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3. Circulating Metabolome and White Matter Hyperintensities in Women and Men

Author

Sliz, Eeva, Shin, Jean, Ahmad, Shahzad, Williams, Dylan M, Frenzel, Stefan, Gauß, Friederike, Harris, Sarah E, Henning, Ann-Kristin, Hernandez, Maria Valdes, Hu, Yi-Han, Jiménez, Beatriz, Sargurupremraj, Muralidharan, Sudre, Carole, Wang, Ruiqi, Wittfeld, Katharina, Yang, Qiong, Wardlaw, Joanna M, Völzke, Henry, Vernooij, Meike W, Schott, Jonathan M, Richards, Marcus, Proitsi, Petroula, Nauck, Matthias, Lewis, Matthew R, Launer, Lenore, Hosten, Norbert, Grabe, Hans J, Ghanbari, Mohsen, Deary, Ian J, Cox, Simon R, Chaturvedi, Nishi, Barnes, Josephine, Rotter, Jerome I, Debette, Stephanie, Ikram, M Arfan, Fornage, Myriam, Paus, Tomas, Seshadri, Sudha, Pausova, Zdenka, and Group, for the NeuroCHARGE Working

Subjects
Epidemiology, Biomedical and Clinical Sciences, Health Sciences, Aging, Neurosciences, Prevention, Aged, Brain, Diabetes Mellitus, Type 2, Female, Humans, Magnetic Resonance Imaging, Male, Metabolome, Middle Aged, White Matter, brain, glucuronic acid, hydroxyphenylpyruvate, lipidomics, lipid ratios, lipids, lysophosphatidylcholines, metabolomics, sphingomyelins, white matter, NeuroCHARGE Working Group, Cardiorespiratory Medicine and Haematology, Clinical Sciences, Public Health and Health Services, Cardiovascular System & Hematology, Cardiovascular medicine and haematology, Clinical sciences, Sports science and exercise
Abstract

BackgroundWhite matter hyperintensities (WMH), identified on T2-weighted magnetic resonance images of the human brain as areas of enhanced brightness, are a major risk factor of stroke, dementia, and death. There are no large-scale studies testing associations between WMH and circulating metabolites.MethodsWe studied up to 9290 individuals (50.7% female, average age 61 years) from 15 populations of 8 community-based cohorts. WMH volume was quantified from T2-weighted or fluid-attenuated inversion recovery images or as hypointensities on T1-weighted images. Circulating metabolomic measures were assessed with mass spectrometry and nuclear magnetic resonance spectroscopy. Associations between WMH and metabolomic measures were tested by fitting linear regression models in the pooled sample and in sex-stratified and statin treatment-stratified subsamples. Our basic models were adjusted for age, sex, age×sex, and technical covariates, and our fully adjusted models were also adjusted for statin treatment, hypertension, type 2 diabetes, smoking, body mass index, and estimated glomerular filtration rate. Population-specific results were meta-analyzed using the fixed-effect inverse variance-weighted method. Associations with false discovery rate (FDR)-adjusted P values (PFDR)

Published
2022

4. Associations of NAFLD with circulating ceramides and impaired glycemia

Author

Gadgil, Meghana D, Sarkar, Monika, Sands, Caroline, Lewis, Matthew R, Herrington, David M, and Kanaya, Alka M

Subjects
Public Health, Biomedical and Clinical Sciences, Nutrition and Dietetics, Health Sciences, Clinical Research, Substance Misuse, Alcoholism, Alcohol Use and Health, Digestive Diseases, Prevention, Women's Health, Nutrition, Liver Disease, 2.1 Biological and endogenous factors, Cardiovascular, Oral and gastrointestinal, Good Health and Well Being, Blood Glucose, Ceramides, Cohort Studies, Female, Humans, Lipidomics, Male, Middle Aged, Non-alcoholic Fatty Liver Disease, NAFLD, South Asian, Type 2 diabetes, Clinical Sciences, Public Health and Health Services, Psychology, Endocrinology & Metabolism, Clinical sciences, Public health, Clinical and health psychology
Abstract

