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Your search keyword '"Nicholas J. Matheson"' showing total 21 results
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1. Proteomic analysis of circulating immune cells identifies cellular phenotypes associated with COVID-19 severity

Author

Martin Potts, Alice Fletcher-Etherington, Katie Nightingale, Federica Mescia, Laura Bergamaschi, Fernando J. Calero-Nieto, Robin Antrobus, James Williamson, Harriet Parsons, Edward L. Huttlin, Nathalie Kingston, Berthold Göttgens, John R. Bradley, Paul J. Lehner, Nicholas J. Matheson, Kenneth G.C. Smith, Mark R. Wills, Paul A. Lyons, and Michael P. Weekes

Subjects
CP: Immunology, Biology (General), QH301-705.5
Abstract

Summary: Certain serum proteins, including C-reactive protein (CRP) and D-dimer, have prognostic value in patients with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Nonetheless, these factors are non-specific, providing limited mechanistic insight into the peripheral blood mononuclear cell (PBMC) populations that drive the pathogenesis of severe COVID-19. To identify cellular phenotypes associated with disease, we performed a comprehensive, unbiased analysis of total and plasma-membrane PBMC proteomes from 40 unvaccinated individuals with SARS-CoV-2, spanning the whole disease spectrum. Combined with RNA sequencing (RNA-seq) and flow cytometry from the same donors, we define a comprehensive multi-omic profile for each severity level, revealing that immune-cell dysregulation progresses with increasing disease. The cell-surface proteins CEACAMs1, 6, and 8, CD177, CD63, and CD89 are strongly associated with severe COVID-19, corresponding to the emergence of atypical CD3+CD4+CEACAM1/6/8+CD177+CD63+CD89+ and CD16+CEACAM1/6/8+ mononuclear cells. Utilization of these markers may facilitate real-time patient assessment by flow cytometry and identify immune populations that could be targeted to ameliorate immunopathology.

Published
2023
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2. LRRC15 mediates an accessory interaction with the SARS-CoV-2 spike protein

Author

Jarrod Shilts, Thomas W. M. Crozier, Ana Teixeira-Silva, Ildar Gabaev, Pehuén Pereyra Gerber, Edward J. D. Greenwood, Samuel James Watson, Brian M. Ortmann, Christian M. Gawden-Bone, Tekle Pauzaite, Markus Hoffmann, James A. Nathan, Stefan Pöhlmann, Nicholas J. Matheson, Paul J. Lehner, and Gavin J. Wright

Subjects
Biology (General), QH301-705.5
Abstract

The interactions between Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) and human host factors enable the virus to propagate infections that lead to Coronavirus Disease 2019 (COVID-19). The spike protein is the largest structural component of the virus and mediates interactions essential for infection, including with the primary angiotensin-converting enzyme 2 (ACE2) receptor. We performed two independent cell-based systematic screens to determine whether there are additional proteins by which the spike protein of SARS-CoV-2 can interact with human cells. We discovered that in addition to ACE2, expression of LRRC15 also causes spike protein binding. This interaction is distinct from other known spike attachment mechanisms such as heparan sulfates or lectin receptors. Measurements of orthologous coronavirus spike proteins implied the interaction was functionally restricted to SARS-CoV-2 by accessibility. We localized the interaction to the C-terminus of the S1 domain and showed that LRRC15 shares recognition of the ACE2 receptor binding domain. From analyzing proteomics and single-cell transcriptomics, we identify LRRC15 expression as being common in human lung vasculature cells and fibroblasts. Levels of LRRC15 were greatly elevated by inflammatory signals in the lungs of COVID-19 patients. Although infection assays demonstrated that LRRC15 alone is not sufficient to permit viral entry, we present evidence that it can modulate infection of human cells. This unexpected interaction merits further investigation to determine how SARS-CoV-2 exploits host LRRC15 and whether it could account for any of the distinctive features of COVID-19. A systematic search for human proteins that can bind to the spike protein of SARS-CoV-2 reveals that LRRC15 can act as a host factor for the virus, and may therefore modulate infection with potential implications for COVID-19.

