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6. Constructing custom-made radiotranscriptomic signatures of vascular inflammation from routine CT angiograms: a prospective outcomes validation study in COVID-19

Author

Ahern, David J, Ai, Zhichao, Ainsworth, Mark, Allan, Chris, Allcock, Alice, Angus, Brian, Ansari, M Azim, Arancibia-Cárcamo, Carolina, Aschenbrenner, Dominik, Attar, Moustafa, Baillie, J Kenneth, Barnes, Eleanor, Bashford-Rogers, Rachael, Bashyal, Archana, Beer, Sally, Berridge, Georgina, Beveridge, Amy, Bibi, Sagida, Bicanic, Tihana, Blackwell, Luke, Bowness, Paul, Brent, Andrew, Brown, Andrew, Broxholme, John, Buck, David, Burnham, Katie, Byrne, Helen, Camara, Susana, Ferreira, Ivan Candido, Charles, Philip, Chen, Wentao, Chen, Yi-Ling, Chong, Amanda, Clutterbuck, Elizabeth, Coles, Mark, Conlon, Christopher, Cornall, Richard, Cribbs, Adam, Curion, Fabiola, Davenport, Emma, Davidson, Neil, Davis, Simon, Dendrou, Calliope, Dequaire, Julie, Dib, Lea, Docker, James, Dold, Christina, Dong, Tao, Downes, Damien, Drakesmith, Hal, Dunachie, Susanna, Duncan, David, Eijsbouts, Chris, Esnouf, Robert, Espinosa, Alexis, Etherington, Rachel, Fairfax, Benjamin, Fairhead, Rory, Fang, Hai, Fassih, Shayan, Felle, Sally, Fernandez Mendoza, Maria, Ferreira, Ricardo, Fischer, Roman, Foord, Thomas, Forrow, Aden, Frater, John, Fries, Anastasia, Gallardo Sanchez, Veronica, Garner, Lucy, Geeves, Clementine, Georgiou, Dominique, Godfrey, Leila, Golubchik, Tanya, Gomez Vazquez, Maria, Green, Angie, Harper, Hong, Harrington, Heather, Heilig, Raphael, Hester, Svenja, Hill, Jennifer, Hinds, Charles, Hird, Clare, Ho, Ling-Pei, Hoekzema, Renee, Hollis, Benjamin, Hughes, Jim, Hutton, Paula, Jackson-Wood, Matthew, Jainarayanan, Ashwin, James-Bott, Anna, Jansen, Kathrin, Jeffery, Katie, Jones, Elizabeth, Jostins, Luke, Kerr, Georgina, Kim, David, Klenerman, Paul, Knight, Julian, Kumar, Vinod, Kumar Sharma, Piyush, Kurupati, Prathiba, Kwok, Andrew, Lee, Angela, Linder, Aline, Lockett, Teresa, Lonie, Lorne, Lopopolo, Maria, Lukoseviciute, Martyna, Luo, Jian, Marinou, Spyridoula, Marsden, Brian, Martinez, Jose, Matthews, Philippa, Mazurczyk, Michalina, McGowan, Simon, McKechnie, Stuart, Mead, Adam, Mentzer, Alexander, Mi, Yuxin, Monaco, Claudia, Montadon, Ruddy, Napolitani, Giorgio, Nassiri, Isar, Novak, Alex, O'Brien, Darragh, O'Connor, Daniel, O'Donnell, Denise, Ogg, Graham, Overend, Lauren, Park, Inhye, Pavord, Ian, Peng, Yanchun, Penkava, Frank, Pereira Pinho, Mariana, Perez, Elena, Pollard, Andrew, Powrie, Fiona, Psaila, Bethan, Quan, T Phuong, Repapi, Emmanouela, Revale, Santiago, Silva-Reyes, Laura, Richard, Jean-Baptiste, Rich-Griffin, Charlotte, Ritter, Thomas, Rollier, Christine, Rowland, Matthew, Ruehle, Fabian, Salio, Mariolina, Sansom, Stephen Nicholas, Sanches Peres, Raphael, Santos Delgado, Alberto, Sauka-Spengler, Tatjana, Schwessinger, Ron, Scozzafava, Giuseppe, Screaton, Gavin, Seigal, Anna, Semple, Malcolm, Sergeant, Martin, Simoglou Karali, Christina, Sims, David, Skelly, Donal, Slawinski, Hubert, Sobrinodiaz, Alberto, Sousos, Nikolaos, Stafford, Lizzie, Stockdale, Lisa, Strickland, Marie, Sumray, Otto, Sun, Bo, Taylor, Chelsea, Taylor, Stephen, Taylor, Adan, Thongjuea, Supat, Thraves, Hannah, Todd, John, Tomic, Adriana, Tong, Orion, Trebes, Amy, Trzupek, Dominik, Tucci, Felicia Anna, Turtle, Lance, Udalova, Irina, Uhlig, Holm, van Grinsven, Erinke, Vendrell, Iolanda, Verheul, Marije, Voda, Alexandru, Wang, Guanlin, Wang, Lihui, Wang, Dapeng, Watkinson, Peter, Watson, Robert, Weinberger, Michael, Whalley, Justin, Witty, Lorna, Wray, Katherine, Xue, Luzheng, Yuen Yeung, Hing, Yin, Zixi, Young, Rebecca, Youngs, Jonathan, Zhang, Ping, Zurke, Yasemin-Xiomara, Banning, Adrian, Antonopoulos, Alexios, Bajaj, Amrita, Kelion, Andrew, Deshpande, Aparna, Kardos, Attila, Hudson, Benjamin, Koo, Bon-Kwon, Shirodaria, Cheerag, Xie, Cheng, Kotanidis, Christos, Mahon, Ciara, Berry, Colin, Adlam, David, Newby, David, Connolly, Derek, Scaletta, Diane, Alexander, Donna, Nicol, Ed, McAlindon, Elisa, Oikonomou, Evangelos, Pugliese, Francesca, Pontone, Gianluca, Benedetti, Giulia, He, Guo-Wei, West, Henry, Kondo, Hidekazu, Benedek, Imre, Das, Intrajeet, Deanfield, John, Graby, John, Greenwood, John, Rodrigues, Jonathan, Ge, Junbo, Channon, Keith, Fabritz, Larissa, Fan, Li-Juan, Kingham, Lucy, Guglielmo, Marco, Lyasheva, Maria, Schmitt, Matthias, Beer, Meinrad, Anderson, Michelle, Desai, Milind, Marwan, Mohamed, Takahashi, Naohiko, Mehta, Nehal, Dai, Neng, Screaton, Nicholas, Sabharwal, Nikant, Maurovich-Horvat, Pál, Rao, Praveen, Kotronias, Rafail, Kharbanda, Rajesh, Preston, Rebecca, Wood, Richard, Blankstein, Ron, Rajani, Ronak, Mirsadraee, Saeed, Munir, Shahzad, Thomas, Sheena, Neubauer, Stefan, Klömpken, Steffen, Petersen, Steffen, Achenbach, Stephan, Anthony, Susan, Mak, Sze, Mittal, Tarun, Benedek, Theodora, Sharma, Vinoda, Lin, Wen-Hua, Kotanidis, Christos P, Rodrigues, Jonathan C L, O’Connor, Daniel, Siddique, Muhammad, Lockstone, Helen, Oikonomou, Evangelos K, Badi, Ileana, Lumley, Sheila F, Constantinides, Bede, Sanderson, Nicholas, Rodger, Gillian, Chau, Kevin K, Lodge, Archie, Tsakok, Maria, Gleeson, Fergus, Indrajeet, Das, Hudson, Benjamin J, Srivastava, Vivek, Farid, Shakil, Krasopoulos, George, Sayeed, Rana, Newby, David E, Channon, Keith M, and Antoniades, Charalambos

