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Damhofer H, Tatar T, Southgate B, Scarneo S, Agger K, Shlyueva D, Uhrbom L, Morrison GM, Hughes PF, Haystead T, Pollard SM, Helin K. TAK1 inhibition leads to RIPK1-dependent apoptosis in immune-activated cancers. Cell Death Dis 2024; 15:273. [PMID: 38632238 PMCID: PMC11024179 DOI: 10.1038/s41419-024-06654-1] [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: 11/18/2023] [Revised: 04/02/2024] [Accepted: 04/05/2024] [Indexed: 04/19/2024]
Abstract
Poor survival and lack of treatment response in glioblastoma (GBM) is attributed to the persistence of glioma stem cells (GSCs). To identify novel therapeutic approaches, we performed CRISPR/Cas9 knockout screens and discovered TGFβ activated kinase (TAK1) as a selective survival factor in a significant fraction of GSCs. Loss of TAK1 kinase activity results in RIPK1-dependent apoptosis via Caspase-8/FADD complex activation, dependent on autocrine TNFα ligand production and constitutive TNFR signaling. We identify a transcriptional signature associated with immune activation and the mesenchymal GBM subtype to be a characteristic of cancer cells sensitive to TAK1 perturbation and employ this signature to accurately predict sensitivity to the TAK1 kinase inhibitor HS-276. In addition, exposure to pro-inflammatory cytokines IFNγ and TNFα can sensitize resistant GSCs to TAK1 inhibition. Our findings reveal dependency on TAK1 kinase activity as a novel vulnerability in immune-activated cancers, including mesenchymal GBMs that can be exploited therapeutically.
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Affiliation(s)
- Helene Damhofer
- Division of Cancer Biology, The Institute of Cancer Research, London, UK
- Cell Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Biotech Research and Innovation Centre, University of Copenhagen, Copenhagen, Denmark
| | - Tülin Tatar
- Division of Cancer Biology, The Institute of Cancer Research, London, UK
- Biotech Research and Innovation Centre, University of Copenhagen, Copenhagen, Denmark
| | - Benjamin Southgate
- Centre for Regenerative Medicine, University of Edinburgh, Edinburgh, UK
| | - Scott Scarneo
- Department of Pharmacology and Cancer Biology, Duke University School of Medicine, Durham, NC, USA
- EydisBio Inc., Durham, NC, USA
| | - Karl Agger
- Biotech Research and Innovation Centre, University of Copenhagen, Copenhagen, Denmark
| | - Daria Shlyueva
- Cell Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Biotech Research and Innovation Centre, University of Copenhagen, Copenhagen, Denmark
| | - Lene Uhrbom
- Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden
| | - Gillian M Morrison
- Centre for Regenerative Medicine, University of Edinburgh, Edinburgh, UK
| | - Philip F Hughes
- Department of Pharmacology and Cancer Biology, Duke University School of Medicine, Durham, NC, USA
- EydisBio Inc., Durham, NC, USA
| | - Timothy Haystead
- Department of Pharmacology and Cancer Biology, Duke University School of Medicine, Durham, NC, USA
- EydisBio Inc., Durham, NC, USA
| | - Steven M Pollard
- Centre for Regenerative Medicine, University of Edinburgh, Edinburgh, UK
| | - Kristian Helin
- Division of Cancer Biology, The Institute of Cancer Research, London, UK.
- Cell Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
- Biotech Research and Innovation Centre, University of Copenhagen, Copenhagen, Denmark.