Published
2023

3. Recurrent emergence of SARS-CoV-2 spike deletion H69/V70 and its role in the Alpha variant B.1.1.7

Author

Bo Meng, Steven A. Kemp, Guido Papa, Rawlings Datir, Isabella A.T.M. Ferreira, Sara Marelli, William T. Harvey, Spyros Lytras, Ahmed Mohamed, Giulia Gallo, Nazia Thakur, Dami A. Collier, Petra Mlcochova, Lidia M. Duncan, Alessandro M. Carabelli, Julia C. Kenyon, Andrew M. Lever, Anna De Marco, Christian Saliba, Katja Culap, Elisabetta Cameroni, Nicholas J. Matheson, Luca Piccoli, Davide Corti, Leo C. James, David L. Robertson, Dalan Bailey, Ravindra K. Gupta, Samuel C. Robson, Nicholas J. Loman, Thomas R. Connor, Tanya Golubchik, Rocio T. Martinez Nunez, Catherine Ludden, Sally Corden, Ian Johnston, David Bonsall, Colin P. Smith, Ali R. Awan, Giselda Bucca, M. Estee Torok, Kordo Saeed, Jacqui A. Prieto, David K. Jackson, William L. Hamilton, Luke B. Snell, Catherine Moore, Ewan M. Harrison, Sonia Goncalves, Derek J. Fairley, Matthew W. Loose, Joanne Watkins, Rich Livett, Samuel Moses, Roberto Amato, Sam Nicholls, Matthew Bull, Darren L. Smith, Jeff Barrett, David M. Aanensen, Martin D. Curran, Surendra Parmar, Dinesh Aggarwal, James G. Shepherd, Matthew D. Parker, Sharon Glaysher, Matthew Bashton, Anthony P. Underwood, Nicole Pacchiarini, Katie F. Loveson, Kate E. Templeton, Cordelia F. Langford, John Sillitoe, Thushan I. de Silva, Dennis Wang, Dominic Kwiatkowski, Andrew Rambaut, Justin O’Grady, Simon Cottrell, Matthew T.G. Holden, Emma C. Thomson, Husam Osman, Monique Andersson, Anoop J. Chauhan, Mohammed O. Hassan-Ibrahim, Mara Lawniczak, Alex Alderton, Meera Chand, Chrystala Constantinidou, Meera Unnikrishnan, Alistair C. Darby, Julian A. Hiscox, Steve Paterson, Inigo Martincorena, Erik M. Volz, Andrew J. Page, Oliver G. Pybus, Andrew R. Bassett, Cristina V. Ariani, Michael H. Spencer Chapman, Kathy K. Li, Rajiv N. Shah, Natasha G. Jesudason, Yusri Taha, Martin P. McHugh, Rebecca Dewar, Aminu S. Jahun, Claire McMurray, Sarojini Pandey, James P. McKenna, Andrew Nelson, Gregory R. Young, Clare M. McCann, Scott Elliott, Hannah Lowe, Ben Temperton, Sunando Roy, Anna Price, Sara Rey, Matthew Wyles, Stefan Rooke, Sharif Shaaban, Mariateresa de Cesare, Laura Letchford, Siona Silveira, Emanuela Pelosi, Eleri Wilson-Davies, Myra Hosmillo, Áine O’Toole, Andrew R. Hesketh, Richard Stark, Louis du Plessis, Chris Ruis, Helen Adams, Yann Bourgeois, Stephen L. Michell, Dimitris Gramatopoulos, Jonathan Edgeworth, Judith Breuer, John A. Todd, Christophe Fraser, David Buck, Michaela John, Gemma L. Kay, Steve Palmer, Sharon J. Peacock, David Heyburn, Danni Weldon, Esther Robinson, Alan McNally, Peter Muir, Ian B. Vipond, John Boyes, Venkat Sivaprakasam, Tranprit Salluja, Samir Dervisevic, Emma J. Meader, Naomi R. Park, Karen Oliver, Aaron R. Jeffries, Sascha Ott, Ana da Silva Filipe, David A. Simpson, Chris Williams, Jane A.H. Masoli, Bridget A. Knight, Christopher R. Jones, Cherian Koshy, Amy Ash, Anna Casey, Andrew Bosworth, Liz Ratcliffe, Li Xu-McCrae, Hannah M. Pymont, Stephanie Hutchings, Lisa Berry, Katie Jones, Fenella Halstead, Thomas Davis, Christopher Holmes, Miren Iturriza-Gomara, Anita O. Lucaci, Paul Anthony Randell, Alison Cox, Pinglawathee Madona, Kathryn Ann Harris, Julianne Rose Brown, Tabitha W. Mahungu, Dianne Irish-Tavares, Tanzina Haque, Jennifer Hart, Eric Witele, Melisa Louise Fenton, Steven Liggett, Clive Graham, Emma Swindells, Jennifer Collins, Gary Eltringham, Sharon Campbell, Patrick C. McClure, Gemma Clark, Tim J. Sloan, Carl Jones, Jessica Lynch, Ben Warne, Steven Leonard, Jillian Durham, Thomas Williams, Sam T. Haldenby, Nathaniel Storey, Nabil-Fareed Alikhan, Nadine Holmes, Christopher Moore, Matthew Carlile, Malorie Perry, Noel Craine, Ronan A. Lyons, Angela H. Beckett, Salman Goudarzi, Christopher Fearn, Kate Cook, Hannah Dent, Hannah Paul, Robert Davies, Beth Blane, Sophia T. Girgis, Mathew A. Beale, Katherine L. Bellis, Matthew J. Dorman, Eleanor Drury, Leanne Kane, Sally Kay, Samantha McGuigan, Rachel Nelson, Liam Prestwood, Shavanthi Rajatileka, Rahul Batra, Rachel J. Williams, Mark Kristiansen, Angie Green, Anita Justice, Adhyana I.K. Mahanama, Buddhini Samaraweera, Nazreen F. Hadjirin, Joshua Quick, Radoslaw Poplawski, Leanne M. Kermack, Nicola Reynolds, Grant Hall, Yasmin Chaudhry, Malte L. Pinckert, Iliana Georgana, Robin J. Moll, Alicia Thornton, Richard Myers, Joanne Stockton, Charlotte A. Williams, Wen C. Yew, Alexander J. Trotter, Amy Trebes, George MacIntyre-Cockett, Alec Birchley, Alexander Adams, Amy Plimmer, Bree Gatica-Wilcox, Caoimhe McKerr, Ember Hilvers, Hannah Jones, Hibo Asad, Jason Coombes, Johnathan M. Evans, Laia Fina, Lauren Gilbert, Lee Graham, Michelle Cronin, Sara Kumziene-Summerhayes, Sarah Taylor, Sophie Jones, Danielle C. Groves, Peijun Zhang, Marta Gallis, Stavroula F. Louka, Igor Starinskij, Chris Jackson, Marina Gourtovaia, Gerry Tonkin-Hill, Kevin Lewis, Jaime M. Tovar-Corona, Keith James, Laura Baxter, Mohammad T. Alam, Richard J. Orton, Joseph Hughes, Sreenu Vattipally, Manon Ragonnet-Cronin, Fabricia F. Nascimento, David Jorgensen, Olivia Boyd, Lily Geidelberg, Alex E. Zarebski, Jayna Raghwani, Moritz U.G. Kraemer, Joel Southgate, Benjamin B. Lindsey, Timothy M. Freeman, Jon-Paul Keatley, Joshua B. Singer, Leonardo de Oliveira Martins, Corin A. Yeats, Khalil Abudahab, Ben E.W. Taylor, Mirko Menegazzo, John Danesh, Wendy Hogsden, Sahar Eldirdiri, Anita Kenyon, Jenifer Mason, Trevor I. Robinson, Alison Holmes, James Price, John A. Hartley, Tanya Curran, Alison E. Mather, Giri Shankar, Rachel Jones, Robin Howe, Sian Morgan, Elizabeth Wastenge, Michael R. Chapman, Siddharth Mookerjee, Rachael Stanley, Wendy Smith, Timothy Peto, David Eyre, Derrick Crook, Gabrielle Vernet, Christine Kitchen, Huw Gulliver, Ian Merrick, Martyn Guest, Robert Munn, Declan T. Bradley, Tim Wyatt, Charlotte Beaver, Luke Foulser, Sophie Palmer, Carol M. Churcher, Ellena Brooks, Kim S. Smith, Katerina Galai, Georgina M. McManus, Frances Bolt, Francesc Coll, Lizzie Meadows, Stephen W. Attwood, Alisha Davies, Elen De Lacy, Fatima Downing, Sue Edwards, Garry P. Scarlett, Sarah Jeremiah, Nikki Smith, Danielle Leek, Sushmita Sridhar, Sally Forrest, Claire Cormie, Harmeet K. Gill, Joana Dias, Ellen E. Higginson, Mailis Maes, Jamie Young, Michelle Wantoch, Dorota Jamrozy, Stephanie Lo, Minal Patel, Verity Hill, Claire M. Bewshea, Sian Ellard, Cressida Auckland, Ian Harrison, Chloe Bishop, Vicki Chalker, Alex Richter, Andrew Beggs, Angus Best, Benita Percival, Jeremy Mirza, Oliver Megram, Megan Mayhew, Liam Crawford, Fiona Ashcroft, Emma Moles-Garcia, Nicola Cumley, Richard Hopes, Patawee Asamaphan, Marc O. Niebel, Rory N. Gunson, Amanda Bradley, Alasdair Maclean, Guy Mollett, Rachel Blacow, Paul Bird, Thomas Helmer, Karlie Fallon, Julian Tang, Antony D. Hale, Louissa R. Macfarlane-Smith, Katherine L. Harper, Holli Carden, Nicholas W. Machin, Kathryn A. Jackson, Shazaad S.Y. Ahmad, Ryan P. George, Lance Turtle, Elaine O’Toole, Joanne Watts, Cassie Breen, Angela Cowell, Adela Alcolea-Medina, Themoula Charalampous, Amita Patel, Lisa J. Levett, Judith Heaney, Aileen Rowan, Graham P. Taylor, Divya Shah, Laura Atkinson, Jack