Published
2022
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7. Species‐level, metagenomic and proteomic analysis of microbe‐immune interactions in severe asthma.

Author

Jabeen, Maisha F., Sanderson, Nicholas D., Tinè, Mariaenrica, Donachie, Gillian, Barber, Clair, Azim, Adnan, Lau, Laurie C. K., Brown, Thomas, Pavord, Ian D., Chauhan, Anoop, Klenerman, Paul, Street, Teresa L., Marchi, Emanuele, Howarth, Peter H., and Hinks, Timothy S. C.

Subjects
*BASIC proteins, *NASAL irrigation, *INFLAMMATORY mediators, *MICROBIAL diversity, *BAYESIAN analysis, *MYCOPLASMA pneumoniae infections
Abstract

Background Methods Results Conclusions The airway microbiome in severe asthma has not been characterised at species‐level by metagenomic sequencing, nor have the relationships between specific species and mucosal immune responses in ‘type‐2 low’, neutrophilic asthma been defined. We performed an integrated species‐level metagenomic data with inflammatory mediators to characterise prevalence of dominant potentially pathogenic organisms and host immune responses.Sputum and nasal lavage samples were analysed using long‐read metagenomic sequencing with Nanopore and qPCR in two cross‐sectional adult severe asthma cohorts, Wessex (n = 66) and Oxford (n = 30). We integrated species‐level data with clinical parameters and 39 selected airway proteins measured by immunoassay and O‐link.The sputum microbiome in health and mild asthma displayed comparable microbial diversity. By contrast, 23% (19/81) of severe asthma microbiomes were dominated by a single respiratory pathogen, namely H. influenzae (n = 10), M. catarrhalis (n = 4), S. pneumoniae (n = 4) and P. aeruginosa (n = 1). Neutrophilic asthma was associated with H. influenzae, M. catarrhalis, S. pneumoniae and T. whipplei with elevated type‐1 cytokines and proteases; eosinophilic asthma with higher M. catarrhalis, but lower H. influenzae, and S. pneumoniae abundance. H. influenzae load correlated with Eosinophil Cationic Protein, elastase and IL‐10. R. mucilaginosa associated positively with IL‐6 and negatively with FGF. Bayesian network analysis also revealed close and distinct relationships of H. influenzae and M. catarrhalis with type‐1 airway inflammation. The microbiomes and cytokine milieu were distinct between upper and lower airways.This species‐level integrated analysis reveals central, but distinct associations between potentially pathogenic bacteria and airways inflammation in severe asthma. [ABSTRACT FROM AUTHOR]

Published
2024
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8. Long-read sequencing for fast and robust identification of correct genome-edited alleles: PCR-based and Cas9 capture methods

Author

McCabe, Christopher V., primary, Price, Peter D., additional, Codner, Gemma F., additional, Allan, Alasdair J., additional, Caulder, Adam, additional, Christou, Skevoulla, additional, Loeffler, Jorik, additional, Mackenzie, Matthew, additional, Malzer, Elke, additional, Mianné, Joffrey, additional, Nowicki, Krystian J., additional, O’Neill, Edward J., additional, Pike, Fran J., additional, Hutchison, Marie, additional, Petit-Demoulière, Benoit, additional, Stewart, Michelle E., additional, Gates, Hilary, additional, Wells, Sara, additional, Sanderson, Nicholas D., additional, and Teboul, Lydia, additional

Published
2024
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10. Cell-binding IgM in CSF is distinctive of multiple sclerosis and targets the iron transporter SCARA5

Author

Callegari, Ilaria, primary, Oechtering, Johanna, additional, Schneider, Mika, additional, Perriot, Sylvain, additional, Mathias, Amandine, additional, Voortman, Margarete M, additional, Cagol, Alessandro, additional, Lanner, Ulrike, additional, Diebold, Martin, additional, Holdermann, Sebastian, additional, Kreiner, Victor, additional, Becher, Burkhard, additional, Granziera, Cristina, additional, Junker, Andreas, additional, Du Pasquier, Renaud, additional, Khalil, Michael, additional, Kuhle, Jens, additional, Kappos, Ludwig, additional, Sanderson, Nicholas S R, additional, and Derfuss, Tobias, additional