AimDetermine the association of circulating ceramides with NAFLD and glycemic impairment.MethodsSample: 669 participants in the Mediators of Atherosclerosis in South Asians Living in America (MASALA) cohort aged 40-84 years without cardiovascular disease, cirrhosis, or significant alcohol intake.Clinical measuresComputed tomography scans at baseline for hepatic attenuation. Fasting serum specimens at baseline and after 5 years. Lipidomics: LC-MS-based analysis of 19 known ceramide signals.Statistical analysisLinear and logistic regression models of log-transformed ceramides, hepatic attenuation and glucose adjusted for age, sex, calories, study site, BMI, exercise, diet quality, alcohol, saturated fat, lipid-lowering medications and fasting glucose.ResultsAverage age was 55 years, 44% were women, mean BMI was 25.9 kg/m2, and 8% had NAFLD. In adjusted models, Cer(d16:1/20:0) and Cer(d18:1/18:0) were associated with lower mean hepatic attenuation (increased liver fat) (β -4.29; 95% CI [-5.98, -2.59]) and (β -3.40; 95% CI [-5.11, -1.70]), and LacCer(d18:1/16:0) with higher attenuation (β 4.44; 95% CI [2.15, 6.73]). All three ceramides partially mediated the relationship between hepatic attenuation and fasting glucose by 16%, 11% and 5%, respectively, after 5-years.ConclusionsThree circulating ceramides were strongly associated with NAFLD and fasting glucose after 5 years, and partially mediated this association.

Published
2022

5. A Comprehensive Line-Spread Function Error Budget for the Off-Plane Grating Rocket Experiment

Author

Donovan, Benjamin D., McEntaffer, Randall L., Tutt, James H., O'Meara, Bridget C., Grisé, Fabien, Zhang, William W., Biskach, Michael P., Saha, Timo T., Holland, Andrew D., Evan, Daniel, Lewis, Matthew R., Soman, Matthew R., Holland, Karen, Colebrook, David, Cooper, Fraser, and Farn, David

Subjects
Astrophysics - Instrumentation and Methods for Astrophysics
Abstract

The Off-plane Grating Rocket Experiment (OGRE) is a soft X-ray grating spectrometer to be flown on a suborbital rocket. The payload is designed to obtain the highest-resolution soft X-ray spectrum of Capella to date with a resolution goal of $R(\lambda/\Delta\lambda)>2000$ at select wavelengths in its 10--55 Angstrom bandpass of interest. The optical design of the spectrometer realizes a theoretical maximum resolution of $R\approx5000$, but this performance does not consider the finite performance of the individual spectrometer components, misalignments between components, and in-flight pointing errors. These errors all degrade the performance of the spectrometer from its theoretical maximum. A comprehensive line-spread function (LSF) error budget has been constructed for the OGRE spectrometer to identify contributions to the LSF, to determine how each of these affects the LSF, and to inform performance requirements and alignment tolerances for the spectrometer. In this document, the comprehensive LSF error budget for the OGRE spectrometer is presented, the resulting errors are validated via raytrace simulations, and the implications of these results are discussed., Comment: 26 pages, 9 figures, preprint of a manuscript accepted for publication in the Journal of Astronomical Telescopes, Instruments, and Systems (JATIS)

Published
2021

6. Pathobionts in the tumour microbiota predict survival following resection for colorectal cancer

Author

Alexander, James L., Posma, Joram M., Scott, Alasdair, Poynter, Liam, Mason, Sam E., Doria, M. Luisa, Herendi, Lili, Roberts, Lauren, McDonald, Julie A. K., Cameron, Simon, Hughes, David J., Liska, Vaclav, Susova, Simona, Soucek, Pavel, der Sluis, Verena Horneffer-van, Gomez-Romero, Maria, Lewis, Matthew R., Hoyles, Lesley, Woolston, Andrew, Cunningham, David, Darzi, Ara, Gerlinger, Marco, Goldin, Robert, Takats, Zoltan, Marchesi, Julian R., Teare, Julian, and Kinross, James