C.D. Lee, Adam P. Westhorpe, Riaz Jannoo, Helen L. Lowe, Angeliki Karamani, Leah Ensell, Wendy Chatterton, Monika Pusok, Ashok Dadrah, Amanda Symmonds, Graciela Sluga, Zoltan Molnar, Paul Baker, Stephen Bonner, Sarah Essex, Edward Barton, Debra Padgett, Garren Scott, Jane Greenaway, Brendan A.I. Payne, Shirelle Burton-Fanning, Sheila Waugh, Veena Raviprakash, Nicola Sheriff, Victoria Blakey, Lesley-Anne Williams, Jonathan Moore, Susanne Stonehouse, Louise Smith, Rose K. Davidson, Luke Bedford, Lindsay Coupland, Victoria Wright, Joseph G. Chappell, Theocharis Tsoleridis, Jonathan Ball, Manjinder Khakh, Vicki M. Fleming, Michelle M. Lister, Hannah C. Howson-Wells, Louise Berry, Tim Boswell, Amelia Joseph, Iona Willingham, Nichola Duckworth, Sarah Walsh, Emma Wise, Nathan Moore, Matilde Mori, Nick Cortes, Stephen Kidd, Rebecca Williams, Laura Gifford, Kelly Bicknell, Sarah Wyllie, Allyson Lloyd, Robert Impey, Cassandra S. Malone, Benjamin J. Cogger, Nick Levene, Lynn Monaghan, Alexander J. Keeley, David G. Partridge, Mohammad Raza, Cariad Evans, Kate Johnson, Emma Betteridge, Ben W. Farr, Scott Goodwin, Michael A. Quail, Carol Scott, Lesley Shirley, Scott A.J. Thurston, Diana Rajan, Iraad F. Bronner, Louise Aigrain, Nicholas M. Redshaw, Stefanie V. Lensing, Shane McCarthy, Alex Makunin, Carlos E. Balcazar, Michael D. Gallagher, Kathleen A. Williamson, Thomas D. Stanton, Michelle L. Michelsen, Joanna Warwick-Dugdale, Robin Manley, Audrey Farbos, James W. Harrison, Christine M. Sambles, David J. Studholme, Angie Lackenby, Tamyo Mbisa, Steven Platt, Shahjahan Miah, David Bibby, Carmen Manso, Jonathan Hubb, Gavin Dabrera, Mary Ramsay, Daniel Bradshaw, Ulf Schaefer, Natalie Groves, Eileen Gallagher, David Lee, David Williams, Nicholas Ellaby, Hassan Hartman, Nikos Manesis, Vineet Patel, Juan Ledesma, Katherine A. Twohig, Elias Allara, Clare Pearson, Jeffrey K.J. Cheng, Hannah E. Bridgewater, Lucy R. Frost, Grace Taylor-Joyce, Paul E. Brown, Lily Tong, Alice Broos, Daniel Mair, Jenna Nichols, Stephen N. Carmichael, Katherine L. Smollett, Kyriaki Nomikou, Elihu Aranday-Cortes, Natasha Johnson, Seema Nickbakhsh, Edith E. Vamos, Margaret Hughes, Lucille Rainbow, Richard Eccles, Charlotte Nelson, Mark Whitehead, Richard Gregory, Matthew Gemmell, Claudia Wierzbicki, Hermione J. Webster, Chloe L. Fisher, Adrian W. Signell, Gilberto Betancor, Harry D. Wilson, Gaia Nebbia, Flavia Flaviani, Alberto C. Cerda, Tammy V. Merrill, Rebekah E. Wilson, Marius Cotic, Nadua Bayzid, Thomas Thompson, Erwan Acheson, Steven Rushton, Sarah O’Brien, David J. Baker, Steven Rudder, Alp Aydin, Fei Sang, Johnny Debebe, Sarah Francois, Tetyana I. Vasylyeva, Marina Escalera Zamudio, Bernardo Gutierrez, Angela Marchbank, Joshua Maksimovic, Karla Spellman, Kathryn McCluggage, Mari Morgan, Robert Beer, Safiah Afifi, Trudy Workman, William Fuller, Catherine Bresner, Adrienn Angyal, Luke R. Green, Paul J. Parsons, Rachel M. Tucker, Rebecca Brown, Max Whiteley, James Bonfield, Christoph Puethe, Andrew Whitwham, Jennifier Liddle, Will Rowe, Igor Siveroni, Thanh Le-Viet, Amy Gaskin, Rob Johnson, Irina Abnizova, Mozam Ali, Laura Allen, Ralph Anderson, Cristina Ariani, Siobhan Austin-Guest, Sendu Bala, Jeffrey Barrett, Andrew Bassett, Kristina Battleday, James Beal, Mathew Beale, Sam Bellany, Tristram Bellerby, Katie Bellis, Duncan Berger, Matt Berriman, Paul Bevan, Simon Binley, Jason Bishop, Kirsty Blackburn, Nick Boughton, Sam Bowker, Timothy Brendler-Spaeth, Iraad Bronner, Tanya Brooklyn, Sarah Kay Buddenborg, Robert Bush, Catarina Caetano, Alex Cagan, Nicola Carter, Joanna Cartwright, Tiago Carvalho Monteiro, Liz Chapman, Tracey-Jane Chillingworth, Peter Clapham, Richard Clark, Adrian Clarke, Catriona Clarke, Daryl Cole, Elizabeth Cook, Maria Coppola, Linda Cornell, Clare Cornwell, Craig Corton, Abby Crackett, Alison Cranage, Harriet Craven, Sarah Craw, Mark Crawford, Tim Cutts, Monika Dabrowska, Matt Davies, Joseph Dawson, Callum Day, Aiden Densem, Thomas Dibling, Cat Dockree, David Dodd, Sunil Dogga, Matthew Dorman, Gordon Dougan, Martin Dougherty, Alexander Dove, Lucy Drummond, Monika Dudek, Laura Durrant, Elizabeth Easthope, Sabine Eckert, Pete Ellis, Ben Farr, Michael Fenton, Marcella Ferrero, Neil Flack, Howerd Fordham, Grace Forsythe, Matt Francis, Audrey Fraser, Adam Freeman, Anastasia Galvin, Maria Garcia-Casado, Alex Gedny, Sophia Girgis, James Glover, Oliver Gould, Andy Gray, Emma Gray, Coline Griffiths, Yong Gu, Florence Guerin, Will Hamilton, Hannah Hanks, Ewan Harrison, Alexandria Harrott, Edward Harry, Julia Harvison, Paul Heath, Anastasia Hernandez-Koutoucheva, Rhiannon Hobbs, Dave Holland, Sarah Holmes, Gary Hornett, Nicholas Hough, Liz Huckle, Lena Hughes-Hallet, Adam Hunter, Stephen Inglis, Sameena Iqbal, Adam Jackson, David Jackson, Carlos Jimenez Verdejo, Matthew Jones, Kalyan Kallepally, Keely Kay, Jon Keatley, Alan Keith, Alison King, Lucy Kitchin, Matt Kleanthous, Martina Klimekova, Petra Korlevic, Ksenia Krasheninnkova, Greg Lane, Cordelia Langford, Adam Laverack, Katharine Law, Stefanie Lensing, Amanah Lewis-Wade, Jennifer Liddle, Quan Lin, Sarah Lindsay, Sally Linsdell, Rhona Long, Jamie Lovell, Jon Lovell, James Mack, Mark Maddison, Aleksei Makunin, Irfan Mamun, Jenny Mansfield, Neil Marriott, Matt Martin, Matthew Mayho, Jo McClintock, Sandra McHugh, Liz MapcMinn, Carl Meadows, Emily Mobley, Robin Moll, Maria Morra, Leanne Morrow, Kathryn Murie, Sian Nash, Claire Nathwani, Plamena Naydenova, Alexandra Neaverson, Ed Nerou, Jon Nicholson, Tabea Nimz, Guillaume G. Noell, Sarah O’Meara, Valeriu Ohan, Charles Olney, Doug Ormond, Agnes Oszlanczi, Yoke Fei Pang, Barbora Pardubska, Naomi Park, Aaron Parmar, Gaurang Patel, Maggie Payne, Sharon Peacock, Arabella Petersen, Deborah Plowman, Tom Preston, Michael Quail, Richard Rance, Suzannah Rawlings, Nicholas Redshaw, Joe Reynolds, Mark Reynolds, Simon Rice, Matt Richardson, Connor Roberts, Katrina Robinson, Melanie Robinson, David Robinson, Hazel Rogers, Eduardo Martin Rojo, Daljit Roopra, Mark Rose, Luke Rudd, Ramin Sadri, Nicholas Salmon, David Saul, Frank Schwach, Phil Seekings, Alison Simms, Matt Sinnott, Shanthi Sivadasan, Bart Siwek, Dale Sizer, Kenneth Skeldon, Jason Skelton, Joanna Slater-Tunstill, Lisa Sloper, Nathalie Smerdon, Chris Smith, Christen Smith, James Smith, Katie Smith, Michelle Smith, Sean Smith, Tina Smith, Leighton Sneade, Carmen Diaz Soria, Catarina Sousa, Emily Souster, Andrew Sparkes, Michael Spencer-Chapman, Janet Squares, Robert Stanley, Claire Steed, Tim Stickland, Ian Still, Mike Stratton, Michelle Strickland, Allen Swann, Agnieszka Swiatkowska, Neil Sycamore, Emma Swift, Edward Symons, Suzanne Szluha, Emma Taluy, Nunu Tao, Katy Taylor, Sam Taylor, Stacey Thompson, Mark Thompson, Mark Thomson, Nicholas Thomson, Scott Thurston, Dee Toombs, Benjamin Topping, Jaime Tovar-Corona, Daniel Ungureanu, James Uphill, Jana Urbanova, Philip Jansen Van, Valerie Vancollie, Paul Voak, Danielle Walker, Matthew Walker, Matt Waller, Gary Ward, Charlie Weatherhogg, Niki Webb, Alan Wells, Eloise Wells, Luke Westwood, Theo Whipp, Thomas Whiteley, Georgia Whitton, Sara Widaa, Mia Williams, Mark Wilson, and Sean Wright