Published
2023
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11. B cell depletion attenuates CD27 signaling of T helper cells in multiple sclerosis

Author

Ulutekin, Can, primary, Galli, Edoardo, additional, Schreiner, Bettina, additional, Khademi, Mohsen, additional, Callegari, Ilaria, additional, Piehl, Fredrik, additional, Sanderson, Nicholas, additional, Kirschenbaum, Daniel, additional, Mundt, Sarah, additional, Filippi, Massimo, additional, Furlan, Roberto, additional, Olsson, Tomas, additional, Derfuss, Tobias, additional, Ingelfinger, Florian, additional, and Becher, Burkhard, additional

Published
2023
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13. Nanopore sequencing of influenza A and B in Oxfordshire and the United Kingdom, 2022-23

Author

Cane, Jennifer, primary, Sanderson, Nicholas, additional, Barnett, Sophie, additional, Vaughan, Ali, additional, Pott, Megan, additional, Kapel, Natalia, additional, Morgan, Marcus, additional, Jesuthasan, Gerald, additional, Samuel, Reggie, additional, Ehsaan, Muhammad, additional, Boothe, Hugh, additional, Haduli, Eric, additional, Studley, Ruth, additional, Rourke, Emma, additional, Diamond, Ian, additional, Fowler, Tom, additional, Watson, Conall, additional, Stoesser, Nicole, additional, Walker, Ann Sarah, additional, Street, Teresa, additional, and Eyre, David William, additional

Published
2023
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14. Determination of the genetic mechanisms responsible for generating diversity in the cattle NK cell receptor repertoire

Author

Sanderson, Nicholas, Skinner, Mike, and Hammond, John

Subjects
610
Abstract

Cattle have expanded the KIR gene repertoire, a polymorphic and polygenic im- munoglobulin family that encode Natural Killer cell receptors specific to MHC class I ligands. In humans, KIR are important mediators of innate immunity to viral pathogens such as HCV and HIV, and there is potential for exploiting cattle KIR diversity as a means of improving animal health. Cattle KIR expansion has occurred independently to humans, the result is a cattle KIR haplotype (CKH) with a completely different gene content. Successful sequencing and assembly of the CKH using whole genome techniques has failed. To interrogate cattle KIR, their function and comparative evolution, the content of a CKH must be estab- lished, then the extent of polymorphism and gene presence/absence variation can be studied. In this project the first CKH has been sequenced and assembled using second generation sequencing of BAC clones. This has provided a reference sequence for whole genome sequence data to be aligned revealing the KIR content of different Bovidae species, including the aurochs, the ancestor to all domesticated cattle. Furthermore genome capture and enrichment was performed to determine polymorphic and polygenic KIR variation within 24 different cattle genomes. The sheep KIR haplotype (SKH) was sequenced using PacBio of BAC clones to enable comparative analysis with cattle. The CKH has expanded through block duplications resulting in 16 discrete KIR loci. The haplotype is dominated by functional inhibitory receptor genes and the attenuated remains of activating KIR. Predicted similarity between au- rochs and modern CKH suggests KIR blocks expanded through natural selection and not artificial selection generated through centuries of domestication. Com- parative analysis of the SKH and CKH reveals that sheep have independently expanded at least five of the shared KIR that cattle have expanded. Cattle KIR are extremely polymorphic, with diversity focused within the Ig domains, regions predicted to interact with ligand.

Published
2014
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15. Cell-binding IgM in CSF is distinctive of multiple sclerosis and targets the iron transporter SCARA5.

Author

Callegari, Ilaria, Oechtering, Johanna, Schneider, Mika, Perriot, Sylvain, Mathias, Amandine, Voortman, Margarete M, Cagol, Alessandro, Lanner, Ulrike, Diebold, Martin, Holdermann, Sebastian, Kreiner, Victor, Becher, Burkhard, Granziera, Cristina, Junker, Andreas, Pasquier, Renaud Du, Khalil, Michael, Kuhle, Jens, Kappos, Ludwig, Sanderson, Nicholas S R, and Derfuss, Tobias

Subjects
IMMUNOGLOBULIN M, MULTIPLE sclerosis, IRON, CELL surface antigens, RECOMBINANT antibodies, CELL migration
Abstract

Intrathecal IgM production in multiple sclerosis is associated with a worse disease course. To investigate pathogenic relevance of autoreactive IgM in multiple sclerosis, CSF from two independent cohorts, including multiple sclerosis patients and controls, were screened for antibody binding to induced pluripotent stem cell-derived neurons and astrocytes, and a panel of CNS-related cell lines. IgM binding to a primitive neuro-ectodermal tumour cell line discriminated 10% of multiple sclerosis donors from controls. Transcriptomes of single IgM producing CSF B cells from patients with cell-binding IgM were sequenced and used to produce recombinant monoclonal antibodies for characterization and antigen identification. We produced five cell-binding recombinant IgM antibodies, of which one, cloned from an HLA-DR + plasma-like B cell, mediated antigen-dependent complement activation. Immunoprecipitation and mass spectrometry, and biochemical and transcriptome analysis of the target cells identified the iron transport scavenger protein SCARA5 as the antigen target of this antibody. Intrathecal injection of a SCARA5 antibody led to an increased T cell infiltration in an experimental autoimmune encephalomyelitis (EAE) model. CSF IgM might contribute to CNS inflammation in multiple sclerosis by binding to cell surface antigens like SCARA5 and activating complement, or by facilitating immune cell migration into the brain. [ABSTRACT FROM AUTHOR]

Published
2024
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17. An integrative study of differing relational patterns produced around the experience of disappointment : theoretical and clinical implications of the distinctive significance and nature of the role of disappointment in the schizoid and depressive processes during childhood development