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2
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Marqués-Torrejón MÁ, Williams CAC, Southgate B, Alfazema N, Clements MP, Garcia-Diaz C, Blin C, Arranz-Emparan N, Fraser J, Gammoh N, Parrinello S, Pollard SM. LRIG1 is a gatekeeper to exit from quiescence in adult neural stem cells. Nat Commun 2021; 12:2594. [PMID: 33972529 PMCID: PMC8110534 DOI: 10.1038/s41467-021-22813-w] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [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: 12/20/2019] [Accepted: 03/26/2021] [Indexed: 01/17/2023] Open
Abstract
Adult neural stem cells (NSCs) must tightly regulate quiescence and proliferation. Single-cell analysis has suggested a continuum of cell states as NSCs exit quiescence. Here we capture and characterize in vitro primed quiescent NSCs and identify LRIG1 as an important regulator. We show that BMP-4 signaling induces a dormant non-cycling quiescent state (d-qNSCs), whereas combined BMP-4/FGF-2 signaling induces a distinct primed quiescent state poised for cell cycle re-entry. Primed quiescent NSCs (p-qNSCs) are defined by high levels of LRIG1 and CD9, as well as an interferon response signature, and can efficiently engraft into the adult subventricular zone (SVZ) niche. Genetic disruption of Lrig1 in vivo within the SVZ NSCs leads an enhanced proliferation. Mechanistically, LRIG1 primes quiescent NSCs for cell cycle re-entry and EGFR responsiveness by enabling EGFR protein levels to increase but limiting signaling activation. LRIG1 is therefore an important functional regulator of NSC exit from quiescence.
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Affiliation(s)
| | - Charles A C Williams
- MRC Centre for Regenerative Medicine & Cancer Research UK Edinburgh Centre, University of Edinburgh, Edinburgh, UK
| | - Benjamin Southgate
- MRC Centre for Regenerative Medicine & Cancer Research UK Edinburgh Centre, University of Edinburgh, Edinburgh, UK
| | - Neza Alfazema
- MRC Centre for Regenerative Medicine & Cancer Research UK Edinburgh Centre, University of Edinburgh, Edinburgh, UK
| | - Melanie P Clements
- Samantha Dickson Brain Cancer Unit, UCL Cancer Institute, University College London, London, UK
| | - Claudia Garcia-Diaz
- Samantha Dickson Brain Cancer Unit, UCL Cancer Institute, University College London, London, UK
| | - Carla Blin
- MRC Centre for Regenerative Medicine & Cancer Research UK Edinburgh Centre, University of Edinburgh, Edinburgh, UK
| | - Nerea Arranz-Emparan
- MRC Centre for Regenerative Medicine & Cancer Research UK Edinburgh Centre, University of Edinburgh, Edinburgh, UK
| | - Jane Fraser
- Cancer Research UK Edinburgh Centre, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, UK
| | - Noor Gammoh
- Cancer Research UK Edinburgh Centre, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, UK
| | - Simona Parrinello
- Samantha Dickson Brain Cancer Unit, UCL Cancer Institute, University College London, London, UK
| | - Steven M Pollard
- MRC Centre for Regenerative Medicine & Cancer Research UK Edinburgh Centre, University of Edinburgh, Edinburgh, UK.
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3
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Bressan RB, Southgate B, Ferguson KM, Blin C, Grant V, Alfazema N, Wills JC, Marques-Torrejon MA, Morrison GM, Ashmore J, Robertson F, Williams CAC, Bradley L, von Kriegsheim A, Anderson RA, Tomlinson SR, Pollard SM. Regional identity of human neural stem cells determines oncogenic responses to histone H3.3 mutants. Cell Stem Cell 2021; 28:877-893.e9. [PMID: 33631116 PMCID: PMC8110245 DOI: 10.1016/j.stem.2021.01.016] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [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: 06/22/2020] [Revised: 10/22/2020] [Accepted: 01/20/2021] [Indexed: 01/06/2023]
Abstract
Point mutations within the histone H3.3 are frequent in aggressive childhood brain tumors known as pediatric high-grade gliomas (pHGGs). Intriguingly, distinct mutations arise in discrete anatomical regions: H3.3-G34R within the forebrain and H3.3-K27M preferentially within the hindbrain. The reasons for this contrasting etiology are unknown. By engineering human fetal neural stem cell cultures from distinct brain regions, we demonstrate here that cell-intrinsic regional identity provides differential responsiveness to each mutant that mirrors the origins of pHGGs. Focusing on H3.3-G34R, we find that the oncohistone supports proliferation of forebrain cells while inducing a cytostatic response in the hindbrain. Mechanistically, H3.3-G34R does not impose widespread transcriptional or epigenetic changes but instead impairs recruitment of ZMYND11, a transcriptional repressor of highly expressed genes. We therefore propose that H3.3-G34R promotes tumorigenesis by focally stabilizing the expression of key progenitor genes, thereby locking initiating forebrain cells into their pre-existing immature state.