Subjects
SARS-CoV-2, COVID-19, antibody escape, neutralizing antibodies, infectivity, spike mutation, Biology (General), QH301-705.5
Abstract

Summary: We report severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) spike ΔH69/V70 in multiple independent lineages, often occurring after acquisition of receptor binding motif replacements such as N439K and Y453F, known to increase binding affinity to the ACE2 receptor and confer antibody escape. In vitro, we show that, although ΔH69/V70 itself is not an antibody evasion mechanism, it increases infectivity associated with enhanced incorporation of cleaved spike into virions. ΔH69/V70 is able to partially rescue infectivity of spike proteins that have acquired N439K and Y453F escape mutations by increased spike incorporation. In addition, replacement of the H69 and V70 residues in the Alpha variant B.1.1.7 spike (where ΔH69/V70 occurs naturally) impairs spike incorporation and entry efficiency of the B.1.1.7 spike pseudotyped virus. Alpha variant B.1.1.7 spike mediates faster kinetics of cell-cell fusion than wild-type Wuhan-1 D614G, dependent on ΔH69/V70. Therefore, as ΔH69/V70 compensates for immune escape mutations that impair infectivity, continued surveillance for deletions with functional effects is warranted.

Published
2021
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4. Promiscuous Targeting of Cellular Proteins by Vpr Drives Systems-Level Proteomic Remodeling in HIV-1 Infection

Author

Edward J.D. Greenwood, James C. Williamson, Agata Sienkiewicz, Adi Naamati, Nicholas J. Matheson, and Paul J. Lehner

Subjects
Biology (General), QH301-705.5
Abstract

Summary: HIV-1 encodes four “accessory proteins” (Vif, Vpr, Vpu, and Nef), dispensable for viral replication in vitro but essential for viral pathogenesis in vivo. Well characterized cellular targets have been associated with Vif, Vpu, and Nef, which counteract host restriction and promote viral replication. Conversely, although several substrates of Vpr have been described, their biological significance remains unclear. Here, we use complementary unbiased mass spectrometry-based approaches to demonstrate that Vpr is both necessary and sufficient for the DCAF1/DDB1/CUL4 E3 ubiquitin ligase-mediated degradation of at least 38 cellular proteins, causing systems-level changes to the cellular proteome. We therefore propose that promiscuous targeting of multiple host factors underpins complex Vpr-dependent cellular phenotypes and validate this in the case of G2/M cell cycle arrest. Our model explains how Vpr modulates so many cell biological processes and why the functional consequences of previously described Vpr targets, identified and studied in isolation, have proved elusive. : HIV infection results in global changes to the cellular proteome. Greenwood et al. show that one HIV protein, Vpr, is directly or indirectly responsible for almost all of these changes by targeting multiple proteins for degradation. This broad substrate specificity explains the difficulties to date in understanding this enigmatic protein. Keywords: HIV, Vpr, proteomics, Vpx, SIV, TMT, pulsed SILAC, mass spectrometry, IP-MS

Published
2019
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5. Efficacy of FFP3 respirators for prevention of SARS-CoV-2 infection in healthcare workers

Author

Ashley Shaw, Jo Wright, Chris Workman, Christopher J. R. Illingworth, Emma Goldesgeyme, Christine Moody, Rebecca Ferris, Geraldine Martell, Eoin O'Connor, Mark Ferris, David A Enoch, Nicholas J. Matheson, Michael P. Weekes, Parth Patel, Natalie Quinnell, Ferris, Mark [0000-0001-5040-4263], O'Connor, Eoin [0000-0002-6846-6881], Illingworth, Christopher [0000-0002-0030-2784], Matheson, Nicholas [0000-0002-3318-1851], Weekes, Michael [0000-0003-3196-5545], and Apollo - University of Cambridge Repository

Subjects
business.product_category, global health, 0302 clinical medicine, Pandemic, Epidemiology, Health care, Global health, 030212 general & internal medicine, Biology (General), Respiratory Protective Devices, Respirator, FFP3, Microbiology and Infectious Disease, 0303 health sciences, Incidence, General Neuroscience, Masks, General Medicine, Middle Aged, 3. Good health, Viruses, Medicine, PPE, epidemiology, Adult, medicine.medical_specialty, QH301-705.5, infectious disease, Science, Health Personnel, Context (language use), General Biochemistry, Genetics and Molecular Biology, Young Adult, 03 medical and health sciences, healthcare worker, medicine, Humans, Aged, 030304 developmental biology, Aerosols, Infection Control, General Immunology and Microbiology, SARS-CoV-2, business.industry, microbiology, COVID-19, Models, Theoretical, United Kingdom, mask, Surgical mask, Epidemiology and Global Health, Family medicine, Observational study, Research Advance, business
Abstract

Background:Respiratory protective equipment recommended in the UK for healthcare workers (HCWs) caring for patients with COVID-19 comprises a fluid-resistant surgical mask (FRSM), except in the context of aerosol generating procedures (AGPs). We previously demonstrated frequent pauci- and asymptomatic severe acute respiratory syndrome coronavirus 2 infection HCWs during the first wave of the COVID-19 pandemic in the UK, using a comprehensive PCR-based HCW screening programme (Rivett et al., 2020; Jones et al., 2020).Methods:Here, we use observational data and mathematical modelling to analyse infection rates amongst HCWs working on ‘red’ (coronavirus disease 2019, COVID-19) and ‘green’ (non-COVID-19) wards during the second wave of the pandemic, before and after the substitution of filtering face piece 3 (FFP3) respirators for FRSMs.Results:Whilst using FRSMs, HCWs working on red wards faced an approximately 31-fold (and at least fivefold) increased risk of direct, ward-based infection. Conversely, after changing to FFP3 respirators, this risk was significantly reduced (52–100% protection).Conclusions:FFP3 respirators may therefore provide more effective protection than FRSMs for HCWs caring for patients with COVID-19, whether or not AGPs are undertaken.Funding:Wellcome Trust, Medical Research Council, Addenbrooke’s Charitable Trust, NIHR Cambridge Biomedical Research Centre, NHS Blood and Transfusion, UKRI.

Published
2021
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6. Single-dose BNT162b2 vaccine protects against asymptomatic SARS-CoV-2 infection

Author

Jo Wright, Shaun R. Seaman, Rob Howes, Giles Wright, Mark Ferris, Paul J. Lehner, Ashley Shaw, Natalie Quinnell, Lucy Rivett, Nick K Jones, Richard J. Samworth, Michael P. Weekes, Chris Workman, Nicholas J Matheson, Ian Goodfellow, Ben Warne, Jones, Nick K [0000-0003-4475-7761], Rivett, Lucy [0000-0002-2781-9345], Goodfellow, Ian G [0000-0002-9483-510X], Lehner, Paul J [0000-0001-9383-1054], Matheson, Nicholas J [0000-0002-3318-1851], Weekes, Michael P [0000-0003-3196-5545], and Apollo - University of Cambridge Repository

Subjects
0301 basic medicine, global health, Disease, 0302 clinical medicine, Pandemic, Epidemiology, Global health, Medicine, Biology (General), Asymptomatic Infections, Microbiology and Infectious Disease, Transmission (medicine), General Neuroscience, Vaccination, General Medicine, 3. Good health, epidemiology, medicine.symptom, Human, medicine.medical_specialty, COVID-19 Vaccines, QH301-705.5, Science, infectious disease, Health Personnel, Immunization, Secondary, Asymptomatic, General Biochemistry, Genetics and Molecular Biology, 03 medical and health sciences, Internal medicine, Humans, asymptomatic, Infectious disease (athletes), BNT162 Vaccine, Immunization Schedule, General Immunology and Microbiology, SARS-CoV-2, business.industry, microbiology, COVID-19, Epidemiology and Global Health, 030104 developmental biology, BNT162b2, Pfizer-BioNTech, Research Advance, business, 030217 neurology & neurosurgery
Abstract

The BNT162b2 mRNA COVID-19 vaccine (Pfizer-BioNTech) is being utilised internationally for mass COVID-19 vaccination. Evidence of single-dose protection against symptomatic disease has encouraged some countries to opt for delayed booster doses of BNT162b2, but the effect of this strategy on rates of asymptomatic SARS-CoV-2 infection remains unknown. We previously demonstrated frequent pauci- and asymptomatic SARS-CoV-2 infection amongst healthcare workers (HCWs) during the UK’s first wave of the COVID-19 pandemic, using a comprehensive PCR-based HCW screening programme (Rivett et al., 2020; Jones et al., 2020). Here, we evaluate the effect of first-dose BNT162b2 vaccination on test positivity rates and find a fourfold reduction in asymptomatic infection amongst HCWs ≥12 days post-vaccination. These data provide real-world evidence of short-term protection against asymptomatic SARS-CoV-2 infection following a single dose of BNT162b2 vaccine, suggesting that mass first-dose vaccination will reduce SARS-CoV-2 transmission, as well as the burden of COVID-19 disease.

Published
2021
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7. Neural stem cells traffic functional mitochondria via extracellular vesicles

Author

Erika Fernandez-Vizarra, Carlo Viscomi, Ágnes Kittel, Sisareuth Tan, Christian Frezza, Stefano Pluchino, Cristiane Benincá, Nunzio Vicario, Massimo Zeviani, Tommaso Leonardi, Ben Peacock, Paul J. Lehner, Alice Braga, Joshua D. Bernstock, Aletta Van Den Bosch, Jayden A. Smith, Karin H. Muller, Carlos Bastos, Edit I. Buzás, Luca Peruzzotti-Jametti, Giulia Manferrari, Cory M. Willis, Alain Brisson, Nunzio Iraci, Rebecca Rogall, Nuno Faria, Grzegorz Krzak, James C Williamson, Nicholas J Matheson, Iacopo Bicci, Chimie et Biologie des Membranes et des Nanoobjets (CBMN), École Nationale d'Ingénieurs des Travaux Agricoles - Bordeaux (ENITAB)-Institut de Chimie du CNRS (INC)-Université de Bordeaux (UB)-Centre National de la Recherche Scientifique (CNRS), European Project: 258803, Peruzzotti-Jametti, Luca [0000-0002-9396-5607], Bernstock, Joshua D [0000-0002-7814-3867], Willis, Cory M [0000-0001-7938-7276], Manferrari, Giulia [0000-0001-7062-1142], Rogall, Rebecca [0000-0003-0605-2322], Fernandez-Vizarra, Erika [0000-0002-2469-142X], Williamson, James C [0000-0002-2009-189X], Braga, Alice [0000-0003-3273-9742], van den Bosch, Aletta [0000-0001-8886-8928], Leonardi, Tommaso [0000-0002-4449-1863], Benincá, Cristiane [0000-0001-7933-860X], Vicario, Nunzio [0000-0001-5934-3962], Tan, Sisareuth [0000-0003-3633-6318], Bicci, Iacopo [0000-0001-6994-3857], Iraci, Nunzio [0000-0003-2146-9329], Smith, Jayden A [0000-0003-2307-8452], Peacock, Ben [0000-0002-7823-8719], Muller, Karin H [0000-0003-4693-8558], Brisson, Alain [0000-0003-0342-352X], Matheson, Nicholas J [0000-0002-3318-1851], Apollo - University of Cambridge Repository, Université de Bordeaux (UB)-École Nationale d'Ingénieurs des Travaux Agricoles - Bordeaux (ENITAB)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS), Bernstock, Joshua D. [0000-0002-7814-3867], Willis, Cory M. [0000-0001-7938-7276], Williamson, James C. [0000-0002-2009-189X], Smith, Jayden A. [0000-0003-2307-8452], Muller, Karin H. [0000-0003-4693-8558], and Matheson, Nicholas J. [0000-0002-3318-1851]