Author

Sanderson, Nicholas Andrew

Subjects
150
Abstract

The subject of this thesis is the child's experience of the disappointment of its wishes during the early, most formative years of its psychological development. This is a common area of study in psychoanalytic developmental theories and a range of these established understandings will be discussed. My research on the child's experience of disappointment, which is presented in the context of these previous theories, endeavours to be original, however, by attempting to establish whether or not the experience is, in the context of the Kleinian object relational understanding of childhood development, significant in a way that has yet to be fully considered. In order to research whether my particular arguments, as to the importance of a child's disappointment, might be valid or not, I firstly explore the experience from the perspective of the relevant psychoanalytical literature on child developmental theory. From this position, I am then able to present my own series of theoretical arguments, and it is from these that a set of hypotheses, about the meaning of disappointment in childhood development, are then able to be proposed. Following this, the thesis describes my examination of these hypotheses by some preliminary clinical research. The overall findings of this research are then presented and applied in support of my theoretical arguments.

Published
2010

18. GM-CSF and CXCR4 define a T helper cell signature in multiple sclerosis

Author

Galli, Edoardo, Hartmann, Felix J., Schreiner, Bettina, Ingelfinger, Florian, Arvaniti, Eirini, Diebold, Martin, Mrdjen, Dunja, van der Meer, Franziska, Krieg, Carsten, Nimer, Faiez Al, Sanderson, Nicholas, Stadelmann, Christine, Khademi, Mohsen, Piehl, Fredrik, Claassen, Manfred, Derfuss, Tobias, Olsson, Tomas, and Becher, Burkhard

Published
2019
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21. Nomenclature for the KIR of non-human species

Author

Robinson, James, Guethlein, Lisbeth A., Maccari, Giuseppe, Blokhuis, Jeroen, Bimber, Benjamin N., de Groot, Natasja G., Sanderson, Nicholas D., Abi-Rached, Laurent, Walter, Lutz, Bontrop, Ronald E., Hammond, John A., Marsh, Steven G. E., and Parham, Peter

Published
2018
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22. Data from Antiglioma Immunological Memory in Response to Conditional Cytotoxic/Immune-Stimulatory Gene Therapy: Humoral and Cellular Immunity Lead to Tumor Regression

Author

Ghulam Muhammad, A.K.M., primary, Candolfi, Marianela, primary, King, Gwendalyn D., primary, Yagiz, Kader, primary, Foulad, David, primary, Mineharu, Yohei, primary, Kroeger, Kurt M., primary, Treuer, Katherine A., primary, Nichols, W. Stephen, primary, Sanderson, Nicholas S., primary, Yang, Jieping, primary, Khayznikov, Maksim, primary, Van Rooijen, Nico, primary, Lowenstein, Pedro R., primary, and Castro, Maria G., primary

Published
2023
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23. Supplementary Data from Antiglioma Immunological Memory in Response to Conditional Cytotoxic/Immune-Stimulatory Gene Therapy: Humoral and Cellular Immunity Lead to Tumor Regression

Author

Ghulam Muhammad, A.K.M., primary, Candolfi, Marianela, primary, King, Gwendalyn D., primary, Yagiz, Kader, primary, Foulad, David, primary, Mineharu, Yohei, primary, Kroeger, Kurt M., primary, Treuer, Katherine A., primary, Nichols, W. Stephen, primary, Sanderson, Nicholas S., primary, Yang, Jieping, primary, Khayznikov, Maksim, primary, Van Rooijen, Nico, primary, Lowenstein, Pedro R., primary, and Castro, Maria G., primary

Published
2023
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25. Natalizumab in cerebrospinal fluid and breastmilk of patients with multiple sclerosis

Author

Callegari, Ilaria, primary, Schneider, Mika, additional, Aebischer, Vera, additional, Voortman, Margarete M., additional, Proschmann, Undine, additional, Ziemssen, Tjalf, additional, Lindberg, Raija, additional, Fischer-Barnicol, Bettina, additional, Khalil, Michael, additional, Kappos, Ludwig, additional, Kuhle, Jens, additional, Sanderson, Nicholas S.R., additional, and Derfuss, Tobias, additional

Published
2023
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27. Constructing custom-made radiotranscriptomic signatures of vascular inflammation from routine CT angiograms: a prospective outcomes validation study in COVID-19