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Affiliation(s)
- Raul Bardini Bressan
- Centre for Regenerative Medicine and Institute for Regeneration and Repair, University of Edinburgh, Edinburgh EH16 4UU, UK; Biotech Research and Innovation Centre, University of Copenhagen, Copenhagen 2200, Denmark
| | - Benjamin Southgate
- Centre for Regenerative Medicine and Institute for Regeneration and Repair, University of Edinburgh, Edinburgh EH16 4UU, UK; Cancer Research UK Edinburgh Centre, University of Edinburgh, Edinburgh EH4 2XR, UK
| | - Kirsty M Ferguson
- Centre for Regenerative Medicine and Institute for Regeneration and Repair, University of Edinburgh, Edinburgh EH16 4UU, UK; Cancer Research UK Edinburgh Centre, University of Edinburgh, Edinburgh EH4 2XR, UK
| | - Carla Blin
- Centre for Regenerative Medicine and Institute for Regeneration and Repair, University of Edinburgh, Edinburgh EH16 4UU, UK
| | - Vivien Grant
- Centre for Regenerative Medicine and Institute for Regeneration and Repair, University of Edinburgh, Edinburgh EH16 4UU, UK
| | - Neza Alfazema
- Centre for Regenerative Medicine and Institute for Regeneration and Repair, University of Edinburgh, Edinburgh EH16 4UU, UK; Cancer Research UK Edinburgh Centre, University of Edinburgh, Edinburgh EH4 2XR, UK
| | - Jimi C Wills
- Cancer Research UK Edinburgh Centre, University of Edinburgh, Edinburgh EH4 2XR, UK
| | - Maria Angeles Marques-Torrejon
- Centre for Regenerative Medicine and Institute for Regeneration and Repair, University of Edinburgh, Edinburgh EH16 4UU, UK
| | - Gillian M Morrison
- Centre for Regenerative Medicine and Institute for Regeneration and Repair, University of Edinburgh, Edinburgh EH16 4UU, UK; Cancer Research UK Edinburgh Centre, University of Edinburgh, Edinburgh EH4 2XR, UK
| | - James Ashmore
- Centre for Regenerative Medicine and Institute for Regeneration and Repair, University of Edinburgh, Edinburgh EH16 4UU, UK
| | - Faye Robertson
- Centre for Regenerative Medicine and Institute for Regeneration and Repair, University of Edinburgh, Edinburgh EH16 4UU, UK; Cancer Research UK Edinburgh Centre, University of Edinburgh, Edinburgh EH4 2XR, UK
| | - Charles A C Williams
- Centre for Regenerative Medicine and Institute for Regeneration and Repair, University of Edinburgh, Edinburgh EH16 4UU, UK; Cancer Research UK Edinburgh Centre, University of Edinburgh, Edinburgh EH4 2XR, UK
| | - Leanne Bradley
- Centre for Regenerative Medicine and Institute for Regeneration and Repair, University of Edinburgh, Edinburgh EH16 4UU, UK; Cancer Research UK Edinburgh Centre, University of Edinburgh, Edinburgh EH4 2XR, UK
| | - Alex von Kriegsheim
- Cancer Research UK Edinburgh Centre, University of Edinburgh, Edinburgh EH4 2XR, UK
| | - Richard A Anderson
- MRC Centre for Reproductive Health, Queens Medical Research Institute, University of Edinburgh, Edinburgh EH16 4TJ, UK
| | - Simon R Tomlinson
- Centre for Regenerative Medicine and Institute for Regeneration and Repair, University of Edinburgh, Edinburgh EH16 4UU, UK; Institute for Stem Cell Research, University of Edinburgh, Edinburgh EH16 4UU, UK
| | - Steven M Pollard
- Centre for Regenerative Medicine and Institute for Regeneration and Repair, University of Edinburgh, Edinburgh EH16 4UU, UK; Cancer Research UK Edinburgh Centre, University of Edinburgh, Edinburgh EH4 2XR, UK.