Subjects
0301 basic medicine, Central Nervous System, Proteomics, [SDV.NEU.NB]Life Sciences [q-bio]/Neurons and Cognition [q-bio.NC]/Neurobiology, Cell Membranes, Artificial Gene Amplification and Extension, Mitochondrion, Outer membrane proteins, Inbred C57BL, Exosomes, Biochemistry, Nervous System, Transgenic, White Blood Cells, Database and Informatics Methods, Mice, 0302 clinical medicine, Neural Stem Cells, Animal Cells, Medicine and Health Sciences, Computer software, Biology (General), Energy-Producing Organelles, Cells, Cultured, Phagocytes, Cultured, Proteomic Databases, General Neuroscience, Neural stem cell, Cell biology, Mitochondria, Polymerase chain reaction, medicine.anatomical_structure, Female, Stem cell, Cellular Structures and Organelles, Cellular Types, Anatomy, General Agricultural and Biological Sciences, Research Article, QH301-705.5, Cells, Immune Cells, Central nervous system, Immunology, Green Fluorescent Proteins, Mice, Transgenic, Biology, Bioenergetics, Research and Analysis Methods, General Biochemistry, Genetics and Molecular Biology, 03 medical and health sciences, Extracellular Vesicles, [SDV.BBM.GTP]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN], Organelle, medicine, Animals, Vesicles, Molecular Biology Techniques, Molecular Biology, Blood Cells, General Immunology and Microbiology, Biology and Life Sciences, Membrane Proteins, Biological Transport, Mesenchymal Stem Cells, Cell Biology, Microvesicles, Transplantation, Mice, Inbred C57BL, 030104 developmental biology, Biological Databases, 030217 neurology & neurosurgery
Abstract

Neural stem cell (NSC) transplantation induces recovery in animal models of central nervous system (CNS) diseases. Although the replacement of lost endogenous cells was originally proposed as the primary healing mechanism of NSC grafts, it is now clear that transplanted NSCs operate via multiple mechanisms, including the horizontal exchange of therapeutic cargoes to host cells via extracellular vesicles (EVs). EVs are membrane particles trafficking nucleic acids, proteins, metabolites and metabolic enzymes, lipids, and entire organelles. However, the function and the contribution of these cargoes to the broad therapeutic effects of NSCs are yet to be fully understood. Mitochondrial dysfunction is an established feature of several inflammatory and degenerative CNS disorders, most of which are potentially treatable with exogenous stem cell therapeutics. Herein, we investigated the hypothesis that NSCs release and traffic functional mitochondria via EVs to restore mitochondrial function in target cells. Untargeted proteomics revealed a significant enrichment of mitochondrial proteins spontaneously released by NSCs in EVs. Morphological and functional analyses confirmed the presence of ultrastructurally intact mitochondria within EVs with conserved membrane potential and respiration. We found that the transfer of these mitochondria from EVs to mtDNA-deficient L929 Rho0 cells rescued mitochondrial function and increased Rho0 cell survival. Furthermore, the incorporation of mitochondria from EVs into inflammatory mononuclear phagocytes restored normal mitochondrial dynamics and cellular metabolism and reduced the expression of pro-inflammatory markers in target cells. When transplanted in an animal model of multiple sclerosis, exogenous NSCs actively transferred mitochondria to mononuclear phagocytes and induced a significant amelioration of clinical deficits. Our data provide the first evidence that NSCs deliver functional mitochondria to target cells via EVs, paving the way for the development of novel (a)cellular approaches aimed at restoring mitochondrial dysfunction not only in multiple sclerosis, but also in degenerative neurological diseases., This study shows that neural stem cells are able to transfer functional mitochondria via extracellular vesicles to target cells both in vitro and in vivo, suggesting that functional mitochondrial transfer via extracellular vesicles is a signaling mechanism used by neural stem cells to modulate the physiology and metabolism of target cells.

Published
2021
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8. Dissecting cell-type-specific metabolism in pancreatic ductal adenocarcinoma

Author

David A. Tuveson, Nicholas J Matheson, Giulia Biffi, Evan C. Lien, Alicia M. Darnell, Laura V. Danai, Tyler Jacks, Shawn M. Davidson, Matthew G. Vander Heiden, Kiera M. Sapp, Ömer H. Yilmaz, Vasilena Gocheva, Sharanya Sivanand, Anna M. Westermark, Zhaoqi Li, Christopher R. Chin, Allison N. Lau, Raphael Ferreira, Jared R. Mayers, Lau, Allison N [0000-0003-4250-7355], Ferreira, Raphael [0000-0001-9881-6232], Mayers, Jared R [0000-0002-8607-1787], Matheson, Nicholas J [0000-0002-3318-1851], Vander Heiden, Matthew G [0000-0002-6702-4192], and Apollo - University of Cambridge Repository

Subjects
0301 basic medicine, Male, Cell type, Mouse, QH301-705.5, Science, Population, pancreatic cancer, pyruvate carboxylase, General Biochemistry, Genetics and Molecular Biology, 03 medical and health sciences, Mice, 0302 clinical medicine, Immune system, Pancreatic cancer, Organoid, medicine, Tumor Microenvironment, Animals, Biology (General), Fibroblast, education, Cancer Biology, education.field_of_study, malic enzyme 1, General Immunology and Microbiology, Chemistry, General Neuroscience, PDAC, General Medicine, metabolic heterogeneity, medicine.disease, Pyruvate carboxylase, Cell biology, Mice, Inbred C57BL, Pancreatic Neoplasms, 030104 developmental biology, medicine.anatomical_structure, organoid culture, 030220 oncology & carcinogenesis, Cancer cell, Medicine, Female, Carcinoma, Pancreatic Ductal, Research Article
Abstract

Funder: Jane Coffin Childs Memorial Fund for Medical Research; FundRef: http://dx.doi.org/10.13039/100001033, Funder: Swedish Foundation for Strategic Research; FundRef: http://dx.doi.org/10.13039/501100001729, Funder: Knut and Alice Wallenberg Foundation; FundRef: http://dx.doi.org/10.13039/501100004063, Funder: Barbro Osher Pro Suecia Foundation; FundRef: http://dx.doi.org/10.13039/100008483, Funder: Howard Hughes Medical Institute; FundRef: http://dx.doi.org/10.13039/100000011, Funder: NIHR Cambridge BRC, Funder: Lustgarten Foundation; FundRef: http://dx.doi.org/10.13039/100005979, Funder: Stand Up To Cancer; FundRef: http://dx.doi.org/10.13039/100009730, Funder: MIT Center for Precision Cancer Medicine, Funder: Ludwig Center at MIT, Funder: Emerald Foundation, Tumors are composed of many different cell types including cancer cells, fibroblasts, and immune cells. Dissecting functional metabolic differences between cell types within a mixed population can be challenging due to the rapid turnover of metabolites relative to the time needed to isolate cells. To overcome this challenge, we traced isotope-labeled nutrients into macromolecules that turn over more slowly than metabolites. This approach was used to assess differences between cancer cell and fibroblast metabolism in murine pancreatic cancer organoid-fibroblast co-cultures and tumors. Pancreatic cancer cells exhibited increased pyruvate carboxylation relative to fibroblasts, and this flux depended on both pyruvate carboxylase and malic enzyme 1 activity. Consequently, expression of both enzymes in cancer cells was necessary for organoid and tumor growth, demonstrating that dissecting the metabolism of specific cell populations within heterogeneous systems can identify dependencies that may not be evident from studying isolated cells in culture or bulk tissue.