Author

Kotanidis, Christos P, primary, Xie, Cheng, additional, Alexander, Donna, additional, Rodrigues, Jonathan C L, additional, Burnham, Katie, additional, Mentzer, Alexander, additional, O’Connor, Daniel, additional, Knight, Julian, additional, Siddique, Muhammad, additional, Lockstone, Helen, additional, Thomas, Sheena, additional, Kotronias, Rafail, additional, Oikonomou, Evangelos K, additional, Badi, Ileana, additional, Lyasheva, Maria, additional, Shirodaria, Cheerag, additional, Lumley, Sheila F, additional, Constantinides, Bede, additional, Sanderson, Nicholas, additional, Rodger, Gillian, additional, Chau, Kevin K, additional, Lodge, Archie, additional, Tsakok, Maria, additional, Gleeson, Fergus, additional, Adlam, David, additional, Rao, Praveen, additional, Indrajeet, Das, additional, Deshpande, Aparna, additional, Bajaj, Amrita, additional, Hudson, Benjamin J, additional, Srivastava, Vivek, additional, Farid, Shakil, additional, Krasopoulos, George, additional, Sayeed, Rana, additional, Ho, Ling-Pei, additional, Neubauer, Stefan, additional, Newby, David E, additional, Channon, Keith M, additional, Deanfield, John, additional, Antoniades, Charalambos, additional, Ahern, David J, additional, Ai, Zhichao, additional, Ainsworth, Mark, additional, Allan, Chris, additional, Allcock, Alice, additional, Angus, Brian, additional, Ansari, M Azim, additional, Arancibia-Cárcamo, Carolina, additional, Aschenbrenner, Dominik, additional, Attar, Moustafa, additional, Baillie, J Kenneth, additional, Barnes, Eleanor, additional, Bashford-Rogers, Rachael, additional, Bashyal, Archana, additional, Beer, Sally, additional, Berridge, Georgina, additional, Beveridge, Amy, additional, Bibi, Sagida, additional, Bicanic, Tihana, additional, Blackwell, Luke, additional, Bowness, Paul, additional, Brent, Andrew, additional, Brown, Andrew, additional, Broxholme, John, additional, Buck, David, additional, Byrne, Helen, additional, Camara, Susana, additional, Ferreira, Ivan Candido, additional, Charles, Philip, additional, Chen, Wentao, additional, Chen, Yi-Ling, additional, Chong, Amanda, additional, Clutterbuck, Elizabeth, additional, Coles, Mark, additional, Conlon, Christopher, additional, Cornall, Richard, additional, Cribbs, Adam, additional, Curion, Fabiola, additional, Davenport, Emma, additional, Davidson, Neil, additional, Davis, Simon, additional, Dendrou, Calliope, additional, Dequaire, Julie, additional, Dib, Lea, additional, Docker, James, additional, Dold, Christina, additional, Dong, Tao, additional, Downes, Damien, additional, Drakesmith, Hal, additional, Dunachie, Susanna, additional, Duncan, David, additional, Eijsbouts, Chris, additional, Esnouf, Robert, additional, Espinosa, Alexis, additional, Etherington, Rachel, additional, Fairfax, Benjamin, additional, Fairhead, Rory, additional, Fang, Hai, additional, Fassih, Shayan, additional, Felle, Sally, additional, Fernandez Mendoza, Maria, additional, Ferreira, Ricardo, additional, Fischer, Roman, additional, Foord, Thomas, additional, Forrow, Aden, additional, Frater, John, additional, Fries, Anastasia, additional, Gallardo Sanchez, Veronica, additional, Garner, Lucy, additional, Geeves, Clementine, additional, Georgiou, Dominique, additional, Godfrey, Leila, additional, Golubchik, Tanya, additional, Gomez Vazquez, Maria, additional, Green, Angie, additional, Harper, Hong, additional, Harrington, Heather, additional, Heilig, Raphael, additional, Hester, Svenja, additional, Hill, Jennifer, additional, Hinds, Charles, additional, Hird, Clare, additional, Hoekzema, Renee, additional, Hollis, Benjamin, additional, Hughes, Jim, additional, Hutton, Paula, additional, Jackson-Wood, Matthew, additional, Jainarayanan, Ashwin, additional, James-Bott, Anna, additional, Jansen, Kathrin, additional, Jeffery, Katie, additional, Jones, Elizabeth, additional, Jostins, Luke, additional, Kerr, Georgina, additional, Kim, David, additional, Klenerman, Paul, additional, Kumar, Vinod, additional, Kumar Sharma, Piyush, additional, Kurupati, Prathiba, additional, Kwok, Andrew, additional, Lee, Angela, additional, Linder, Aline, additional, Lockett, Teresa, additional, Lonie, Lorne, additional, Lopopolo, Maria, additional, Lukoseviciute, Martyna, additional, Luo, Jian, additional, Marinou, Spyridoula, additional, Marsden, Brian, additional, Martinez, Jose, additional, Matthews, Philippa, additional, Mazurczyk, Michalina, additional, McGowan, Simon, additional, McKechnie, Stuart, additional, Mead, Adam, additional, Mi, Yuxin, additional, Monaco, Claudia, additional, Montadon, Ruddy, additional, Napolitani, Giorgio, additional, Nassiri, Isar, additional, Novak, Alex, additional, O'Brien, Darragh, additional, O'Connor, Daniel, additional, O'Donnell, Denise, additional, Ogg, Graham, additional, Overend, Lauren, additional, Park, Inhye, additional, Pavord, Ian, additional, Peng, Yanchun, additional, Penkava, Frank, additional, Pereira Pinho, Mariana, additional, Perez, Elena, additional, Pollard, Andrew, additional, Powrie, Fiona, additional, Psaila, Bethan, additional, Quan, T Phuong, additional, Repapi, Emmanouela, additional, Revale, Santiago, additional, Silva-Reyes, Laura, additional, Richard, Jean-Baptiste, additional, Rich-Griffin, Charlotte, additional, Ritter, Thomas, additional, Rollier, Christine, additional, Rowland, Matthew, additional, Ruehle, Fabian, additional, Salio, Mariolina, additional, Sansom, Stephen Nicholas, additional, Sanches Peres, Raphael, additional, Santos Delgado, Alberto, additional, Sauka-Spengler, Tatjana, additional, Schwessinger, Ron, additional, Scozzafava, Giuseppe, additional, Screaton, Gavin, additional, Seigal, Anna, additional, Semple, Malcolm, additional, Sergeant, Martin, additional, Simoglou Karali, Christina, additional, Sims, David, additional, Skelly, Donal, additional, Slawinski, Hubert, additional, Sobrinodiaz, Alberto, additional, Sousos, Nikolaos, additional, Stafford, Lizzie, additional, Stockdale, Lisa, additional, Strickland, Marie, additional, Sumray, Otto, additional, Sun, Bo, additional, Taylor, Chelsea, additional, Taylor, Stephen, additional, Taylor, Adan, additional, Thongjuea, Supat, additional, Thraves, Hannah, additional, Todd, John, additional, Tomic, Adriana, additional, Tong, Orion, additional, Trebes, Amy, additional, Trzupek, Dominik, additional, Tucci, Felicia Anna, additional, Turtle, Lance, additional, Udalova, Irina, additional, Uhlig, Holm, additional, van Grinsven, Erinke, additional, Vendrell, Iolanda, additional, Verheul, Marije, additional, Voda, Alexandru, additional, Wang, Guanlin, additional, Wang, Lihui, additional, Wang, Dapeng, additional, Watkinson, Peter, additional, Watson, Robert, additional, Weinberger, Michael, additional, Whalley, Justin, additional, Witty, Lorna, additional, Wray, Katherine, additional, Xue, Luzheng, additional, Yuen Yeung, Hing, additional, Yin, Zixi, additional, Young, Rebecca, additional, Youngs, Jonathan, additional, Zhang, Ping, additional, Zurke, Yasemin-Xiomara, additional, Banning, Adrian, additional, Antonopoulos, Alexios, additional, Kelion, Andrew, additional, Kardos, Attila, additional, Hudson, Benjamin, additional, Koo, Bon-Kwon, additional, Kotanidis, Christos, additional, Mahon, Ciara, additional, Berry, Colin, additional, Newby, David, additional, Connolly, Derek, additional, Scaletta, Diane, additional, Nicol, Ed, additional, McAlindon, Elisa, additional, Oikonomou, Evangelos, additional, Pugliese, Francesca, additional, Pontone, Gianluca, additional, Benedetti, Giulia, additional, He, Guo-Wei, additional, West, Henry, additional, Kondo, Hidekazu, additional, Benedek, Imre, additional, Das, Intrajeet, additional, Graby, John, additional, Greenwood, John, additional, Rodrigues, Jonathan, additional, Ge, Junbo, additional, Channon, Keith, additional, Fabritz, Larissa, additional, Fan, Li-Juan, additional, Kingham, Lucy, additional, Guglielmo, Marco, additional, Schmitt, Matthias, additional, Beer, Meinrad, additional, Anderson, Michelle, additional, Desai, Milind, additional, Marwan, Mohamed, additional, Takahashi, Naohiko, additional, Mehta, Nehal, additional, Dai, Neng, additional, Screaton, Nicholas, additional, Sabharwal, Nikant, additional, Maurovich-Horvat, Pál, additional, Kharbanda, Rajesh, additional, Preston, Rebecca, additional, Wood, Richard, additional, Blankstein, Ron, additional, Rajani, Ronak, additional, Mirsadraee, Saeed, additional, Munir, Shahzad, additional, Klömpken, Steffen, additional, Petersen, Steffen, additional, Achenbach, Stephan, additional, Anthony, Susan, additional, Mak, Sze, additional, Mittal, Tarun, additional, Benedek, Theodora, additional, Sharma, Vinoda, additional, and Lin, Wen-Hua, additional