Published
2023
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7. Metabolome-wide association study on ABCA7 indicates a role of ceramide metabolism in Alzheimer’s disease

Author

Dehghan, Abbas, Pinto, Rui Climaco, Karaman, Ibrahim, Huang, Jian, Durainayagam, Brenan R., Ghanbari, Mohsen, Nazeer, Areesha, Zhong, Qi, Liggi, Sonia, Whiley, Luke, Mustafa, Rima, Kivipelto, Miia, Solomon, Alina, Ngandu, Tiia, Kanekiyo, Takahisa, Aikawa, Tomonori, Radulescu, Carola I., Barnes, Samuel J., Graça, Gonçalo, Chekmeneva, Elena, Camuzeaux, Stephane, Lewis, Matthew R., Kaluarachchi, Manuja R., Ikram, M. Arfan, Holmes, Elaine, Tzoulaki, Ioanna, Matthews, Paul M., Griffin, Julian L., and Elliott, Paul

Published
2022

9. Circulating metabolites and lipids are associated with glycaemic measures in South Asians

Author

Gadgil, Meghana D, Kanaya, Alka M, Sands, Caroline, Lewis, Matthew R, Kandula, Namratha R, and Herrington, David M

Subjects
Medical Biochemistry and Metabolomics, Biomedical and Clinical Sciences, Minority Health, Diabetes, Prevention, Nutrition, Women's Health, 2.4 Surveillance and distribution, Cancer, Stroke, Metabolic and endocrine, Adult, Aged, Aged, 80 and over, Asia, Western, Betaine, Blood Glucose, Carnitine, Chromatography, Liquid, Cohort Studies, Diabetes Mellitus, Diglycerides, Female, Glycated Hemoglobin, Humans, Linear Models, Lipidomics, Logistic Models, Male, Mass Spectrometry, Metabolomics, Middle Aged, Proline, Sphingomyelins, Triglycerides, United States, diabetes, metabolomics, South Asian, Clinical Sciences, Public Health and Health Services, Psychology, Endocrinology & Metabolism, Clinical sciences
Abstract

BackgroundSouth Asians are at higher risk for diabetes (DM) than many other racial/ethnic groups. Circulating metabolites are measurable products of metabolic processes that may explain the aetiology of elevated risk. We characterized metabolites associated with prevalent DM and glycaemic measures in South Asians.MethodsWe included 717 participants from the Mediators of Atherosclerosis in South Asians Living in America (MASALA) study, aged 40-84 years. We used baseline fasting serum for metabolomics and demographic, behavioural, glycaemic data from baseline and at 5 years. We performed LC-MS untargeted metabolomic and lipidomic analysis with targeted integration of known signals. Individual linear and ordinal logistic regression models were adjusted for age, sex, BMI, diet, exercise, alcohol, smoking and family history of DM followed by elastic net regression to identify metabolites most associated with the outcome.ResultsThere were 258 metabolites with detectable signal in >98% of samples. Thirty-four metabolites were associated with prevalent DM in an elastic net model. Predominant metabolites associated with DM were sphingomyelins, proline (OR 15.86; 95% CI 4.72, 53.31) and betaine (OR 0.03; 0.004, 0.14). Baseline tri- and di-acylglycerols [DG (18:0/16:0) (18.36; 11.79, 24.92)] were positively associated with fasting glucose and long-chain acylcarnitines [CAR 26:1 (-0.40; -0.54, -0.27)] were inversely associated with prevalent DM and HbA1c at follow-up.DiscussionA metabolomic signature in South Asians may help determine the unique aetiology of diabetes in this high-risk ethnic group. Future work will externally validate our findings and determine the effects of modifiable risk factors for DM.