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4
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Gangoso E, Southgate B, Bradley L, Rus S, Galvez-Cancino F, McGivern N, Güç E, Kapourani CA, Byron A, Ferguson KM, Alfazema N, Morrison G, Grant V, Blin C, Sou I, Marques-Torrejon MA, Conde L, Parrinello S, Herrero J, Beck S, Brandner S, Brennan PM, Bertone P, Pollard JW, Quezada SA, Sproul D, Frame MC, Serrels A, Pollard SM. Glioblastomas acquire myeloid-affiliated transcriptional programs via epigenetic immunoediting to elicit immune evasion. Cell 2021; 184:2454-2470.e26. [PMID: 33857425 PMCID: PMC8099351 DOI: 10.1016/j.cell.2021.03.023] [Citation(s) in RCA: 132] [Impact Index Per Article: 44.0] [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: 01/27/2020] [Revised: 12/18/2020] [Accepted: 03/11/2021] [Indexed: 12/22/2022]
Abstract
Glioblastoma multiforme (GBM) is an aggressive brain tumor for which current immunotherapy approaches have been unsuccessful. Here, we explore the mechanisms underlying immune evasion in GBM. By serially transplanting GBM stem cells (GSCs) into immunocompetent hosts, we uncover an acquired capability of GSCs to escape immune clearance by establishing an enhanced immunosuppressive tumor microenvironment. Mechanistically, this is not elicited via genetic selection of tumor subclones, but through an epigenetic immunoediting process wherein stable transcriptional and epigenetic changes in GSCs are enforced following immune attack. These changes launch a myeloid-affiliated transcriptional program, which leads to increased recruitment of tumor-associated macrophages. Furthermore, we identify similar epigenetic and transcriptional signatures in human mesenchymal subtype GSCs. We conclude that epigenetic immunoediting may drive an acquired immune evasion program in the most aggressive mesenchymal GBM subtype by reshaping the tumor immune microenvironment.
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Affiliation(s)
- Ester Gangoso
- Centre for Regenerative Medicine, Institute for Regeneration and Repair, University of Edinburgh, 5 Little France Drive, Edinburgh EH16 4UU, UK; CRUK Edinburgh Centre, Institute of Genetics and Molecular Medicine, Crewe Road South, University of Edinburgh, Edinburgh EH42XR, UK
| | - Benjamin Southgate
- Centre for Regenerative Medicine, Institute for Regeneration and Repair, University of Edinburgh, 5 Little France Drive, Edinburgh EH16 4UU, UK; CRUK Edinburgh Centre, Institute of Genetics and Molecular Medicine, Crewe Road South, University of Edinburgh, Edinburgh EH42XR, UK
| | - Leanne Bradley
- Centre for Regenerative Medicine, Institute for Regeneration and Repair, University of Edinburgh, 5 Little France Drive, Edinburgh EH16 4UU, UK; CRUK Edinburgh Centre, Institute of Genetics and Molecular Medicine, Crewe Road South, University of Edinburgh, Edinburgh EH42XR, UK
| | - Stefanie Rus
- Centre for Regenerative Medicine, Institute for Regeneration and Repair, University of Edinburgh, 5 Little France Drive, Edinburgh EH16 4UU, UK; CRUK Edinburgh Centre, Institute of Genetics and Molecular Medicine, Crewe Road South, University of Edinburgh, Edinburgh EH42XR, UK
| | - Felipe Galvez-Cancino
- Cancer Immunology Unit, Research Department of Haematology, University College London Cancer Institute, London WC1E 6BT, UK
| | - Niamh McGivern
- CRUK Edinburgh Centre, Institute of Genetics and Molecular Medicine, Crewe Road South, University of Edinburgh, Edinburgh EH42XR, UK
| | - Esra Güç
- Centre for Reproductive Health, The University of Edinburgh, The Queen's Medical Research Institute, Edinburgh Little France Crescent, Edinburgh EH16 4TJ, UK
| | - Chantriolnt-Andreas Kapourani
- Centre for Regenerative Medicine, Institute for Regeneration and Repair, University of Edinburgh, 5 Little France Drive, Edinburgh EH16 4UU, UK; CRUK Edinburgh Centre, Institute of Genetics and Molecular Medicine, Crewe Road South, University of Edinburgh, Edinburgh EH42XR, UK
| | - Adam Byron
- CRUK Edinburgh Centre, Institute of Genetics and Molecular Medicine, Crewe Road South, University of Edinburgh, Edinburgh EH42XR, UK
| | - Kirsty M Ferguson