Published
2020
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9. Antagonism of PP2A is an independent and conserved function of HIV-1 Vif and causes cell cycle arrest

Author

Paul J. Lehner, Edward J. D. Greenwood, Janet E. Deane, Sara Marelli, Anna V. Protasio, Adi Naamati, James C Williamson, Nicholas J Matheson, Greenwood, Edward Jd [0000-0002-5224-0263], Deane, Janet E [0000-0002-4863-0330], Lehner, Paul J [0000-0001-9383-1054], Matheson, Nicholas J [0000-0002-3318-1851], Apollo - University of Cambridge Repository, and Greenwood, Edward JD [0000-0002-5224-0263]

Subjects
Cell cycle checkpoint, QH301-705.5, Science, viruses, infectious disease, Phosphatase, Mutant, virus, Biology, General Biochemistry, Genetics and Molecular Biology, 03 medical and health sciences, vif Gene Products, Human Immunodeficiency Virus, Humans, Point Mutation, APOBEC Deaminases, Protein Phosphatase 2, Biology (General), APOBEC3G, 030304 developmental biology, chemistry.chemical_classification, 0303 health sciences, Microbiology and Infectious Disease, General Immunology and Microbiology, Host Microbial Interactions, General Neuroscience, 030302 biochemistry & molecular biology, microbiology, virus diseases, HIV, General Medicine, Protein phosphatase 2, Cell Cycle Checkpoints, Cell cycle, biochemical phenomena, metabolism, and nutrition, Flow Cytometry, Vif, 3. Good health, Cell biology, Amino acid, PP2A, chemistry, HIV-1, Medicine, cell cycle, Antagonism, Research Advance, Function (biology)
Abstract

The seminal description of cellular restriction factor APOBEC3G and its antagonism by HIV-1 Vif has underpinned two decades of research on the host-virus interaction. As well as APOBEC3G and its homologues, however, we have recently discovered that Vif is also able to degrade the PPP2R5 family of regulatory subunits of key cellular phosphatase PP2A (PPP2R5A-E) (Greenwood et al., 2016; Naamati et al., 2019). We now identify amino acid polymorphisms at positions 31 and 128 of HIV-1 Vif which selectively regulate the degradation of PPP2R5 family proteins. These residues covary across HIV-1 virusesin vivo, favouring depletion of PPP2R5A-E. Through analysis of point mutants and naturally occurring Vif variants, we further show that degradation of PPP2R5 family subunits is both necessary and sufficient for Vif-dependent G2/M cell cycle arrest. Antagonism of PP2A by HIV-1 Vif is therefore independent of APOBEC3 family proteins, and regulates cell cycle progression in HIV-infected cells.

Published
2020

10. Functional proteomic atlas of HIV-infection in primary human CD4+ T cells

Author

Paul J. Lehner, Sara Marelli, Adi Naamati, James C Williamson, Edward J. D. Greenwood, Nicholas J Matheson, Greenwood, Edward Jd [0000-0002-5224-0263], Lehner, Paul J [0000-0001-9383-1054], Matheson, Nicholas J [0000-0002-3318-1851], and Apollo - University of Cambridge Repository

Subjects
CD4-Positive T-Lymphocytes, Proteomics, Proteome, Viral pathogenesis, viruses, Human immunodeficiency virus (HIV), Host factors, HIV Infections, Cell Separation, medicine.disease_cause, Lymphocyte Activation, Virus Replication, Cellular protein, immunology, Fragile X Mental Retardation Protein, 0302 clinical medicine, vif Gene Products, Human Immunodeficiency Virus, Cluster Analysis, Biology (General), Cellular proteins, 0303 health sciences, virus diseases, Hydrogen-Ion Concentration, 3. Good health, DNA-Binding Proteins, medicine.anatomical_structure, 030220 oncology & carcinogenesis, Medicine, Protein Binding, Cell physiology, QH301-705.5, Science, T cell, infectious disease, Green Fluorescent Proteins, virus, Biology, Virus, primary human CD4+ T cell, 03 medical and health sciences, Magnetics, medicine, Humans, human, 030304 developmental biology, magnetic cell selection, microbiology, Lentivirus, HIV, Protein Tyrosine Phosphatase, Non-Receptor Type 22, Methyltransferases, Virology, Gene Expression Regulation, inflammation, HIV-1, Streptavidin
Abstract

Viruses manipulate host cells to enhance their replication, and the identification of host factors targeted by viruses has led to key insights in both viral pathogenesis and cellular physiology. We previously described global changes in cellular protein levels during human immunodeficiency virus (HIV) infection using transformed CEM-T4 T cells as a model. In this study, we develop an HIV reporter virus displaying a streptavidin-binding affinity tag at the surface of infected cells, allowing facile one-step selection with streptavidin-conjugated magnetic beads. We use this system to obtain pure populations of HIV-infected primary human CD4+ T cells for detailed proteomic analysis, including quantitation of >9,000 proteins across 4 different donors, and temporal profiling during T cell activation. Remarkably, amongst 650 cellular proteins significantly perturbed during HIV infection of primary T cells (q

Published
2018
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11. Temporal proteomic analysis of HIV infection reveals remodelling of the host phosphoproteome by lentiviral Vif variants

Author

Paul J. Lehner, Nicholas J Matheson, James C Williamson, Dick J. H. van den Boomen, Kim Wals, Robin Antrobus, Edward J. D. Greenwood, Greenwood, Edward [0000-0002-5224-0263], Matheson, Nicholas [0000-0002-3318-1851], Van Den Boomen, Dick [0000-0001-6474-3661], Williamson, James [0000-0002-2009-189X], Lehner, Paul [0000-0001-9383-1054], and Apollo - University of Cambridge Repository

Subjects
0301 basic medicine, Time Factors, Proteome, QH301-705.5, Science, viruses, infectious disease, Phosphatase, Hyperphosphorylation, HIV Infections, Proteomics, Tandem mass tag, General Biochemistry, Genetics and Molecular Biology, 03 medical and health sciences, proteomics, lentivirus, vif Gene Products, Human Immunodeficiency Virus, Humans, human, Biology (General), Cells, Cultured, Microbiology and Infectious Disease, General Immunology and Microbiology, biology, Kinase, phosphorylation, General Neuroscience, microbiology, HIV, General Medicine, Protein phosphatase 2, Phosphoproteins, biology.organism_classification, Virology, Vif, 3. Good health, Cell biology, PP2A, 030104 developmental biology, Host-Pathogen Interactions, Lentivirus, Medicine, Phosphorylation, Research Article
Abstract

Viruses manipulate host factors to enhance their replication and evade cellular restriction. We used multiplex tandem mass tag (TMT)-based whole cell proteomics to perform a comprehensive time course analysis of >6500 viral and cellular proteins during HIV infection. To enable specific functional predictions, we categorized cellular proteins regulated by HIV according to their patterns of temporal expression. We focussed on proteins depleted with similar kinetics to APOBEC3C, and found the viral accessory protein Vif to be necessary and sufficient for CUL5-dependent proteasomal degradation of all members of the B56 family of regulatory subunits of the key cellular phosphatase PP2A (PPP2R5A-E). Quantitative phosphoproteomic analysis of HIV-infected cells confirmed Vif-dependent hyperphosphorylation of >200 cellular proteins, particularly substrates of the aurora kinases. The ability of Vif to target PPP2R5 subunits is found in primate and non-primate lentiviral lineages, and remodeling of the cellular phosphoproteome is therefore a second ancient and conserved Vif function. DOI: http://dx.doi.org/10.7554/eLife.18296.001, eLife digest About 100 years since it was first transmitted to humans, the Human Immunodeficiency Virus (HIV) infects almost 40 million people worldwide and causes more than a million AIDS-related deaths every year. It is therefore critical to understand how HIV has been able to multiply and spread, and why infection with HIV causes AIDS. In the evolutionary “arms race” between viruses like HIV and the cells they infect, viruses try to enhance their ability to multiply, and cells try to resist. These interactions emphasise the processes that are most important for cells and viruses, and suggest new ways to treat HIV and other viral infections. Proteomics is the large-scale study of molecules known as proteins, the critical building blocks of both cells and viruses. Greenwood, Matheson et al. use proteomics to measure how the abundance of proteins in human cells change during HIV infection, and identify new interactions between the virus and its host. The experiments distinguish more than 6500 proteins, and reveal that an HIV protein called Vif destroys several key components of a cellular protein called PP2A. Previous studies have demonstrated that PP2A plays a critical role in regulating the activities of numerous other proteins and processes in cells. Greenwood, Matheson et al. further show that other HIV-related viruses that infect monkeys, apes and even sheep can also counteract PP2A, suggesting that this interaction has been important during host and virus evolution. The next steps following on from this work are to find out why HIV attacks PP2A, and whether drugs that interfere with this interaction may help to treat HIV infection. A future challenge will be to investigate how HIV interacts with other cellular proteins highlighted by the proteomics approach. DOI: http://dx.doi.org/10.7554/eLife.18296.002

Published
2016

12. A protease-activatable luminescent biosensor and reporter cell line for authentic SARS-CoV-2 infection.

Author

Pehuén Pereyra Gerber, Lidia M Duncan, Edward Jd Greenwood, Sara Marelli, Adi Naamati, Ana Teixeira-Silva, Thomas Wm Crozier, Ildar Gabaev, Jun R Zhan, Thomas E Mulroney, Emily C Horner, Rainer Doffinger, Anne E Willis, James Ed Thaventhiran, Anna V Protasio, and Nicholas J Matheson

Subjects
Immunologic diseases. Allergy, RC581-607, Biology (General), QH301-705.5
Abstract

Efforts to define serological correlates of protection against COVID-19 have been hampered by the lack of a simple, scalable, standardised assay for SARS-CoV-2 infection and antibody neutralisation. Plaque assays remain the gold standard, but are impractical for high-throughput screening. In this study, we show that expression of viral proteases may be used to quantitate infected cells. Our assays exploit the cleavage of specific oligopeptide linkers, leading to the activation of cell-based optical biosensors. First, we characterise these biosensors using recombinant SARS-CoV-2 proteases. Next, we confirm their ability to detect viral protease expression during replication of authentic virus. Finally, we generate reporter cells stably expressing an optimised luciferase-based biosensor, enabling viral infection to be measured within 24 h in a 96- or 384-well plate format, including variants of concern. We have therefore developed a luminescent SARS-CoV-2 reporter cell line, and demonstrated its utility for the relative quantitation of infectious virus and titration of neutralising antibodies.

Published
2022
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13. Efficacy of FFP3 respirators for prevention of SARS-CoV-2 infection in healthcare workers

Author

Mark Ferris, Rebecca Ferris, Chris Workman, Eoin O'Connor, David A Enoch, Emma Goldesgeyme, Natalie Quinnell, Parth Patel, Jo Wright, Geraldine Martell, Christine Moody, Ashley Shaw, Christopher JR Illingworth, Nicholas J Matheson, and Michael P Weekes

Subjects
COVID-19, SARS-CoV-2, healthcare worker, PPE, mask, FFP3, Medicine, Science, Biology (General), QH301-705.5
Abstract

Background: Respiratory protective equipment recommended in the UK for healthcare workers (HCWs) caring for patients with COVID-19 comprises a fluid-resistant surgical mask (FRSM), except in the context of aerosol generating procedures (AGPs). We previously demonstrated frequent pauci- and asymptomatic severe acute respiratory syndrome coronavirus 2 infection HCWs during the first wave of the COVID-19 pandemic in the UK, using a comprehensive PCR-based HCW screening programme (Rivett et al., 2020; Jones et al., 2020). Methods: Here, we use observational data and mathematical modelling to analyse infection rates amongst HCWs working on ‘red’ (coronavirus disease 2019, COVID-19) and ‘green’ (non-COVID-19) wards during the second wave of the pandemic, before and after the substitution of filtering face piece 3 (FFP3) respirators for FRSMs. Results: Whilst using FRSMs, HCWs working on red wards faced an approximately 31-fold (and at least fivefold) increased risk of direct, ward-based infection. Conversely, after changing to FFP3 respirators, this risk was significantly reduced (52–100% protection). Conclusions: FFP3 respirators may therefore provide more effective protection than FRSMs for HCWs caring for patients with COVID-19, whether or not AGPs are undertaken. Funding: Wellcome Trust, Medical Research Council, Addenbrooke’s Charitable Trust, NIHR Cambridge Biomedical Research Centre, NHS Blood and Transfusion, UKRI.

Published
2021
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14. Neural stem cells traffic functional mitochondria via extracellular vesicles.

Author

Luca Peruzzotti-Jametti, Joshua D Bernstock, Cory M Willis, Giulia Manferrari, Rebecca Rogall, Erika Fernandez-Vizarra, James C Williamson, Alice Braga, Aletta van den Bosch, Tommaso Leonardi, Grzegorz Krzak, Ágnes Kittel, Cristiane Benincá, Nunzio Vicario, Sisareuth Tan, Carlos Bastos, Iacopo Bicci, Nunzio Iraci, Jayden A Smith, Ben Peacock, Karin H Muller, Paul J Lehner, Edit Iren Buzas, Nuno Faria, Massimo Zeviani, Christian Frezza, Alain Brisson, Nicholas J Matheson, Carlo Viscomi, and Stefano Pluchino

Subjects
Biology (General), QH301-705.5
Abstract

Neural stem cell (NSC) transplantation induces recovery in animal models of central nervous system (CNS) diseases. Although the replacement of lost endogenous cells was originally proposed as the primary healing mechanism of NSC grafts, it is now clear that transplanted NSCs operate via multiple mechanisms, including the horizontal exchange of therapeutic cargoes to host cells via extracellular vesicles (EVs). EVs are membrane particles trafficking nucleic acids, proteins, metabolites and metabolic enzymes, lipids, and entire organelles. However, the function and the contribution of these cargoes to the broad therapeutic effects of NSCs are yet to be fully understood. Mitochondrial dysfunction is an established feature of several inflammatory and degenerative CNS disorders, most of which are potentially treatable with exogenous stem cell therapeutics. Herein, we investigated the hypothesis that NSCs release and traffic functional mitochondria via EVs to restore mitochondrial function in target cells. Untargeted proteomics revealed a significant enrichment of mitochondrial proteins spontaneously released by NSCs in EVs. Morphological and functional analyses confirmed the presence of ultrastructurally intact mitochondria within EVs with conserved membrane potential and respiration. We found that the transfer of these mitochondria from EVs to mtDNA-deficient L929 Rho0 cells rescued mitochondrial function and increased Rho0 cell survival. Furthermore, the incorporation of mitochondria from EVs into inflammatory mononuclear phagocytes restored normal mitochondrial dynamics and cellular metabolism and reduced the expression of pro-inflammatory markers in target cells. When transplanted in an animal model of multiple sclerosis, exogenous NSCs actively transferred mitochondria to mononuclear phagocytes and induced a significant amelioration of clinical deficits. Our data provide the first evidence that NSCs deliver functional mitochondria to target cells via EVs, paving the way for the development of novel (a)cellular approaches aimed at restoring mitochondrial dysfunction not only in multiple sclerosis, but also in degenerative neurological diseases.

Published
2021
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15. Single-dose BNT162b2 vaccine protects against asymptomatic SARS-CoV-2 infection

Author

Nick K Jones, Lucy Rivett, Shaun Seaman, Richard J Samworth, Ben Warne, Chris Workman, Mark Ferris, Jo Wright, Natalie Quinnell, Ashley Shaw, Cambridge COVID-19 Collaboration, Ian G Goodfellow, Paul J Lehner, Rob Howes, Giles Wright, Nicholas J Matheson, and Michael P Weekes

Subjects
SARS-CoV-2, COVID-19, BNT162b2, vaccination, asymptomatic, Pfizer-BioNTech, Medicine, Science, Biology (General), QH301-705.5
Abstract

The BNT162b2 mRNA COVID-19 vaccine (Pfizer-BioNTech) is being utilised internationally for mass COVID-19 vaccination. Evidence of single-dose protection against symptomatic disease has encouraged some countries to opt for delayed booster doses of BNT162b2, but the effect of this strategy on rates of asymptomatic SARS-CoV-2 infection remains unknown. We previously demonstrated frequent pauci- and asymptomatic SARS-CoV-2 infection amongst healthcare workers (HCWs) during the UK’s first wave of the COVID-19 pandemic, using a comprehensive PCR-based HCW screening programme (Rivett et al., 2020; Jones et al., 2020). Here, we evaluate the effect of first-dose BNT162b2 vaccination on test positivity rates and find a fourfold reduction in asymptomatic infection amongst HCWs ≥12 days post-vaccination. These data provide real-world evidence of short-term protection against asymptomatic SARS-CoV-2 infection following a single dose of BNT162b2 vaccine, suggesting that mass first-dose vaccination will reduce SARS-CoV-2 transmission, as well as the burden of COVID-19 disease.

Published
2021
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16. Dissecting cell-type-specific metabolism in pancreatic ductal adenocarcinoma

Author

Allison N Lau, Zhaoqi Li, Laura V Danai, Anna M Westermark, Alicia M Darnell, Raphael Ferreira, Vasilena Gocheva, Sharanya Sivanand, Evan C Lien, Kiera M Sapp, Jared R Mayers, Giulia Biffi, Christopher R Chin, Shawn M Davidson, David A Tuveson, Tyler Jacks, Nicholas J Matheson, Omer Yilmaz, and Matthew G Vander Heiden

Subjects
pancreatic cancer, organoid culture, malic enzyme 1, PDAC, pyruvate carboxylase, metabolic heterogeneity, Medicine, Science, Biology (General), QH301-705.5
Abstract

Tumors are composed of many different cell types including cancer cells, fibroblasts, and immune cells. Dissecting functional metabolic differences between cell types within a mixed population can be challenging due to the rapid turnover of metabolites relative to the time needed to isolate cells. To overcome this challenge, we traced isotope-labeled nutrients into macromolecules that turn over more slowly than metabolites. This approach was used to assess differences between cancer cell and fibroblast metabolism in murine pancreatic cancer organoid-fibroblast co-cultures and tumors. Pancreatic cancer cells exhibited increased pyruvate carboxylation relative to fibroblasts, and this flux depended on both pyruvate carboxylase and malic enzyme 1 activity. Consequently, expression of both enzymes in cancer cells was necessary for organoid and tumor growth, demonstrating that dissecting the metabolism of specific cell populations within heterogeneous systems can identify dependencies that may not be evident from studying isolated cells in culture or bulk tissue.

Published
2020
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17. Effective control of SARS-CoV-2 transmission between healthcare workers during a period of diminished community prevalence of COVID-19

Author

Nick K Jones, Lucy Rivett, Dominic Sparkes, Sally Forrest, Sushmita Sridhar, Jamie Young, Joana Pereira-Dias, Claire Cormie, Harmeet Gill, Nicola Reynolds, Michelle Wantoch, Matthew Routledge, Ben Warne, Jack Levy, William David Córdova Jiménez, Fathima Nisha Begum Samad, Chris McNicholas, Mark Ferris, Jane Gray, Michael Gill, The CITIID-NIHR COVID-19 BioResource Collaboration, Martin D Curran, Stewart Fuller, Afzal Chaudhry, Ashley Shaw, John R Bradley, Gregory J Hannon, Ian G Goodfellow, Gordon Dougan, Kenneth GC Smith, Paul J Lehner, Giles Wright, Nicholas J Matheson, Stephen Baker, and Michael P Weekes

Subjects
COVID-19, SARS-CoV-2, infectious disease, virology, occupational health, emerging pathogens, Medicine, Science, Biology (General), QH301-705.5
Abstract

Previously, we showed that 3% (31/1032)of asymptomatic healthcare workers (HCWs) from a large teaching hospital in Cambridge, UK, tested positive for SARS-CoV-2 in April 2020. About 15% (26/169) HCWs with symptoms of coronavirus disease 2019 (COVID-19) also tested positive for SARS-CoV-2 (Rivett et al., 2020). Here, we show that the proportion of both asymptomatic and symptomatic HCWs testing positive for SARS-CoV-2 rapidly declined to near-zero between 25th April and 24th May 2020, corresponding to a decline in patient admissions with COVID-19 during the ongoing UK ‘lockdown’. These data demonstrate how infection prevention and control measures including staff testing may help prevent hospitals from becoming independent ‘hubs’ of SARS-CoV-2 transmission, and illustrate how, with appropriate precautions, organizations in other sectors may be able to resume on-site work safely.

Published
2020
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18. Screening of healthcare workers for SARS-CoV-2 highlights the role of asymptomatic carriage in COVID-19 transmission

Author

Lucy Rivett, Sushmita Sridhar, Dominic Sparkes, Matthew Routledge, Nick K Jones, Sally Forrest, Jamie Young, Joana Pereira-Dias, William L Hamilton, Mark Ferris, M Estee Torok, Luke Meredith, The CITIID-NIHR COVID-19 BioResource Collaboration, Martin D Curran, Stewart Fuller, Afzal Chaudhry, Ashley Shaw, Richard J Samworth, John R Bradley, Gordon Dougan, Kenneth GC Smith, Paul J Lehner, Nicholas J Matheson, Giles Wright, Ian G Goodfellow, Stephen Baker, and Michael P Weekes

Subjects
COVID-19, SARS-CoV-2, infectious disease, virology, occupational health, emerging pathogens, Medicine, Science, Biology (General), QH301-705.5
Abstract

Significant differences exist in the availability of healthcare worker (HCW) SARS-CoV-2 testing between countries, and existing programmes focus on screening symptomatic rather than asymptomatic staff. Over a 3 week period (April 2020), 1032 asymptomatic HCWs were screened for SARS-CoV-2 in a large UK teaching hospital. Symptomatic staff and symptomatic household contacts were additionally tested. Real-time RT-PCR was used to detect viral RNA from a throat+nose self-swab. 3% of HCWs in the asymptomatic screening group tested positive for SARS-CoV-2. 17/30 (57%) were truly asymptomatic/pauci-symptomatic. 12/30 (40%) had experienced symptoms compatible with coronavirus disease 2019 (COVID-19)>7 days prior to testing, most self-isolating, returning well. Clusters of HCW infection were discovered on two independent wards. Viral genome sequencing showed that the majority of HCWs had the dominant lineage B∙1. Our data demonstrates the utility of comprehensive screening of HCWs with minimal or no symptoms. This approach will be critical for protecting patients and hospital staff.

Published
2020
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19. Antagonism of PP2A is an independent and conserved function of HIV-1 Vif and causes cell cycle arrest

Author

Sara Marelli, James C Williamson, Anna V Protasio, Adi Naamati, Edward JD Greenwood, Janet E Deane, Paul J Lehner, and Nicholas J Matheson

Subjects
HIV, Vif, PP2A, cell cycle, Medicine, Science, Biology (General), QH301-705.5
Abstract

The seminal description of the cellular restriction factor APOBEC3G and its antagonism by HIV-1 Vif has underpinned two decades of research on the host-virus interaction. We recently reported that HIV-1 Vif is also able to degrade the PPP2R5 family of regulatory subunits of key cellular phosphatase PP2A (PPP2R5A-E; Greenwood et al., 2016; Naamati et al., 2019). We now identify amino acid polymorphisms at positions 31 and 128 of HIV-1 Vif which selectively regulate the degradation of PPP2R5 family proteins. These residues covary across HIV-1 viruses in vivo, favouring depletion of PPP2R5A-E. Through analysis of point mutants and naturally occurring Vif variants, we further show that degradation of PPP2R5 family subunits is both necessary and sufficient for Vif-dependent G2/M cell cycle arrest. Antagonism of PP2A by HIV-1 Vif is therefore independent of APOBEC3 family proteins, and regulates cell cycle progression in HIV-infected cells.

Published
2020
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20. Functional proteomic atlas of HIV infection in primary human CD4+ T cells

Author

Adi Naamati, James C Williamson, Edward JD Greenwood, Sara Marelli, Paul J Lehner, and Nicholas J Matheson

Subjects
HIV, primary human CD4+ T cell, magnetic cell selection, proteomics, Medicine, Science, Biology (General), QH301-705.5
Abstract

Viruses manipulate host cells to enhance their replication, and the identification of cellular factors targeted by viruses has led to key insights into both viral pathogenesis and cell biology. In this study, we develop an HIV reporter virus (HIV-AFMACS) displaying a streptavidin-binding affinity tag at the surface of infected cells, allowing facile one-step selection with streptavidin-conjugated magnetic beads. We use this system to obtain pure populations of HIV-infected primary human CD4+ T cells for detailed proteomic analysis, and quantitate approximately 9000 proteins across multiple donors on a dynamic background of T cell activation. Amongst 650 HIV-dependent changes (q < 0.05), we describe novel Vif-dependent targets FMR1 and DPH7, and 192 proteins not identified and/or regulated in T cell lines, such as ARID5A and PTPN22. We therefore provide a high-coverage functional proteomic atlas of HIV infection, and a mechanistic account of host factors subverted by the virus in its natural target cell.

Published
2019
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21. Temporal proteomic analysis of HIV infection reveals remodelling of the host phosphoproteome by lentiviral Vif variants

Author

Edward JD Greenwood, Nicholas J Matheson, Kim Wals, Dick JH van den Boomen, Robin Antrobus, James C Williamson, and Paul J Lehner

Subjects
proteomics, HIV, Vif, PP2A, phosphorylation, lentivirus, Medicine, Science, Biology (General), QH301-705.5
Abstract

Viruses manipulate host factors to enhance their replication and evade cellular restriction. We used multiplex tandem mass tag (TMT)-based whole cell proteomics to perform a comprehensive time course analysis of >6500 viral and cellular proteins during HIV infection. To enable specific functional predictions, we categorized cellular proteins regulated by HIV according to their patterns of temporal expression. We focussed on proteins depleted with similar kinetics to APOBEC3C, and found the viral accessory protein Vif to be necessary and sufficient for CUL5-dependent proteasomal degradation of all members of the B56 family of regulatory subunits of the key cellular phosphatase PP2A (PPP2R5A-E). Quantitative phosphoproteomic analysis of HIV-infected cells confirmed Vif-dependent hyperphosphorylation of >200 cellular proteins, particularly substrates of the aurora kinases. The ability of Vif to target PPP2R5 subunits is found in primate and non-primate lentiviral lineages, and remodeling of the cellular phosphoproteome is therefore a second ancient and conserved Vif function.

Published
2016
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