Published
2021

13. 1581-P: Circulating Metabolites Are Associated with Glycemic Measures in South Asians

Author

GADGIL, MEGHANA D, SANDS, CAROLINE, LEWIS, MATTHEW R, KANAYA, ALKA M, KANDULA, NAMRATHA R, and HERRINGTON, DAVID M

Subjects
Diabetes, Nutrition, Prevention, Metabolic and endocrine, Cardiovascular, Good Health and Well Being, Medical and Health Sciences, Endocrinology & Metabolism
Abstract

South Asians are at higher risk for diabetes (DM) than many other racial/ethnic groups. Circulating metabolites are measurable products of metabolic processes that may explain the etiology of elevated risk. We characterized metabolites associated with prevalent DM and incident glycemic measures in South Asians. We included 717 participants in the Mediators of Atherosclerosis in South Asians Living in America (MASALA) study, aged 40-84 years. We used baseline fasting serum for metabolomics and demographic, behavioral, glycemic data from baseline and at 5 years. We performed LC-MS untargeted metabolomic and lipidomic analysis with targeted integration of known signals. Individual linear and ordinal logistic regression models were adjusted for age, sex, BMI, diet, exercise, alcohol, smoking and family history of DM followed by elastic net regression to identify metabolites most contributory to the outcome. There were 258 metabolites with detectable signal in >98% of samples. Fifty-nine metabolites were associated with prevalent DM, 32 with fasting glucose and 45 with HbA1c at follow-up [FDR < 0.05]. An elastic net model identified a subset of important metabolites (Table 1). Predominant metabolites associated with glycemic measures in South Asians were sphingomyelins, tri- and di-acylglycerols and carnitines. Future work will externally validate our findings and determine the effects of modifiable risk factors for DM. Disclosure: M.D. Gadgil: None. C. Sands: None. M.R. Lewis: None. A.M. Kanaya: None. N.R. Kandula: None. D.M. Herrington: None. Funding: National Institutes of Health (1K23DK119404-01A1)

Published
2020

14. Metabolomics research group brings the power of TIMS to bear on understanding human health and disease: How utilising trapped ion mobility spectrometry (TIMS) has enhanced the use of mass spectrometry (MS) for accurate metabolite analysis at the Novo Nordisk Foundation Center for Basic Metabolic Research (CBMR) to increase our understanding of the metabolic processes in human health and disease

Author

Moritz, Thomas and Lewis, Matthew R.

Subjects
Metabolites -- Usage, Spectrum analysis -- Usage, Business, Chemicals, plastics and rubber industries, Engineering and manufacturing industries, Business, international
Abstract

Metabolomics offers the opportunity to profile major genomic and epigenomic pathways, making it a crucial step in many areas of life science research. From a clinical standpoint, metabolomics allows scientists [...]