- Centre for Regenerative Medicine, Institute for Regeneration and Repair, University of Edinburgh, 5 Little France Drive, Edinburgh EH16 4UU, UK; CRUK Edinburgh Centre, Institute of Genetics and Molecular Medicine, Crewe Road South, University of Edinburgh, Edinburgh EH42XR, UK
| | - Neza Alfazema
- Centre for Regenerative Medicine, Institute for Regeneration and Repair, University of Edinburgh, 5 Little France Drive, Edinburgh EH16 4UU, UK; CRUK Edinburgh Centre, Institute of Genetics and Molecular Medicine, Crewe Road South, University of Edinburgh, Edinburgh EH42XR, UK
| | - Gillian Morrison
- Centre for Regenerative Medicine, Institute for Regeneration and Repair, University of Edinburgh, 5 Little France Drive, Edinburgh EH16 4UU, UK; CRUK Edinburgh Centre, Institute of Genetics and Molecular Medicine, Crewe Road South, University of Edinburgh, Edinburgh EH42XR, UK
| | - Vivien Grant
- Centre for Regenerative Medicine, Institute for Regeneration and Repair, University of Edinburgh, 5 Little France Drive, Edinburgh EH16 4UU, UK; CRUK Edinburgh Centre, Institute of Genetics and Molecular Medicine, Crewe Road South, University of Edinburgh, Edinburgh EH42XR, UK
| | - Carla Blin
- Centre for Regenerative Medicine, Institute for Regeneration and Repair, University of Edinburgh, 5 Little France Drive, Edinburgh EH16 4UU, UK; CRUK Edinburgh Centre, Institute of Genetics and Molecular Medicine, Crewe Road South, University of Edinburgh, Edinburgh EH42XR, UK
| | - IengFong Sou
- Centre for Regenerative Medicine, Institute for Regeneration and Repair, University of Edinburgh, 5 Little France Drive, Edinburgh EH16 4UU, UK; CRUK Edinburgh Centre, Institute of Genetics and Molecular Medicine, Crewe Road South, University of Edinburgh, Edinburgh EH42XR, UK
| | - Maria Angeles Marques-Torrejon
- Centre for Regenerative Medicine, Institute for Regeneration and Repair, University of Edinburgh, 5 Little France Drive, Edinburgh EH16 4UU, UK; CRUK Edinburgh Centre, Institute of Genetics and Molecular Medicine, Crewe Road South, University of Edinburgh, Edinburgh EH42XR, UK
| | - Lucia Conde
- Bill Lyons Informatics Centre, Department of Cancer Biology, University College London Cancer Institute, London WC1E 6BT
| | - Simona Parrinello
- Samantha Dickson Brain Cancer Unit, Department of Cancer Biology, University College London Cancer Institute, London WC1E 6BT, UK
| | - Javier Herrero
- Bill Lyons Informatics Centre, Department of Cancer Biology, University College London Cancer Institute, London WC1E 6BT
| | - Stephan Beck
- Medical Genomics Research Group, Department of Cancer Biology, University College London Cancer Institute, London, WC1E 6BT
| | - Sebastian Brandner
- Division of Neuropathology and Department of Neurodegenerative Disease, UCL Queen Square Institute of Neurology, UCL, London, UK
| | - Paul M Brennan
- Centre for Regenerative Medicine, Institute for Regeneration and Repair, University of Edinburgh, 5 Little France Drive, Edinburgh EH16 4UU, UK; CRUK Edinburgh Centre, Institute of Genetics and Molecular Medicine, Crewe Road South, University of Edinburgh, Edinburgh EH42XR, UK
| | - Paul Bertone
- Department of Medicine, Alpert Medical School, Brown University, Providence, RI 02903, USA
| | - Jeffrey W Pollard
- Centre for Reproductive Health, The University of Edinburgh, The Queen's Medical Research Institute, Edinburgh Little France Crescent, Edinburgh EH16 4TJ, UK
| | - Sergio A Quezada
- Cancer Immunology Unit, Research Department of Haematology, University College London Cancer Institute, London WC1E 6BT, UK
| | - Duncan Sproul
- CRUK Edinburgh Centre, Institute of Genetics and Molecular Medicine, Crewe Road South, University of Edinburgh, Edinburgh EH42XR, UK
| | - Margaret C Frame
- CRUK Edinburgh Centre, Institute of Genetics and Molecular Medicine, Crewe Road South, University of Edinburgh, Edinburgh EH42XR, UK
| | - Alan Serrels
- Centre for Inflammation Research, The University of Edinburgh, The Queen's Medical Research Institute, Edinburgh Little France Crescent, Edinburgh EH16 4TJ, UK
| | - Steven M Pollard
- Centre for Regenerative Medicine, Institute for Regeneration and Repair, University of Edinburgh, 5 Little France Drive, Edinburgh EH16 4UU, UK; CRUK Edinburgh Centre, Institute of Genetics and Molecular Medicine, Crewe Road South, University of Edinburgh, Edinburgh EH42XR, UK.
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5
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Southgate JA, Bull MJ, Brown CM, Watkins J, Corden S, Southgate B, Moore C, Connor TR. Influenza classification from short reads with VAPOR facilitates robust mapping pipelines and zoonotic strain detection for routine surveillance applications. Bioinformatics 2020; 36:1681-1688. [PMID: 31693070 PMCID: PMC7703727 DOI: 10.1093/bioinformatics/btz814] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2019] [Revised: 08/18/2019] [Accepted: 10/30/2019] [Indexed: 11/23/2022] Open
Abstract
Motivation Influenza viruses represent a global public health burden due to annual epidemics and pandemic potential. Due to a rapidly evolving RNA genome, inter-species transmission, intra-host variation, and noise in short-read data, reads can be lost during mapping, and de novo assembly can be time consuming and result in misassembly. We assessed read loss during mapping and designed a graph-based classifier, VAPOR, for selecting mapping references, assembly validation and detection of strains of non-human origin. Results Standard human reference viruses were insufficient for mapping diverse influenza samples in simulation. VAPOR retrieved references for 257 real whole-genome sequencing samples with a mean of >99.8% identity to assemblies, and increased the proportion of mapped reads by up to 13.3% compared to standard references. VAPOR has the potential to improve the robustness of bioinformatics pipelines for surveillance and could be adapted to other RNA viruses. Availability and implementation VAPOR is available at https://github.com/connor-lab/vapor. Supplementary information Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Joel A Southgate
- Organisms and Environment Division, School of Biosciences, Cardiff University, Cardiff CF10 3AX, UK
| | - Matthew J Bull
- Organisms and Environment Division, School of Biosciences, Cardiff University, Cardiff CF10 3AX, UK.,Public Health Wales, University Hospital of Wales, Cardiff CF14 4XW, UK
| | - Clare M Brown
- Organisms and Environment Division, School of Biosciences, Cardiff University, Cardiff CF10 3AX, UK
| | - Joanne Watkins
- Public Health Wales, University Hospital of Wales, Cardiff CF14 4XW, UK
| | - Sally Corden
- Public Health Wales, University Hospital of Wales, Cardiff CF14 4XW, UK
| | - Benjamin Southgate
- MRC Centre for Regenerative Medicine, University of Edinburgh, Edinburgh EH16 4UU, UK
| | - Catherine Moore
- Public Health Wales, University Hospital of Wales, Cardiff CF14 4XW, UK
| | - Thomas R Connor
- Organisms and Environment Division, School of Biosciences, Cardiff University, Cardiff CF10 3AX, UK.,Public Health Wales, University Hospital of Wales, Cardiff CF14 4XW, UK
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6
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Dewari PS, Southgate B, Mccarten K, Monogarov G, O'Duibhir E, Quinn N, Tyrer A, Leitner MC, Plumb C, Kalantzaki M, Blin C, Finch R, Bressan RB, Morrison G, Jacobi AM, Behlke MA, von Kriegsheim A, Tomlinson S, Krijgsveld J, Pollard SM. An efficient and scalable pipeline for epitope tagging in mammalian stem cells using Cas9 ribonucleoprotein. eLife 2018; 7:e35069. [PMID: 29638216 PMCID: PMC5947990 DOI: 10.7554/elife.35069] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2018] [Accepted: 04/10/2018] [Indexed: 01/09/2023] Open
Abstract
CRISPR/Cas9 can be used for precise genetic knock-in of epitope tags into endogenous genes, simplifying experimental analysis of protein function. However, Cas9-assisted epitope tagging in primary mammalian cell cultures is often inefficient and reliant on plasmid-based selection strategies. Here, we demonstrate improved knock-in efficiencies of diverse tags (V5, 3XFLAG, Myc, HA) using co-delivery of Cas9 protein pre-complexed with two-part synthetic modified RNAs (annealed crRNA:tracrRNA) and single-stranded oligodeoxynucleotide (ssODN) repair templates. Knock-in efficiencies of ~5-30%, were achieved without selection in embryonic stem (ES) cells, neural stem (NS) cells, and brain-tumor-derived stem cells. Biallelic-tagged clonal lines were readily derived and used to define Olig2 chromatin-bound interacting partners. Using our novel web-based design tool, we established a 96-well format pipeline that enabled V5-tagging of 60 different transcription factors. This efficient, selection-free and scalable epitope tagging pipeline enables systematic surveys of protein expression levels, subcellular localization, and interactors across diverse mammalian stem cells.
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Affiliation(s)
- Pooran Singh Dewari
- Edinburgh Cancer Research United Kingdom CentreUniversity of EdinburghEdinburghUnited Kingdom
- MRC Centre for Regenerative MedicineUniversity of EdinburghEdinburghUnited Kingdom
| | - Benjamin Southgate
- Edinburgh Cancer Research United Kingdom CentreUniversity of EdinburghEdinburghUnited Kingdom
- MRC Centre for Regenerative MedicineUniversity of EdinburghEdinburghUnited Kingdom
| | - Katrina Mccarten
- Edinburgh Cancer Research United Kingdom CentreUniversity of EdinburghEdinburghUnited Kingdom
- MRC Centre for Regenerative MedicineUniversity of EdinburghEdinburghUnited Kingdom
| | - German Monogarov
- German Cancer Research CenterUniversity of HeidelbergHeidelbergGermany
| | - Eoghan O'Duibhir
- Edinburgh Cancer Research United Kingdom CentreUniversity of EdinburghEdinburghUnited Kingdom
- MRC Centre for Regenerative MedicineUniversity of EdinburghEdinburghUnited Kingdom
| | - Niall Quinn
- Institute of Genetics and Molecular Medicine, Edinburgh Cancer Research United Kingdom CentreUniversity of EdinburghEdinburghUnited Kingdom
| | - Ashley Tyrer
- Edinburgh Cancer Research United Kingdom CentreUniversity of EdinburghEdinburghUnited Kingdom
- MRC Centre for Regenerative MedicineUniversity of EdinburghEdinburghUnited Kingdom
| | - Marie-Christin Leitner
- Edinburgh Cancer Research United Kingdom CentreUniversity of EdinburghEdinburghUnited Kingdom
- MRC Centre for Regenerative MedicineUniversity of EdinburghEdinburghUnited Kingdom
| | - Colin Plumb
- Edinburgh Cancer Research United Kingdom CentreUniversity of EdinburghEdinburghUnited Kingdom
- MRC Centre for Regenerative MedicineUniversity of EdinburghEdinburghUnited Kingdom
| | - Maria Kalantzaki
- Edinburgh Cancer Research United Kingdom CentreUniversity of EdinburghEdinburghUnited Kingdom
- MRC Centre for Regenerative MedicineUniversity of EdinburghEdinburghUnited Kingdom
| | - Carla Blin
- Edinburgh Cancer Research United Kingdom CentreUniversity of EdinburghEdinburghUnited Kingdom
- MRC Centre for Regenerative MedicineUniversity of EdinburghEdinburghUnited Kingdom
| | - Rebecca Finch
- Edinburgh Cancer Research United Kingdom CentreUniversity of EdinburghEdinburghUnited Kingdom
- MRC Centre for Regenerative MedicineUniversity of EdinburghEdinburghUnited Kingdom
| | - Raul Bardini Bressan
- Edinburgh Cancer Research United Kingdom CentreUniversity of EdinburghEdinburghUnited Kingdom
- MRC Centre for Regenerative MedicineUniversity of EdinburghEdinburghUnited Kingdom
| | - Gillian Morrison
- Edinburgh Cancer Research United Kingdom CentreUniversity of EdinburghEdinburghUnited Kingdom
- MRC Centre for Regenerative MedicineUniversity of EdinburghEdinburghUnited Kingdom
| | | | - Mark A Behlke
- Integrated DNA Technologies, Inc.CoralvilleUnited States
| | - Alex von Kriegsheim
- Institute of Genetics and Molecular Medicine, Edinburgh Cancer Research United Kingdom CentreUniversity of EdinburghEdinburghUnited Kingdom
| | - Simon Tomlinson
- Edinburgh Cancer Research United Kingdom CentreUniversity of EdinburghEdinburghUnited Kingdom
- MRC Centre for Regenerative MedicineUniversity of EdinburghEdinburghUnited Kingdom
| | - Jeroen Krijgsveld
- German Cancer Research CenterUniversity of HeidelbergHeidelbergGermany
| | - Steven M Pollard
- Edinburgh Cancer Research United Kingdom CentreUniversity of EdinburghEdinburghUnited Kingdom
- MRC Centre for Regenerative MedicineUniversity of EdinburghEdinburghUnited Kingdom
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7