Published
2022
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28. High-dimensional immune profiling identifies a biomarker to monitor dimethyl fumarate response in multiple sclerosis

Author

Diebold, Martin, primary, Galli, Edoardo, additional, Kopf, Andreas, additional, Sanderson, Nicholas S R, additional, Callegari, Ilaria, additional, Benkert, Pascal, additional, Gonzalo Núñez, Nicolás, additional, Ingelfinger, Florian, additional, Herms, Stefan, additional, Cichon, Sven, additional, Kappos, Ludwig, additional, Kuhle, Jens, additional, Becher, Burkhard, additional, Claassen, Manfred, additional, and Derfuss, Tobias, additional

Published
2022
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30. Potent neutralization by monoclonal human IgM against SARS‐CoV‐2 is impaired by class switch

Author

Callegari, Ilaria, primary, Schneider, Mika, additional, Berloffa, Giuliano, additional, Mühlethaler, Tobias, additional, Holdermann, Sebastian, additional, Galli, Edoardo, additional, Roloff, Tim, additional, Boss, Renate, additional, Infanti, Laura, additional, Khanna, Nina, additional, Egli, Adrian, additional, Buser, Andreas, additional, Zimmer, Gert, additional, Derfuss, Tobias, additional, and Sanderson, Nicholas S R, additional

Published
2022
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32. Identifying Bacterial Airways Infection in Stable Severe Asthma Using Oxford Nanopore Sequencing Technologies

Author

Jabeen, Maisha F., primary, Sanderson, Nicholas D., additional, Foster, Dona, additional, Crook, Derrick W., additional, Cane, Jennifer L., additional, Borg, Catherine, additional, Connolly, Clare, additional, Thulborn, Samantha, additional, Pavord, Ian D., additional, Klenerman, Paul, additional, Street, Teresa L., additional, and Hinks, Timothy S. C., additional

Published
2022
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33. Clinical Metagenomic Sequencing for Species Identification and Antimicrobial Resistance Prediction in Orthopedic Device Infection

Author

Street, Teresa L., primary, Sanderson, Nicholas D., additional, Kolenda, Camille, additional, Kavanagh, James, additional, Pickford, Hayleah, additional, Hoosdally, Sarah, additional, Cregan, Jack, additional, Taunt, Carol, additional, Jones, Emma, additional, Oakley, Sarah, additional, Atkins, Bridget L., additional, Dudareva, Maria, additional, McNally, Martin A., additional, O’Grady, Justin, additional, Crook, Derrick W., additional, and Eyre, David W., additional

Published
2022
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34. Immunological Predictors of Dimethyl Fumarate-Induced Lymphopenia

Author

Diebold, Martin, Galli, Edoardo, Kopf, Andreas, Sanderson, Nicholas, Callegari, Ilaria, Ingelfinger, Florian, Gonzalo Núñez, Nicolás, Benkert, Pascal, Kappos, Ludwig, Kuhle, Jens, Becher, Burkhard, Claassen, Manfred, and Derfuss, Tobias

Abstract

Treatment with dimethyl fumarate (DMF) leads to lymphopenia and infectious complications in a subset of patients with multiple sclerosis (MS). Here, we aimed to reveal immune markers of DMF-associated lymphopenia. This prospective observational study longitudinally assessed 31 individuals with MS by single-cell mass cytometry before and after 12 and 48 weeks of DMF therapy. Employing a neural network-based representation learning approach, we identified a CCR4-expressing T helper cell population negatively associated with relevant lymphopenia. CCR4-expressing T helper cells represent a candidate prognostic biomarker for the development of relevant lymphopenia in patients undergoing DMF treatment. ANN NEUROL 2022, Annals of Neurology, 91 (5), ISSN:0364-5134, ISSN:1531-8249

Published
2022
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36. Chronic Bacterial Airways Infection in Severe Asthma

Author

Jabeen, Maisha, primary, Sanderson, Nicholas, additional, Barber, Clair, additional, Lau, Laurie C K, additional, Pavord, Ian D, additional, Chauhan, Anoop, additional, Klenerman, Paul, additional, Street, Teresa, additional, Howarth, Peter H, additional, and Hinks, Timothy S C, additional

Published
2022
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37. Rapid turnaround multiplex sequencing of SARS-CoV-2: comparing tiling amplicon protocol performance

Author

Constantinides, Bede, primary, Webster, Hermione, additional, Gentry, Jessica, additional, Bastable, Jasmine, additional, Dunn, Laura, additional, Oakley, Sarah, additional, Swann, Jeremy, additional, Sanderson, Nicholas D, additional, Fowler, Philip W, additional, Ma, Geoffrey, additional, Rodger, Gillian, additional, Barrett, Lucinda, additional, Jeffery, Katie JM, additional, Peto, Timothy EA JM, additional, Stoesser, Nicole, additional, Street, Teresa L, additional, and Crook, Derrick W, additional

Published
2022
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39. Epidemiological data and genome sequencing reveals that nosocomial transmission of SARS-CoV-2 is underestimated and mostly mediated by a small number of highly infectious individuals

Author

Lumley, Sheila F, primary, Constantinides, Bede, additional, Sanderson, Nicholas, additional, Rodger, Gillian, additional, Street, Teresa L, additional, Swann, Jeremy, additional, Chau, Kevin K, additional, O'Donnell, Denise, additional, Warren, Fiona, additional, Hoosdally, Sarah, additional, O'Donnell, Anne-Marie, additional, Walker, Timothy M, additional, Stoesser, Nicole E, additional, Butcher, Lisa, additional, Peto, Tim EA, additional, Crook, Derrick W, additional, Jeffery, Katie, additional, Matthews, Philippa C, additional, and Eyre, David W, additional

Published
2021
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42. Clinical Metagenomic Sequencing for Species Identification and Antimicrobial Resistance Prediction in Orthopaedic Device Infection

Author

Street, Teresa L., primary, Sanderson, Nicholas D., additional, Kolenda, Camille, additional, Kavanagh, James, additional, Pickford, Hayleah, additional, Hoosdally, Sarah, additional, Cregan, Jack, additional, Taunt, Carol, additional, Jones, Emma, additional, Oakley, Sarah, additional, Atkins, Bridget L., additional, Dudareva, Maria, additional, McNally, Martin A., additional, O’Grady, Justin, additional, Crook, Derrick W., additional, and Eyre, David W., additional

Published
2021
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43. Nanopore metagenomic sequencing of influenza virus directly from respiratory samples: diagnosis, drug resistance and nosocomial transmission, United Kingdom, 2018/19 influenza season

Author

Xu, Yifei, primary, Lewandowski, Kuiama, additional, Downs, Louise O, additional, Kavanagh, James, additional, Hender, Thomas, additional, Lumley, Sheila, additional, Jeffery, Katie, additional, Foster, Dona, additional, Sanderson, Nicholas D, additional, Vaughan, Ali, additional, Morgan, Marcus, additional, Vipond, Richard, additional, Carroll, Miles, additional, Peto, Timothy, additional, Crook, Derrick, additional, Walker, A Sarah, additional, Matthews, Philippa C, additional, and Pullan, Steven T, additional

Published
2021
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44. Observational Cohort Study on the Incidence of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) Infection and B.1.1.7 Variant Infection in Healthcare Workers by Antibody and Vaccination Status.

Author

Lumley, Sheila F, Rodger, Gillian, Constantinides, Bede, Sanderson, Nicholas, Chau, Kevin K, Street, Teresa L, O'Donnell, Denise, Howarth, Alison, Hatch, Stephanie B, Marsden, Brian D, Cox, Stuart, James, Tim, Warren, Fiona, Peck, Liam J, Ritter, Thomas G, Toledo, Zoe de, Warren, Laura, Axten, David, Cornall, Richard J, and Jones, E Yvonne

Subjects
NATURAL immunity, COVID-19, IMMUNOGLOBULINS, SCIENTIFIC observation, SEQUENCE analysis, CONFIDENCE intervals, COVID-19 vaccines, GENETIC variation, DISEASE incidence, ANTIBODY formation, DESCRIPTIVE statistics, POLYMERASE chain reaction, LONGITUDINAL method, POISSON distribution
Abstract

Background Natural and vaccine-induced immunity will play a key role in controlling the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic. SARS-CoV-2 variants have the potential to evade natural and vaccine-induced immunity. Methods In a longitudinal cohort study of healthcare workers (HCWs) in Oxfordshire, United Kingdom, we investigated the protection from symptomatic and asymptomatic polymerase chain reaction (PCR)-confirmed SARS-CoV-2 infection conferred by vaccination (Pfizer-BioNTech BNT162b2, Oxford-AstraZeneca ChAdOx1 nCOV-19) and prior infection (determined using anti-spike antibody status), using Poisson regression adjusted for age, sex, temporal changes in incidence and role. We estimated protection conferred after 1 versus 2 vaccinations and from infections with the B.1.1.7 variant identified using whole genome sequencing. Results In total, 13 109 HCWs participated; 8285 received the Pfizer-BioNTech vaccine (1407 two doses), and 2738 the Oxford-AstraZeneca vaccine (49 two doses). Compared to unvaccinated seronegative HCWs, natural immunity and 2 vaccination doses provided similar protection against symptomatic infection: no HCW vaccinated twice had symptomatic infection, and incidence was 98% lower in seropositive HCWs (adjusted incidence rate ratio 0.02 [95% confidence interval {CI} < .01–.18]). Two vaccine doses or seropositivity reduced the incidence of any PCR-positive result with or without symptoms by 90% (0.10 [95% CI.02–.38]) and 85% (0.15 [95% CI.08–.26]), respectively. Single-dose vaccination reduced the incidence of symptomatic infection by 67% (0.33 [95% CI.21–.52]) and any PCR-positive result by 64% (0.36 [95% CI.26–.50]). There was no evidence of differences in immunity induced by natural infection and vaccination for infections with S-gene target failure and B.1.1.7. Conclusions Natural infection resulting in detectable anti-spike antibodies and 2 vaccine doses both provide robust protection against SARS-CoV-2 infection, including against the B.1.1.7 variant. [ABSTRACT FROM AUTHOR]