Published
2023

18. SARS-CoV-2 Omicron-B.1.1.529 leads to widespread escape from neutralizing antibody responses

Author

Conlon, Christopher, Deeks, Alexandra S., Frater, John, Frending, Lisa, Gardiner, Siobhan, Jämsén, Anni, Jeffery, Katie, Malone, Tom, Phillips, Eloise, Rothwell, Lucy, Stafford, Lizzie, Baillie, J Kenneth, Semple, Malcolm G., Openshaw, Peter JM., Carson, Gail, Alex, Beatrice, Andrikopoulos, Petros, Bach, Benjamin, Barclay, Wendy S., Bogaert, Debby, Chand, Meera, Chechi, Kanta, Cooke, Graham S., da Silva Filipe, Ana, de Silva, Thushan, Docherty, Annemarie B., dos Santos Correia, Gonçalo, Dumas, Marc-Emmanuel, Dunning, Jake, Fletcher, Tom, Green, Christoper A., Greenhalf, William, Griffin, Julian L., Gupta, Rishi K., Harrison, Ewen M., Hiscox, Julian A., Wai Ho, Antonia Ying, Horby, Peter W., Ijaz, Samreen, Khoo, Saye, Klenerman, Paul, Law, Andrew, Lewis, Matthew R., Liggi, Sonia, Lim, Wei Shen, Maslen, Lynn, Mentzer, Alexander J., Merson, Laura, Meynert, Alison M., Moore, Shona C., Noursadeghi, Mahdad, Olanipekun, Michael, Osagie, Anthonia, Palmarini, Massimo, Palmieri, Carlo, Paxton, William A., Pollakis, Georgios, Price, Nicholas, Rambaut, Andrew, Robertson, David L., Russell, Clark D., Sancho-Shimizu, Vanessa, Sands, Caroline J., Scott, Janet T., Sigfrid, Louise, Solomon, Tom, Sriskandan, Shiranee, Stuart, David, Summers, Charlotte, Swann, Olivia V., Takats, Zoltan, Takis, Panteleimon, Tedder, Richard S., Thompson, AA Roger, Thomson, Emma C., Thwaites, Ryan S., Turtle, Lance CW., Zambon, Maria, Hardwick, Hayley, Donohue, Chloe, Griffiths, Fiona, Oosthuyzen, Wilna, Donegan, Cara, Spencer, Rebecca G., Norman, Lisa, Pius, Riinu, Drake, Thomas M., Fairfield, Cameron J., Knight, Stephen R., Mclean, Kenneth A., Murphy, Derek, Shaw, Catherine A., Dalton, Jo, Girvan, Michelle, Saviciute, Egle, Roberts, Stephanie, Harrison, Janet, Marsh, Laura, Connor, Marie, Halpin, Sophie, Jackson, Clare, Gamble, Carrol, Plotkin, Daniel, Lee, James, Leeming, Gary, Wham, Murray, Clohisey, Sara, Hendry, Ross, Scott-Brown, James, Shaw, Victoria, McDonald, Sarah E., Keating, Seán, Ahmed, Katie A., Armstrong, Jane A., Ashworth, Milton, Asiimwe, Innocent G., Bakshi, Siddharth, Barlow, Samantha L., Booth, Laura, Brennan, Benjamin, Bullock, Katie, Catterall, Benjamin WA., Clark, Jordan J., Clarke, Emily A., Cole, Sarah, Cooper, Louise, Cox, Helen, Davis, Christopher, Dincarslan, Oslem, Dunn, Chris, Dyer, Philip, Elliott, Angela, Evans, Anthony, Finch, Lorna, Fisher, Lewis WS., Foster, Terry, Garcia-Dorival, Isabel, Gunning, Philip, Hartley, Catherine, Jensen, Rebecca L., Jones, Christopher B., Jones, Trevor R., Khandaker, Shadia, King, Katharine, Kiy, Robyn T., Koukorava, Chrysa, Lake, Annette, Lant, Suzannah, Latawiec, Diane, Lavelle-Langham, Lara, Lefteri, Daniella, Lett, Lauren, Livoti, Lucia A., Mancini, Maria, McDonald, Sarah, McEvoy, Laurence, McLauchlan, John, Metelmann, Soeren, Miah, Nahida S., Middleton, Joanna, Mitchell, Joyce, Murphy, Ellen G., Penrice-Randal, Rebekah, Pilgrim, Jack, Prince, Tessa, Reynolds, Will, Ridley, P. Matthew, Sales, Debby, Shaw, Victoria E., Shears, Rebecca K., Small, Benjamin, Subramaniam, Krishanthi S., Szemiel, Agnieska, Taggart, Aislynn, Tanianis-Hughes, Jolanta, Thomas, Jordan, Trochu, Erwan, van Tonder, Libby, Wilcock, Eve, