidation (FAO). We demonstrate both in vitro and in vivo that pharmacological and genetic impairment of FAO blocks the development of fully differentiated airway epithelial cells, compromising the repair of airway epithelia. Mechanistically, FAO links to the hexosamine biosynthesis pathway to support protein glycosylation in airway epithelial cells. Our findings unveil the metabolic network underpinning the differentiation of airway epithelia and identify novel targets for intervention to promote lung repair.
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Affiliation(s)
- Stefania Crotta
- Immunoregulation Laboratory, Francis Crick Institute, London, UK.
| | - Matteo Villa
- Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany
| | - Jack Major
- Immunoregulation Laboratory, Francis Crick Institute, London, UK
| | | | | | - Peter Carmeliet
- Laboratory of Angiogenesis and Vascular Metabolism, Center for Cancer Biology, VIB, and Department of Oncology, KU Leuven, Leuven, Belgium
- Laboratory of Angiogenesis & Vascular Heterogeneity, Department of Biomedicine, Aarhus University, Aarhus, Denmark
- Center for Biotechnology (BTC), Khalifa University of Science and Technology, PO Box 127788, Abu Dhabi, United Arab Emirates
| | - Joerg Buescher
- Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany
| | - Andreas Wack
- Immunoregulation Laboratory, Francis Crick Institute, London, UK.
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12
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Virdi GS, Choi ML, Evans JR, Yao Z, Athauda D, Strohbuecker S, Nirujogi RS, Wernick AI, Pelegrina-Hidalgo N, Leighton C, Saleeb RS, Kopach O, Alrashidi H, Melandri D, Perez-Lloret J, Angelova PR, Sylantyev S, Eaton S, Heales S, Rusakov DA, Alessi DR, Kunath T, Horrocks MH, Abramov AY, Patani R, Gandhi S. Protein aggregation and calcium dysregulation are hallmarks of familial Parkinson's disease in midbrain dopaminergic neurons. NPJ Parkinsons Dis 2022; 8:162. [PMID: 36424392 PMCID: PMC9691718 DOI: 10.1038/s41531-022-00423-7] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2022] [Accepted: 10/27/2022] [Indexed: 11/27/2022] Open
Abstract
Mutations in the SNCA gene cause autosomal dominant Parkinson's disease (PD), with loss of dopaminergic neurons in the substantia nigra, and aggregation of α-synuclein. The sequence of molecular events that proceed from an SNCA mutation during development, to end-stage pathology is unknown. Utilising human-induced pluripotent stem cells (hiPSCs), we resolved the temporal sequence of SNCA-induced pathophysiological events in order to discover early, and likely causative, events. Our small molecule-based protocol generates highly enriched midbrain dopaminergic (mDA) neurons: molecular identity was confirmed using single-cell RNA sequencing and proteomics, and functional identity was established through dopamine synthesis, and measures of electrophysiological activity. At the earliest stage of differentiation, prior to maturation to mDA neurons, we demonstrate the formation of small β-sheet-rich oligomeric aggregates, in SNCA-mutant cultures. Aggregation persists and progresses, ultimately resulting in the accumulation of phosphorylated α-synuclein aggregates. Impaired intracellular calcium signalling, increased basal calcium, and impairments in mitochondrial calcium handling occurred early at day 34-41 post differentiation. Once midbrain identity fully developed, at day 48-62 post differentiation, SNCA-mutant neurons exhibited mitochondrial dysfunction, oxidative stress, lysosomal swelling and increased autophagy. Ultimately these multiple cellular stresses lead to abnormal excitability, altered neuronal activity, and cell death. Our differentiation paradigm generates an efficient model for studying disease mechanisms in PD and highlights that protein misfolding to generate intraneuronal oligomers is one of the earliest critical events driving disease in human neurons, rather than a late-stage hallmark of the disease.
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Affiliation(s)
- Gurvir S Virdi
- The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK
- Department of Clinical and Movement Neurosciences, UCL Queen Square Institute of Neurology, Queen Square, London, WC1N 3BG, UK
- Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD, 20815, USA
| | - Minee L Choi
- The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK
- Department of Clinical and Movement Neurosciences, UCL Queen Square Institute of Neurology, Queen Square, London, WC1N 3BG, UK
- Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD, 20815, USA
| | - James R Evans
- The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK
- Department of Clinical and Movement Neurosciences, UCL Queen Square Institute of Neurology, Queen Square, London, WC1N 3BG, UK
- Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD, 20815, USA
| | - Zhi Yao
- The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK
- Department of Clinical and Movement Neurosciences, UCL Queen Square Institute of Neurology, Queen Square, London, WC1N 3BG, UK
| | - Dilan Athauda
- The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK
- Department of Clinical and Movement Neurosciences, UCL Queen Square Institute of Neurology, Queen Square, London, WC1N 3BG, UK
| | | | - Raja S Nirujogi
- Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD, 20815, USA
- Medical Research Council (MRC) Protein Phosphorylation and Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dow Street, Dundee, DD1 5EH, UK
| | - Anna I Wernick
- The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK
- Department of Clinical and Movement Neurosciences, UCL Queen Square Institute of Neurology, Queen Square, London, WC1N 3BG, UK
- Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD, 20815, USA
| | - Noelia Pelegrina-Hidalgo
- EaStCHEM School of Chemistry, University of Edinburgh, Edinburgh, EH9 3FJ, UK
- Center for Regenerative Medicine, University of Edinburgh, Edinburgh, EH16 4UU, UK
| | - Craig Leighton
- EaStCHEM School of Chemistry, University of Edinburgh, Edinburgh, EH9 3FJ, UK
- Center for Regenerative Medicine, University of Edinburgh, Edinburgh, EH16 4UU, UK
| | - Rebecca S Saleeb
- EaStCHEM School of Chemistry, University of Edinburgh, Edinburgh, EH9 3FJ, UK
| | - Olga Kopach
- Department of Clinical and Experimental Epilepsy, UCL Queen Square Institute of Neurology, London, WC1N 3BG, UK
| | - Haya Alrashidi
- UCL Great Ormond Street Institute of Child Health, London, WC1N 1EH, UK
| | - Daniela Melandri
- Department of Neurodegenerative Diseases, UCL Queen Square Institute of Neurology, Queen Square, London, WC1N 3BG, UK
| | | | - Plamena R Angelova
- Department of Clinical and Movement Neurosciences, UCL Queen Square Institute of Neurology, Queen Square, London, WC1N 3BG, UK
| | - Sergiy Sylantyev
- Rowett Institute, University of Aberdeen, Ashgrove Rd West, Aberdeen, AB25 2ZD, UK
| | - Simon Eaton
- UCL Great Ormond Street Institute of Child Health, London, WC1N 1EH, UK
| | - Simon Heales
- UCL Great Ormond Street Institute of Child Health, London, WC1N 1EH, UK
| | - Dmitri A Rusakov
- Department of Clinical and Experimental Epilepsy, UCL Queen Square Institute of Neurology, London, WC1N 3BG, UK
| | - Dario R Alessi
- Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD, 20815, USA
- Medical Research Council (MRC) Protein Phosphorylation and Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dow Street, Dundee, DD1 5EH, UK
| | - Tilo Kunath
- Center for Regenerative Medicine, University of Edinburgh, Edinburgh, EH16 4UU, UK
| | - Mathew H Horrocks
- EaStCHEM School of Chemistry, University of Edinburgh, Edinburgh, EH9 3FJ, UK
| | - Andrey Y Abramov
- Department of Clinical and Movement Neurosciences, UCL Queen Square Institute of Neurology, Queen Square, London, WC1N 3BG, UK
| | - Rickie Patani
- The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK.
- Department of Neuromuscular Disease, UCL Queen Square Institute of Neurology, Queen Square, London, WC1N 3BG, UK.
| | - Sonia Gandhi
- The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK.
- Department of Clinical and Movement Neurosciences, UCL Queen Square Institute of Neurology, Queen Square, London, WC1N 3BG, UK.
- Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD, 20815, USA.
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13
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Wu Y, Biswas D, Usaite I, Angelova M, Boeing S, Karasaki T, Veeriah S, Czyzewska-Khan J, Morton C, Joseph M, Hessey S, Reading J, Georgiou A, Al-Bakir M, McGranahan N, Jamal-Hanjani M, Hackshaw A, Quezada SA, Hayday AC, Swanton C. A local human Vδ1 T cell population is associated with survival in nonsmall-cell lung cancer. Nat Cancer 2022; 3:696-709. [PMID: 35637401 PMCID: PMC9236901 DOI: 10.1038/s43018-022-00376-z] [Citation(s) in RCA: 33] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/26/2021] [Accepted: 04/11/2022] [Indexed: 01/26/2023]
Abstract
Murine tissues harbor signature γδ T cell compartments with profound yet differential impacts on carcinogenesis. Conversely, human tissue-resident γδ cells are less well defined. In the present study, we show that human lung tissues harbor a resident Vδ1 γδ T cell population. Moreover, we demonstrate that Vδ1 T cells with resident memory and effector memory phenotypes were enriched in lung tumors compared with nontumor lung tissues. Intratumoral Vδ1 T cells possessed stem-like features and were skewed toward cytolysis and helper T cell type 1 function, akin to intratumoral natural killer and CD8+ T cells considered beneficial to the patient. Indeed, ongoing remission post-surgery was significantly associated with the numbers of CD45RA-CD27- effector memory Vδ1 T cells in tumors and, most strikingly, with the numbers of CD103+ tissue-resident Vδ1 T cells in nonmalignant lung tissues. Our findings offer basic insights into human body surface immunology that collectively support integrating Vδ1 T cell biology into immunotherapeutic strategies for nonsmall cell lung cancer.
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Affiliation(s)
- Yin Wu
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK.
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK.
- Peter Gorer Department of Immunobiology, School of Immunology & Microbial Sciences, King's College London, London, UK.
- Immunosurveillance Laboratory, The Francis Crick Institute, London, UK.
| | - Dhruva Biswas
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK
- Bill Lyons Informatics Centre, University College London Cancer Institute, London, UK
| | - Ieva Usaite
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
| | - Mihaela Angelova
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK
| | - Stefan Boeing
- Bioinformatics & Biostatistics and Software Development & Machine Learning Team, The Francis Crick Institute, London, UK
| | - Takahiro Karasaki
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK
| | - Selvaraju Veeriah
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
| | - Justyna Czyzewska-Khan
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
| | - Cienne Morton
- Peter Gorer Department of Immunobiology, School of Immunology & Microbial Sciences, King's College London, London, UK
| | - Magdalene Joseph
- Peter Gorer Department of Immunobiology, School of Immunology & Microbial Sciences, King's College London, London, UK
- Immunosurveillance Laboratory, The Francis Crick Institute, London, UK
| | - Sonya Hessey
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
- Cancer Metastasis Lab, University College London Cancer Institute, London, UK
| | - James Reading
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
- Cancer Immunology Unit, Research Department of Haematology, University College London Cancer Institute, London, UK
| | - Andrew Georgiou
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
- Cancer Immunology Unit, Research Department of Haematology, University College London Cancer Institute, London, UK
| | - Maise Al-Bakir
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK
| | - Nicholas McGranahan
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
- Cancer Genome Evolution Research Group, University College London Cancer Institute, London, UK
| | - Mariam Jamal-Hanjani
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
- Cancer Metastasis Lab, University College London Cancer Institute, London, UK
| | - Allan Hackshaw
- Cancer Research UK & University College London Cancer Trials Centre, University College London, London, UK
| | - Sergio A Quezada
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
- Cancer Immunology Unit, Research Department of Haematology, University College London Cancer Institute, London, UK
| | - Adrian C Hayday
- Peter Gorer Department of Immunobiology, School of Immunology & Microbial Sciences, King's College London, London, UK.
- Immunosurveillance Laboratory, The Francis Crick Institute, London, UK.
| | - Charles Swanton
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK.
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK.
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14
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Bosch C, Ackels T, Pacureanu A, Zhang Y, Peddie CJ, Berning M, Rzepka N, Zdora MC, Whiteley I, Storm M, Bonnin A, Rau C, Margrie T, Collinson L, Schaefer AT. Functional and multiscale 3D structural investigation of brain tissue through correlative in vivo physiology, synchrotron microtomography and volume electron microscopy. Nat Commun 2022; 13:2923. [PMID: 35614048 PMCID: PMC9132960 DOI: 10.1038/s41467-022-30199-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2021] [Accepted: 04/19/2022] [Indexed: 12/16/2022] Open
Abstract
Understanding the function of biological tissues requires a coordinated study of physiology and structure, exploring volumes that contain complete functional units at a detail that resolves the relevant features. Here, we introduce an approach to address this challenge: Mouse brain tissue sections containing a region where function was recorded using in vivo 2-photon calcium imaging were stained, dehydrated, resin-embedded and imaged with synchrotron X-ray computed tomography with propagation-based phase contrast (SXRT). SXRT provided context at subcellular detail, and could be followed by targeted acquisition of multiple volumes using serial block-face electron microscopy (SBEM). In the olfactory bulb, combining SXRT and SBEM enabled disambiguation of in vivo-assigned regions of interest. In the hippocampus, we found that superficial pyramidal neurons in CA1a displayed a larger density of spine apparati than deeper ones. Altogether, this approach can enable a functional and structural investigation of subcellular features in the context of cells and tissues.
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Affiliation(s)
- Carles Bosch
- Sensory Circuits and Neurotechnology Lab., The Francis Crick Institute, London, UK.
| | - Tobias Ackels
- Sensory Circuits and Neurotechnology Lab., The Francis Crick Institute, London, UK
- Department of Neuroscience, Physiology and Pharmacology, University College, London, UK
| | - Alexandra Pacureanu
- Sensory Circuits and Neurotechnology Lab., The Francis Crick Institute, London, UK
- Department of Neuroscience, Physiology and Pharmacology, University College, London, UK
- ESRF, The European Synchrotron, Grenoble, France
| | - Yuxin Zhang
- Sensory Circuits and Neurotechnology Lab., The Francis Crick Institute, London, UK
- Department of Neuroscience, Physiology and Pharmacology, University College, London, UK
| | | | - Manuel Berning
- Department of Connectomics, Max Planck Institute for Brain Research, Frankfurt am Main, Germany
- Scalable minds GmbH, Potsdam, Germany
| | | | - Marie-Christine Zdora
- Department of Physics and Astronomy, University College London, London, UK
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot, UK
- School of Physics and Astronomy, University of Southampton, Highfield Campus, Southampton, UK
| | - Isabell Whiteley
- Sensory Circuits and Neurotechnology Lab., The Francis Crick Institute, London, UK
- Department of Neuroscience, Physiology and Pharmacology, University College, London, UK
| | - Malte Storm
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot, UK
- Institute of Materials Physics, Helmholtz-Zentrum Hereon, Geesthacht, Germany
| | - Anne Bonnin
- Paul Scherrer Institut, Villigen, Switzerland
| | - Christoph Rau
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot, UK
| | - Troy Margrie
- Sainsbury Wellcome Centre, University College London, London, UK
| | - Lucy Collinson
- Electron Microscopy STP, The Francis Crick Institute, London, UK
| | - Andreas T Schaefer
- Sensory Circuits and Neurotechnology Lab., The Francis Crick Institute, London, UK.
- Department of Neuroscience, Physiology and Pharmacology, University College, London, UK.
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15
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Guglielmi L, Heliot C, Kumar S, Alexandrov Y, Gori I, Papaleonidopoulou F, Barrington C, East P, Economou AD, French PMW, McGinty J, Hill CS. Smad4 controls signaling robustness and morphogenesis by differentially contributing to the Nodal and BMP pathways. Nat Commun 2021; 12:6374. [PMID: 34737283 PMCID: PMC8569018 DOI: 10.1038/s41467-021-26486-3] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2021] [Accepted: 10/07/2021] [Indexed: 12/25/2022] Open
Abstract
The transcriptional effector SMAD4 is a core component of the TGF-β family signaling pathways. However, its role in vertebrate embryo development remains unresolved. To address this, we deleted Smad4 in zebrafish and investigated the consequences of this on signaling by the TGF-β family morphogens, BMPs and Nodal. We demonstrate that in the absence of Smad4, dorsal/ventral embryo patterning is disrupted due to the loss of BMP signaling. However, unexpectedly, Nodal signaling is maintained, but lacks robustness. This Smad4-independent Nodal signaling is sufficient for mesoderm specification, but not for optimal endoderm specification. Furthermore, using Optical Projection Tomography in combination with 3D embryo morphometry, we have generated a BMP morphospace and demonstrate that Smad4 mutants are morphologically indistinguishable from embryos in which BMP signaling has been genetically/pharmacologically perturbed. Smad4 is thus differentially required for signaling by different TGF-β family ligands, which has implications for diseases where Smad4 is mutated or deleted.
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Affiliation(s)
- Luca Guglielmi
- Developmental Signalling Laboratory, The Francis Crick Institute, London, NW1 1AT, UK
| | - Claire Heliot
- Developmental Signalling Laboratory, The Francis Crick Institute, London, NW1 1AT, UK
| | - Sunil Kumar
- Advanced Light Microscopy, The Francis Crick Institute, London, NW1 1AT, UK
| | - Yuriy Alexandrov
- Advanced Light Microscopy, The Francis Crick Institute, London, NW1 1AT, UK
| | - Ilaria Gori
- Developmental Signalling Laboratory, The Francis Crick Institute, London, NW1 1AT, UK
| | | | - Christopher Barrington
- Bioinformatics and Biostatistics Facility, The Francis Crick Institute, London, NW1 1AT, UK
| | - Philip East
- Bioinformatics and Biostatistics Facility, The Francis Crick Institute, London, NW1 1AT, UK
| | - Andrew D Economou
- Developmental Signalling Laboratory, The Francis Crick Institute, London, NW1 1AT, UK
| | - Paul M W French
- Department of Physics, Imperial College London, SW7 2AZ, London, UK
| | - James McGinty
- Department of Physics, Imperial College London, SW7 2AZ, London, UK
| | - Caroline S Hill
- Developmental Signalling Laboratory, The Francis Crick Institute, London, NW1 1AT, UK.
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16
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Barski MS, Vanzo T, Zhao XZ, Smith SJ, Ballandras-Colas A, Cronin NB, Pye VE, Hughes SH, Burke TR, Cherepanov P, Maertens GN. Structural basis for the inhibition of HTLV-1 integration inferred from cryo-EM deltaretroviral intasome structures. Nat Commun 2021; 12:4996. [PMID: 34404793 PMCID: PMC8370991 DOI: 10.1038/s41467-021-25284-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2021] [Accepted: 07/20/2021] [Indexed: 02/07/2023] Open
Abstract
Between 10 and 20 million people worldwide are infected with the human T-cell lymphotropic virus type 1 (HTLV-1). Despite causing life-threatening pathologies there is no therapeutic regimen for this deltaretrovirus. Here, we screened a library of integrase strand transfer inhibitor (INSTI) candidates built around several chemical scaffolds to determine their effectiveness in limiting HTLV-1 infection. Naphthyridines with substituents in position 6 emerged as the most potent compounds against HTLV-1, with XZ450 having highest efficacy in vitro. Using single-particle cryo-electron microscopy we visualised XZ450 as well as the clinical HIV-1 INSTIs raltegravir and bictegravir bound to the active site of the deltaretroviral intasome. The structures reveal subtle differences in the coordination environment of the Mg2+ ion pair involved in the interaction with the INSTIs. Our results elucidate the binding of INSTIs to the HTLV-1 intasome and support their use for pre-exposure prophylaxis and possibly future treatment of HTLV-1 infection.
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Affiliation(s)
- Michal S Barski
- Imperial College London, St. Mary's Hospital, Department of Infectious Disease, Section of Virology, Norfolk Place, London, UK
- International Institute of Molecular Mechanisms and Machines, Polish Academy of Sciences, Warsaw, Poland
| | - Teresa Vanzo
- Imperial College London, St. Mary's Hospital, Department of Infectious Disease, Section of Virology, Norfolk Place, London, UK
- Department CIBIO, University of Trento, Povo-Trento, Italy
| | - Xue Zhi Zhao
- Chemical Biology Laboratory, Centre for Cancer Research, National Cancer Institute, Frederick, MD, USA
| | - Steven J Smith
- Retroviral Replication Laboratory, Centre for Cancer Research, National Cancer Institute, Frederick, MD, USA
| | | | - Nora B Cronin
- LonCEM Facility, The Francis Crick Institute, London, UK
| | - Valerie E Pye
- Chromatin Structure & Mobile DNA Laboratory, The Francis Crick Institute, London, UK
| | - Stephen H Hughes
- Retroviral Replication Laboratory, Centre for Cancer Research, National Cancer Institute, Frederick, MD, USA
| | - Terrence R Burke
- Chemical Biology Laboratory, Centre for Cancer Research, National Cancer Institute, Frederick, MD, USA
| | - Peter Cherepanov
- Imperial College London, St. Mary's Hospital, Department of Infectious Disease, Section of Virology, Norfolk Place, London, UK
- Chromatin Structure & Mobile DNA Laboratory, The Francis Crick Institute, London, UK
| | - Goedele N Maertens
- Imperial College London, St. Mary's Hospital, Department of Infectious Disease, Section of Virology, Norfolk Place, London, UK.
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17
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Au L, Fendler A, Shepherd STC, Rzeniewicz K, Cerrone M, Byrne F, Carlyle E, Edmonds K, Del Rosario L, Shon J, Haynes WA, Ward B, Shum B, Gordon W, Gerard CL, Xie W, Joharatnam-Hogan N, Young K, Pickering L, Furness AJS, Larkin J, Harvey R, Kassiotis G, Gandhi S, Swanton C, Fribbens C, Wilkinson KA, Wilkinson RJ, Lau DK, Banerjee S, Starling N, Chau I, Turajlic S. Cytokine release syndrome in a patient with colorectal cancer after vaccination with BNT162b2. Nat Med 2021; 27:1362-1366. [PMID: 34040262 PMCID: PMC8363501 DOI: 10.1038/s41591-021-01387-6] [Citation(s) in RCA: 57] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2021] [Accepted: 05/07/2021] [Indexed: 02/07/2023]
Abstract
Patients with cancer are currently prioritized in coronavirus disease 2019 (COVID-19) vaccination programs globally, which includes administration of mRNA vaccines. Cytokine release syndrome (CRS) has not been reported with mRNA vaccines and is an extremely rare immune-related adverse event of immune checkpoint inhibitors. We present a case of CRS that occurred 5 d after vaccination with BTN162b2 (tozinameran)-the Pfizer-BioNTech mRNA COVID-19 vaccine-in a patient with colorectal cancer on long-standing anti-PD-1 monotherapy. The CRS was evidenced by raised inflammatory markers, thrombocytopenia, elevated cytokine levels (IFN-γ/IL-2R/IL-18/IL-16/IL-10) and steroid responsiveness. The close temporal association of vaccination and diagnosis of CRS in this case suggests that CRS was a vaccine-related adverse event; with anti-PD1 blockade as a potential contributor. Overall, further prospective pharmacovigillence data are needed in patients with cancer, but the benefit-risk profile remains strongly in favor of COVID-19 vaccination in this population.
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Affiliation(s)
- Lewis Au
- Cancer Dynamics Laboratory, The Francis Crick Institute, London, UK
- Skin and Renal Units, The Royal Marsden NHS Foundation Trust, London, UK
| | - Annika Fendler
- Cancer Dynamics Laboratory, The Francis Crick Institute, London, UK
| | - Scott T C Shepherd
- Cancer Dynamics Laboratory, The Francis Crick Institute, London, UK
- Skin and Renal Units, The Royal Marsden NHS Foundation Trust, London, UK
| | | | - Maddalena Cerrone
- Tuberculosis Laboratory, The Francis Crick Institute, London, UK
- Department of Infectious Disease, Imperial College London, London, UK
| | - Fiona Byrne
- Cancer Dynamics Laboratory, The Francis Crick Institute, London, UK
| | - Eleanor Carlyle
- Skin and Renal Units, The Royal Marsden NHS Foundation Trust, London, UK
| | - Kim Edmonds
- Skin and Renal Units, The Royal Marsden NHS Foundation Trust, London, UK
| | - Lyra Del Rosario
- Skin and Renal Units, The Royal Marsden NHS Foundation Trust, London, UK
| | | | | | - Barry Ward
- Cancer Dynamics Laboratory, The Francis Crick Institute, London, UK
| | - Ben Shum
- Cancer Dynamics Laboratory, The Francis Crick Institute, London, UK
- Skin and Renal Units, The Royal Marsden NHS Foundation Trust, London, UK
| | - William Gordon
- Cancer Dynamics Laboratory, The Francis Crick Institute, London, UK
| | - Camille L Gerard
- Cancer Dynamics Laboratory, The Francis Crick Institute, London, UK
- Precision Oncology Center, Lausanne University Hospital (CHUV), Lausanne, Switzerland
| | - Wenyi Xie
- Cancer Dynamics Laboratory, The Francis Crick Institute, London, UK
| | | | - Kate Young
- Skin and Renal Units, The Royal Marsden NHS Foundation Trust, London, UK
| | - Lisa Pickering
- Skin and Renal Units, The Royal Marsden NHS Foundation Trust, London, UK
| | - Andrew J S Furness
- Skin and Renal Units, The Royal Marsden NHS Foundation Trust, London, UK
| | - James Larkin
- Skin and Renal Units, The Royal Marsden NHS Foundation Trust, London, UK
| | - Ruth Harvey
- Worldwide Influenza Centre, The Francis Crick Institute, London, UK
| | - George Kassiotis
- Retroviral Immunology Laboratory, The Francis Crick Institute, London, UK
| | - Sonia Gandhi
- Neurodegeneration Biology Laboratory, The Francis Crick Institute, London, UK
- UCL Queen Square Institute of Neurology, Queen Square, London, UK
| | - Charles Swanton
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK
| | - Charlotte Fribbens
- Acute Oncology Service, The Royal Marsden NHS Foundation Trust, London, UK
- Gastrointestinal and Lymphoma Unit, The Royal Marsden NHS Foundation Trust, Sutton, UK
| | | | - Robert J Wilkinson
- Tuberculosis Laboratory, The Francis Crick Institute, London, UK
- Department of Infectious Disease, Imperial College London, London, UK
| | - David K Lau
- Gastrointestinal and Lymphoma Unit, The Royal Marsden NHS Foundation Trust, Sutton, UK
| | - Susana Banerjee
- Gynaecology Unit, The Royal Marsden NHS Foundation Trust and Institute of Cancer Research, London, UK
| | - Naureen Starling
- Gastrointestinal and Lymphoma Unit, The Royal Marsden NHS Foundation Trust, Sutton, UK
| | - Ian Chau
- Gastrointestinal and Lymphoma Unit, The Royal Marsden NHS Foundation Trust, Sutton, UK
| | - Samra Turajlic
- Cancer Dynamics Laboratory, The Francis Crick Institute, London, UK.
- Skin and Renal Units, The Royal Marsden NHS Foundation Trust, London, UK.
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18
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Lattke M, Goldstone R, Ellis JK, Boeing S, Jurado-Arjona J, Marichal N, MacRae JI, Berninger B, Guillemot F. Extensive transcriptional and chromatin changes underlie astrocyte maturation in vivo and in culture. Nat Commun 2021; 12:4335. [PMID: 34267208 PMCID: PMC8282848 DOI: 10.1038/s41467-021-24624-5] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2020] [Accepted: 06/16/2021] [Indexed: 11/08/2022] Open
Abstract
Astrocytes have essential functions in brain homeostasis that are established late in differentiation, but the mechanisms underlying the functional maturation of astrocytes are not well understood. Here we identify extensive transcriptional changes that occur during murine astrocyte maturation in vivo that are accompanied by chromatin remodelling at enhancer elements. Investigating astrocyte maturation in a cell culture model revealed that in vitro-differentiated astrocytes lack expression of many mature astrocyte-specific genes, including genes for the transcription factors Rorb, Dbx2, Lhx2 and Fezf2. Forced expression of these factors in vitro induces distinct sets of mature astrocyte-specific transcripts. Culturing astrocytes in a three-dimensional matrix containing FGF2 induces expression of Rorb, Dbx2 and Lhx2 and improves astrocyte maturity based on transcriptional and chromatin profiles. Therefore, extrinsic signals orchestrate the expression of multiple intrinsic regulators, which in turn induce in a modular manner the transcriptional and chromatin changes underlying astrocyte maturation.
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Affiliation(s)
- Michael Lattke
- Neural Stem Cell Biology Laboratory, The Francis Crick Institute, London, UK
| | - Robert Goldstone
- Advanced Sequencing Facility, The Francis Crick Institute, London, UK
| | - James K Ellis
- Metabolomics Science Technology Platform, The Francis Crick Institute, London, UK
| | - Stefan Boeing
- Software Development & Machine Learning Team, The Francis Crick Institute, London, UK
- Bioinformatics & Biostatistics, The Francis Crick Institute, London, UK
| | - Jerónimo Jurado-Arjona
- Institute of Psychiatry, Psychology & Neuroscience, Centre for Developmental Neurobiology, King's College London, London, UK
| | - Nicolás Marichal
- Institute of Psychiatry, Psychology & Neuroscience, Centre for Developmental Neurobiology, King's College London, London, UK
| | - James I MacRae
- Metabolomics Science Technology Platform, The Francis Crick Institute, London, UK
| | - Benedikt Berninger
- Institute of Psychiatry, Psychology & Neuroscience, Centre for Developmental Neurobiology, King's College London, London, UK
- MRC Centre for Neurodevelopmental Disorders, King's College London, London, UK
- Institute of Physiological Chemistry, University Medical Center of the Johannes Gutenberg University Mainz, Mainz, Germany
- The Francis Crick Institute, London, UK
| | - Francois Guillemot
- Neural Stem Cell Biology Laboratory, The Francis Crick Institute, London, UK.
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19
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Danelli L, Cornish G, Merkenschlager J, Kassiotis G. Default polyfunctional T helper 1 response to ample signal 1 alone. Cell Mol Immunol 2021; 18:1809-1822. [PMID: 32313208 PMCID: PMC8245500 DOI: 10.1038/s41423-020-0415-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2019] [Accepted: 03/14/2020] [Indexed: 12/27/2022] Open
Abstract
CD4+ T cells integrate well-defined signals from the T-cell receptor (TCR) (signal 1) and a host of costimulatory molecules (signal 2) to initiate clonal expansion and differentiation into diverse functional T helper (Th) subsets. However, our ability to guide the expansion of context-appropriate Th subsets by deploying these signals in vaccination remains limited. Using cell-based vaccines, we selectively amplified signal 1 by exclusive presentation of an optimized peptide:MHC II (pMHC II) complex in the absence of classic costimulation. Contrary to expectations, amplified signal 1 alone was strongly immunogenic and selectively expanded high-affinity TCR clonotypes, despite delivering intense TCR signals. In contrast to natural infection or standard vaccines, amplified signal 1, presented by a variety of professional and nonprofessional antigen-presenting cells (APCs), induced exclusively polyfunctional Th1 effector and memory cells, which protected against retroviral infection and tumor challenge, and expanded tumor-reactive CD4+ T cells otherwise rendered unresponsive in tumor-bearing hosts. Together, our findings uncover a default Th1 response to ample signal 1 and offer a means to selectively prime such protective responses by vaccination.
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Affiliation(s)
- Luca Danelli
- Retroviral Immunology, The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK
| | - Georgina Cornish
- Retroviral Immunology, The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK
| | - Julia Merkenschlager
- Retroviral Immunology, The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY, 10065, USA
| | - George Kassiotis
- Retroviral Immunology, The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK.
- Department of Medicine, Faculty of Medicine, Imperial College London, London, W2 1PG, UK.
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20
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von Seth J, Dussex N, Díez-Del-Molino D, van der Valk T, Kutschera VE, Kierczak M, Steiner CC, Liu S, Gilbert MTP, Sinding MHS, Prost S, Guschanski K, Nathan SKSS, Brace S, Chan YL, Wheat CW, Skoglund P, Ryder OA, Goossens B, Götherström A, Dalén L. Genomic insights into the conservation status of the world's last remaining Sumatran rhinoceros populations. Nat Commun 2021; 12:2393. [PMID: 33896938 PMCID: PMC8071806 DOI: 10.1038/s41467-021-22386-8] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2020] [Accepted: 03/01/2021] [Indexed: 02/02/2023] Open
Abstract
Small populations are often exposed to high inbreeding and mutational load that can increase the risk of extinction. The Sumatran rhinoceros was widespread in Southeast Asia, but is now restricted to small and isolated populations on Sumatra and Borneo, and most likely extinct on the Malay Peninsula. Here, we analyse 5 historical and 16 modern genomes from these populations to investigate the genomic consequences of the recent decline, such as increased inbreeding and mutational load. We find that the Malay Peninsula population experienced increased inbreeding shortly before extirpation, which possibly was accompanied by purging. The populations on Sumatra and Borneo instead show low inbreeding, but high mutational load. The currently small population sizes may thus in the near future lead to inbreeding depression. Moreover, we find little evidence for differences in local adaptation among populations, suggesting that future inbreeding depression could potentially be mitigated by assisted gene flow among populations.
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Affiliation(s)
- Johanna von Seth
- Centre for Palaeogenetics, Stockholm, Sweden.
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History, Stockholm, Sweden.
- Department of Zoology, Stockholm University, Stockholm, Sweden.
| | - Nicolas Dussex
- Centre for Palaeogenetics, Stockholm, Sweden.
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History, Stockholm, Sweden.
- Department of Zoology, Stockholm University, Stockholm, Sweden.
| | - David Díez-Del-Molino
- Centre for Palaeogenetics, Stockholm, Sweden
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History, Stockholm, Sweden
- Department of Zoology, Stockholm University, Stockholm, Sweden
| | - Tom van der Valk
- Centre for Palaeogenetics, Stockholm, Sweden
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History, Stockholm, Sweden
- Department of Ecology and Genetics, Animal Ecology, Uppsala University, Uppsala, Sweden
| | - Verena E Kutschera
- Department of Biochemistry and Biophysics, National Bioinformatics Infrastructure Sweden, Science for Life Laboratory, Stockholm University, Solna, Sweden
| | - Marcin Kierczak
- Department of Cell and Molecular Biology, National Bioinformatics Infrastructure Sweden, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Cynthia C Steiner
- San Diego Zoo Wildlife Alliance, Beckman Center for Conservation Research, Escondido, CA, USA
| | - Shanlin Liu
- The GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
| | - M Thomas P Gilbert
- The GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
- Norwegian University of Science and Technology, University Museum, Trondheim, Norway
| | - Mikkel-Holger S Sinding
- The GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin, Ireland
| | - Stefan Prost
- LOEWE-Centre for Translational Biodiversity Genomics, Senckenberg, Frankfurt, Germany
- South African National Biodiversity Institute, National Zoological Garden, Pretoria, South Africa
| | - Katerina Guschanski
- Department of Ecology and Genetics, Animal Ecology, Uppsala University, Uppsala, Sweden
- Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, UK
| | | | - Selina Brace
- Department of Earth Sciences, Natural History Museum, London, UK
| | - Yvonne L Chan
- Centre for Palaeogenetics, Stockholm, Sweden
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History, Stockholm, Sweden
| | | | | | - Oliver A Ryder
- San Diego Zoo Wildlife Alliance, Beckman Center for Conservation Research, Escondido, CA, USA
| | - Benoit Goossens
- Sabah Wildlife Department, Kota Kinabalu, Sabah, Malaysia
- Organisms and Environment Division, Cardiff School of Biosciences, Cardiff, UK
- Sustainable Places Research Institute, Cardiff University, Cardiff, UK
- Danau Girang Field Centre, c/o Sabah Wildlife Department, Kota Kinabalu, Sabah, Malaysia
| | - Anders Götherström
- Centre for Palaeogenetics, Stockholm, Sweden
- Department of Archaeology and Classical Studies, Stockholm University, Stockholm, Sweden
| | - Love Dalén
- Centre for Palaeogenetics, Stockholm, Sweden.
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History, Stockholm, Sweden.
- Department of Zoology, Stockholm University, Stockholm, Sweden.
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21
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Campinoti S, Gjinovci A, Ragazzini R, Zanieri L, Ariza-McNaughton L, Catucci M, Boeing S, Park JE, Hutchinson JC, Muñoz-Ruiz M, Manti PG, Vozza G, Villa CE, Phylactopoulos DE, Maurer C, Testa G, Stauss HJ, Teichmann SA, Sebire NJ, Hayday AC, Bonnet D, Bonfanti P. Reconstitution of a functional human thymus by postnatal stromal progenitor cells and natural whole-organ scaffolds. Nat Commun 2020; 11:6372. [PMID: 33311516 PMCID: PMC7732825 DOI: 10.1038/s41467-020-20082-7] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2020] [Accepted: 11/04/2020] [Indexed: 12/22/2022] Open
Abstract
The thymus is a primary lymphoid organ, essential for T cell maturation and selection. There has been long-standing interest in processes underpinning thymus generation and the potential to manipulate it clinically, because alterations of thymus development or function can result in severe immunodeficiency and autoimmunity. Here, we identify epithelial-mesenchymal hybrid cells, capable of long-term expansion in vitro, and able to reconstitute an anatomic phenocopy of the native thymus, when combined with thymic interstitial cells and a natural decellularised extracellular matrix (ECM) obtained by whole thymus perfusion. This anatomical human thymus reconstruction is functional, as judged by its capacity to support mature T cell development in vivo after transplantation into humanised immunodeficient mice. These findings establish a basis for dissecting the cellular and molecular crosstalk between stroma, ECM and thymocytes, and offer practical prospects for treating congenital and acquired immunological diseases.
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Affiliation(s)
- Sara Campinoti
- Epithelial Stem Cell Biology & Regenerative Medicine laboratory, The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK
- UCL Great Ormond Street Institute of Child Health, 30 Guilford Street, London, WC1N 1EH, UK
| | - Asllan Gjinovci
- Epithelial Stem Cell Biology & Regenerative Medicine laboratory, The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK
- Institute of Immunity & Transplantation, Division of Infection & Immunity, UCL, Royal Free Hospital, London, NW3 2PF, UK
| | - Roberta Ragazzini
- Epithelial Stem Cell Biology & Regenerative Medicine laboratory, The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK
- Institute of Immunity & Transplantation, Division of Infection & Immunity, UCL, Royal Free Hospital, London, NW3 2PF, UK
| | - Luca Zanieri
- Epithelial Stem Cell Biology & Regenerative Medicine laboratory, The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK
- Institute of Immunity & Transplantation, Division of Infection & Immunity, UCL, Royal Free Hospital, London, NW3 2PF, UK
| | - Linda Ariza-McNaughton
- Haematopoietic Stem Cell laboratory, The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK
| | - Marco Catucci
- Epithelial Stem Cell Biology & Regenerative Medicine laboratory, The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK
- UCL Great Ormond Street Institute of Child Health, 30 Guilford Street, London, WC1N 1EH, UK
- Division of Immunology, Transplantation and Infectious Diseases, San Raffaele Scientific Institute, DIBIT 20132, Milan, Italy
| | - Stefan Boeing
- Bioinformatics Laboratory, The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK
| | - Jong-Eun Park
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
- Graduate School of Medical Science and Engineering, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, 34141, Republic of Korea
| | - John C Hutchinson
- UCL Great Ormond Street Institute of Child Health, 30 Guilford Street, London, WC1N 1EH, UK
- Department of Histopathology, Great Ormond Street Hospital for Children NHS Foundation Trust, London, WC1N 1EH, UK
| | - Miguel Muñoz-Ruiz
- Immunosurveillance laboratory, The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK
| | - Pierluigi G Manti
- Department of Experimental Oncology, IEO, European Institute of Oncology, IRCCS, Milan, Italy
- Department of Oncology and Hemato-Oncology, University of Milan, Milan, Italy
| | - Gianluca Vozza
- Department of Experimental Oncology, IEO, European Institute of Oncology, IRCCS, Milan, Italy
- Department of Oncology and Hemato-Oncology, University of Milan, Milan, Italy
| | - Carlo E Villa
- Department of Experimental Oncology, IEO, European Institute of Oncology, IRCCS, Milan, Italy
| | - Demetra-Ellie Phylactopoulos
- Epithelial Stem Cell Biology & Regenerative Medicine laboratory, The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK
- UCL Great Ormond Street Institute of Child Health, 30 Guilford Street, London, WC1N 1EH, UK
| | - Constance Maurer
- Epithelial Stem Cell Biology & Regenerative Medicine laboratory, The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK
- UCL Great Ormond Street Institute of Child Health, 30 Guilford Street, London, WC1N 1EH, UK
| | - Giuseppe Testa
- Department of Experimental Oncology, IEO, European Institute of Oncology, IRCCS, Milan, Italy
- Department of Oncology and Hemato-Oncology, University of Milan, Milan, Italy
| | - Hans J Stauss
- Institute of Immunity & Transplantation, Division of Infection & Immunity, UCL, Royal Free Hospital, London, NW3 2PF, UK
| | - Sarah A Teichmann
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
| | - Neil J Sebire
- UCL Great Ormond Street Institute of Child Health, 30 Guilford Street, London, WC1N 1EH, UK
- Department of Histopathology, Great Ormond Street Hospital for Children NHS Foundation Trust, London, WC1N 1EH, UK
| | - Adrian C Hayday
- Immunosurveillance laboratory, The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK
- Peter Gorer Department of Immunobiology, School of Immunology & Microbial Sciences, King's College London, London, UK
| | - Dominique Bonnet
- Haematopoietic Stem Cell laboratory, The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK
| | - Paola Bonfanti
- Epithelial Stem Cell Biology & Regenerative Medicine laboratory, The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK.
- UCL Great Ormond Street Institute of Child Health, 30 Guilford Street, London, WC1N 1EH, UK.
- Institute of Immunity & Transplantation, Division of Infection & Immunity, UCL, Royal Free Hospital, London, NW3 2PF, UK.
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22
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Henderson LD, Matthews-Palmer TRS, Gulbronson CJ, Ribardo DA, Beeby M, Hendrixson DR. Diversification of Campylobacter jejuni Flagellar C-Ring Composition Impacts Its Structure and Function in Motility, Flagellar Assembly, and Cellular Processes. mBio 2020; 11:e02286-19. [PMID: 31911488 PMCID: PMC6946799 DOI: 10.1128/mbio.02286-19] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2019] [Accepted: 11/19/2019] [Indexed: 12/22/2022] Open
Abstract
Bacterial flagella are reversible rotary motors that rotate external filaments for bacterial propulsion. Some flagellar motors have diversified by recruiting additional components that influence torque and rotation, but little is known about the possible diversification and evolution of core motor components. The mechanistic core of flagella is the cytoplasmic C ring, which functions as a rotor, directional switch, and assembly platform for the flagellar type III secretion system (fT3SS) ATPase. The C ring is composed of a ring of FliG proteins and a helical ring of surface presentation of antigen (SPOA) domains from the switch proteins FliM and one of two usually mutually exclusive paralogs, FliN or FliY. We investigated the composition, architecture, and function of the C ring of Campylobacter jejuni, which encodes FliG, FliM, and both FliY and FliN by a variety of interrogative approaches. We discovered a diversified C. jejuni C ring containing FliG, FliM, and both FliY, which functions as a classical FliN-like protein for flagellar assembly, and FliN, which has neofunctionalized into a structural role. Specific protein interactions drive the formation of a more complex heterooligomeric C. jejuni C-ring structure. We discovered that this complex C ring has additional cellular functions in polarly localizing FlhG for numerical regulation of flagellar biogenesis and spatial regulation of division. Furthermore, mutation of the C. jejuni C ring revealed a T3SS that was less dependent on its ATPase complex for assembly than were other systems. Our results highlight considerable evolved flagellar diversity that impacts motor output, biogenesis, and cellular processes in different species.IMPORTANCE The conserved core of bacterial flagellar motors reflects a shared evolutionary history that preserves the mechanisms essential for flagellar assembly, rotation, and directional switching. In this work, we describe an expanded and diversified set of core components in the Campylobacter jejuni flagellar C ring, the mechanistic core of the motor. Our work provides insight into how usually conserved core components may have diversified by gene duplication, enabling a division of labor of the ancestral protein between the two new proteins, acquisition of new roles in flagellar assembly and motility, and expansion of the function of the flagellum beyond motility, including spatial regulation of cell division and numerical control of flagellar biogenesis in C. jejuni Our results highlight that relatively small changes, such as gene duplications, can have substantial ramifications on the cellular roles of a molecular machine.
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Affiliation(s)
- Louie D Henderson
- Department of Life Sciences, Imperial College London, London, United Kingdom
| | | | - Connor J Gulbronson
- Department of Microbiology, University of Texas Southwestern Medical Center, Dallas, Texas, USA
| | - Deborah A Ribardo
- Department of Microbiology, University of Texas Southwestern Medical Center, Dallas, Texas, USA
| | - Morgan Beeby
- Department of Life Sciences, Imperial College London, London, United Kingdom
| | - David R Hendrixson
- Department of Microbiology, University of Texas Southwestern Medical Center, Dallas, Texas, USA
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23
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Tibúrcio M, Yang ASP, Yahata K, Suárez-Cortés P, Belda H, Baumgarten S, van de Vegte-Bolmer M, van Gemert GJ, van Waardenburg Y, Levashina EA, Sauerwein RW, Treeck M. A Novel Tool for the Generation of Conditional Knockouts To Study Gene Function across the Plasmodium falciparum Life Cycle. mBio 2019; 10:e01170-19. [PMID: 31530668 PMCID: PMC6751054 DOI: 10.1128/mbio.01170-19] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2019] [Accepted: 08/21/2019] [Indexed: 01/07/2023] Open
Abstract
Plasmodium falciparum has a complex life cycle that involves interaction with multiple tissues inside the human and mosquito hosts. Identification of essential genes at all different stages of the P. falciparum life cycle is urgently required for clinical development of tools for malaria control and eradication. However, the study of P. falciparum is limited by the inability to genetically modify the parasite throughout its life cycle with the currently available genetic tools. Here, we describe the detailed characterization of a new marker-free P. falciparum parasite line that expresses rapamycin-inducible Cre recombinase across the full life cycle. Using this parasite line, we were able to conditionally delete the essential invasion ligand AMA1 in three different developmental stages for the first time. We further confirm efficient gene deletion by targeting the nonessential kinase FIKK7.1.IMPORTANCE One of the major limitations in studying P. falciparum is that so far only asexual stages are amenable to rapid conditional genetic modification. The most promising drug targets and vaccine candidates, however, have been refractory to genetic modification because they are essential during the blood stage or for transmission in the mosquito vector. This leaves a major gap in our understanding of parasite proteins in most life cycle stages and hinders genetic validation of drug and vaccine targets. Here, we describe a method that supports conditional gene deletion across the P. falciparum life cycle for the first time. We demonstrate its potential by deleting essential and nonessential genes at different parasite stages, which opens up completely new avenues for the study of malaria and drug development. It may also allow the realization of novel vaccination strategies using attenuated parasites.
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Affiliation(s)
- Marta Tibúrcio
- Signalling in Apicomplexan Parasites Laboratory, The Francis Crick Institute, London, United Kingdom
| | - Annie S P Yang
- Department of Medical Microbiology, Radboud University Medical Centre, Nijmegen, Netherlands
| | - Kazuhide Yahata
- Signalling in Apicomplexan Parasites Laboratory, The Francis Crick Institute, London, United Kingdom
- Department of Protozoology, Institute of Tropical Medicine (NEKKEN), Nagasaki University, Nagasaki, Japan
| | - Pablo Suárez-Cortés
- Vector Biology Unit, Max Planck Institute for Infection Biology, Berlin, Germany
| | - Hugo Belda
- Signalling in Apicomplexan Parasites Laboratory, The Francis Crick Institute, London, United Kingdom
| | | | | | - Geert-Jan van Gemert
- Department of Medical Microbiology, Radboud University Medical Centre, Nijmegen, Netherlands
| | - Youri van Waardenburg
- Department of Medical Microbiology, Radboud University Medical Centre, Nijmegen, Netherlands
| | - Elena A Levashina
- Vector Biology Unit, Max Planck Institute for Infection Biology, Berlin, Germany
| | - Robert W Sauerwein
- Department of Medical Microbiology, Radboud University Medical Centre, Nijmegen, Netherlands
| | - Moritz Treeck
- Signalling in Apicomplexan Parasites Laboratory, The Francis Crick Institute, London, United Kingdom
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24
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Young J, Dominicus C, Wagener J, Butterworth S, Ye X, Kelly G, Ordan M, Saunders B, Instrell R, Howell M, Stewart A, Treeck M. A CRISPR platform for targeted in vivo screens identifies Toxoplasma gondii virulence factors in mice. Nat Commun 2019; 10:3963. [PMID: 31481656 PMCID: PMC6722137 DOI: 10.1038/s41467-019-11855-w] [Citation(s) in RCA: 46] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2019] [Accepted: 08/07/2019] [Indexed: 02/08/2023] Open
Abstract
Genome-wide CRISPR screening is a powerful tool to identify genes required under selective conditions. However, the inherent scale of genome-wide libraries can limit their application in experimental settings where cell numbers are restricted, such as in vivo infections or single cell analysis. The use of small scale CRISPR libraries targeting gene subsets circumvents this problem. Here we develop a method for rapid generation of custom guide RNA (gRNA) libraries using arrayed single-stranded oligonucleotides for reproducible pooled cloning of CRISPR/Cas9 libraries. We use this system to generate mutant pools of different sizes in the protozoan parasite Toxoplasma gondi and describe optimised analysis methods for small scale libraries. An in vivo genetic screen in the murine host identifies novel and known virulence factors and we confirm results using cloned knock-out parasites. Our study also reveals a potential trans-rescue of individual knock-out parasites in pools of mutants compared to homogenous knock-out lines of the key virulence factor MYR1.
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Affiliation(s)
- Joanna Young
- Signalling in Apicomplexan Parasites Laboratory, The Francis Crick Institute, 1 Midland Road, NW1 1AT, London, UK
| | - Caia Dominicus
- Signalling in Apicomplexan Parasites Laboratory, The Francis Crick Institute, 1 Midland Road, NW1 1AT, London, UK
| | - Jeanette Wagener
- Signalling in Apicomplexan Parasites Laboratory, The Francis Crick Institute, 1 Midland Road, NW1 1AT, London, UK
| | - Simon Butterworth
- Signalling in Apicomplexan Parasites Laboratory, The Francis Crick Institute, 1 Midland Road, NW1 1AT, London, UK
| | - Xingda Ye
- Signalling in Apicomplexan Parasites Laboratory, The Francis Crick Institute, 1 Midland Road, NW1 1AT, London, UK
| | - Gavin Kelly
- Bioinformatics and Biostatistics Science Technology Platform, The Francis Crick Institute, 1 Midland Road, NW1 1AT, London, UK
| | - Merav Ordan
- Signalling in Apicomplexan Parasites Laboratory, The Francis Crick Institute, 1 Midland Road, NW1 1AT, London, UK
| | - Becky Saunders
- High Throughput Screening Science Technology Platform, The Francis Crick Institute, 1 Midland Road, NW1 1AT, London, UK
| | - Rachael Instrell
- High Throughput Screening Science Technology Platform, The Francis Crick Institute, 1 Midland Road, NW1 1AT, London, UK
| | - Michael Howell
- High Throughput Screening Science Technology Platform, The Francis Crick Institute, 1 Midland Road, NW1 1AT, London, UK
| | - Aengus Stewart
- Bioinformatics and Biostatistics Science Technology Platform, The Francis Crick Institute, 1 Midland Road, NW1 1AT, London, UK
| | - Moritz Treeck
- Signalling in Apicomplexan Parasites Laboratory, The Francis Crick Institute, 1 Midland Road, NW1 1AT, London, UK.
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