Published
2022
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45. Mass Cytometry of CSF Identifies an MS-Associated B-cell Population

Author

Johansson, David, primary, Rauld, Céline, additional, Roux, Julien, additional, Regairaz, Camille, additional, Galli, Edoardo, additional, Callegari, Ilaria, additional, Raad, Layla, additional, Waldt, Annick, additional, Cuttat, Rachel, additional, Roma, Guglielmo, additional, Diebold, Martin, additional, Becher, Burkhard, additional, Kuhle, Jens, additional, Derfuss, Tobias, additional, Carballido, José M., additional, and Sanderson, Nicholas S.R., additional

Published
2021
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47. DNA extraction from primary liquid blood cultures for bloodstream infection diagnosis using whole genome sequencing

Author

Anson, Luke W., Chau, Kevin, Sanderson, Nicholas, Hoosdally, Sarah, Bradley, Phelim, Iqbal, Zamin, Phan, Hang, Foster, Dona, Oakley, Sarah, Morgan, Marcus, Peto, Tim E. A., Crook, Derrick W., and Pankhurst, Louise J.

Subjects
DNA, Bacterial, bacteraemia, whole genome sequencing, Staphylococcus aureus, bloodstream infection, Bacteremia, Microbial Sensitivity Tests, Sequence Analysis, DNA, Disease, Diagnosis and Diagnostics, sepsis, Molecular Diagnostic Techniques, Blood Culture, Catheter-Related Infections, Escherichia coli, Humans, Reagent Kits, Diagnostic, Genome, Bacterial, Research Article
Abstract

Purpose Speed of bloodstream infection diagnosis is vital to reduce morbidity and mortality. Whole genome sequencing (WGS) performed directly from liquid blood culture could provide single-assay species and antibiotic susceptibility prediction; however, high inhibitor and human cell/DNA concentrations limit pathogen recovery. We develop a method for the preparation of bacterial DNA for WGS-based diagnostics direct from liquid blood culture. Methodology We evaluate three commercial DNA extraction kits: BiOstic Bacteraemia, Amplex Hyplex and MolYsis Plus. Differential centrifugation, filtration, selective lysis and solid-phase reversible immobilization bead clean-up are tested to improve human cells/DNA and inhibitor removal. Using WGS (Illumina/MinION), we assess human DNA removal, pathogen recovery, and predict species and antibiotic susceptibility inpositive blood cultures of 44 Gram-negative and 54 Staphylococcus species. Results/Key findings BiOstic kit extractions yield the greatest mean DNA concentration, 94–301 ng µl−1, versus 0–2.5 ng µl−1 using Amplex and MolYsis kits. However, we note higher levels of inhibition (260/280 ratio 0.9–2.1) and human DNA (0.0–4.4×106 copies) in BiOstic extracts. Differential centrifugation (2000 g, 1 min) prior to BiOstic extraction reduces human DNA by 63–89 % with selective lysis minimizing by a further 62 %. Post-extraction bead clean-up lowers inhibition. Overall, 67 % of sequenced samples (Illumina MiSeq) contain 93 % concordance between WGS-based species and susceptibility predictions and clinical diagnosis. If >60 % of sequencing reads are human (7/98 samples) susceptibility prediction becomes compromised. Novel MinION-based WGS (n=9) currently gives rapid species identification but not susceptibility prediction. Conclusion Our method for DNA preparation allows WGS-based diagnosis direct from blood culture bottles, providing species and antibiotic susceptibility prediction in a single assay.

Published
2018

48. Optimized use of Oxford Nanopore flowcells for hybrid assemblies

Author

Lipworth, Samuel, primary, Pickford, Hayleah, additional, Sanderson, Nicholas, additional, Chau, Kevin K., additional, Kavanagh, James, additional, Barker, Leanne, additional, Vaughan, Alison, additional, Swann, Jeremy, additional, Andersson, Monique, additional, Jeffery, Katie, additional, Morgan, Marcus, additional, Peto, Timothy E. A., additional, Crook, Derrick W., additional, Stoesser, Nicole, additional, and Walker, A. Sarah, additional

Published
2020
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49. Multiple novel non-canonically transcribed sub-genomic mRNAs produced by avian coronavirus infectious bronchitis virus

Author

Keep, Sarah, primary, Oade, Michael S., additional, Lidzbarski-Silvestre, Filip, additional, Bentley, Kirsten, additional, Stevenson-Leggett, Phoebe, additional, Freimanis, Graham L., additional, Tennakoon, Chandana, additional, Sanderson, Nicholas, additional, Hammond, John A., additional, Jones, Richard C., additional, Britton, Paul, additional, and Bickerton, Erica, additional

Published
2020
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50. DNA Thermo-Protection Facilitates Whole-Genome Sequencing of Mycobacteria Direct from Clinical Samples

Author

George, Sophie, primary, Xu, Yifei, additional, Rodger, Gillian, additional, Morgan, Marcus, additional, Sanderson, Nicholas D., additional, Hoosdally, Sarah J., additional, Thulborn, Samantha, additional, Robinson, Esther, additional, Rathod, Priti, additional, Walker, A. Sarah, additional, Peto, Timothy E. A., additional, Crook, Derrick W., additional, and Dingle, Kate E., additional

Published
2020
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