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Ximenes RA, Southgate B, Smith PG, Guimaraes Neto L. Social environment, behavior, and schistosomiasis in an urban population in the northeast of Brazil. Rev Panam Salud Publica 2001; 9:13-22. [PMID: 11253273 DOI: 10.1590/s1020-49892001000100005] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
The objective of our study was to gain greater insight into the pattern of water contact in relation to schistosomiasis among residents of São Lourenço da Mata, a town in Pernambuco, a state in the Northeast of Brazil. We had two primary objectives: 1) to identify water contact activities that were more likely to produce infection and 2) to examine the socioeconomic factors behind water contact activities. Using a sample of persons 10-25 years old, we carried out a population-based case-control study to investigate the first objective, and a cross-sectional study for the second objective. We found that leisure water contact with flowing water (stream or river) was significantly associated with schistosomiasis. Variables showing a statistically significant association with leisure water contact were economic sector, income, and level of education of the head of the household; type of housing; possessions inside the house; type of domestic water supply; and method of excreta collection. We introduced these variables into a multivariate model to select the ones that were most closely associated with leisure water contact. We used a stepdown procedure, and two variables were retained in the final model: type of domestic water supply and type of housing. We concluded that a decrease in leisure water contact was associated with better socioeconomic conditions. Our results suggest that with the subjects we studied in São Lourenço da Mata there was a socioeconomic determination for leisure water contact. Our data highlight the importance of a broad and integrated approach in studying water contact activities and in implementing behavioral interventions for schistosomiasis prevention and control.
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Affiliation(s)
- R A Ximenes
- Universidade Federal de Pernambuco, Departamento de Medicina Tropical, Recife, Pernambuco, Brazil
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Ximenes RA, Southgate B, Smith PG, Guimarães Neto L. Migration and urban schistosomiasis. The case of São Lourenço da Mata, northeast of Brazil. Rev Inst Med Trop Sao Paulo 2000; 42:209-17. [PMID: 10968884 DOI: 10.1590/s0036-46652000000400006] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
A population-based case-control design was used to investigate the association between migration, urbanisation and schistosomiasis in the Metropolitan Region of Recife, Northeast of Brazil. 1022 cases and 994 controls, aged 10 to 25, were selected. The natives and the migrants who come from endemic areas have a similar risk of infection. On the other hand, the risk of infection of migrants from nonendemic areas seems to be related with the time elapsed since their arrival in São Lourenço da Mata; those who have been living in that urban area for 5 or more years have a risk of infection similar to that of the natives. Those arriving in the metropolitan region of Recife mostly emigrate from "zona da mata" and "zona do agreste" in the state of Pernambuco. Due to the changes in the sugar agroindustry and to the increase in the area used for cattle grazing these workers were driven to villages and cities. The pattern of urbanisation created the conditions for the establishment of foci of transmission in São Lourenço da Mata.
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Affiliation(s)
- R A Ximenes
- Departamento de Medicina Tropical, Universidade Federal de Pernambuco, Recife, PE, Brasil.
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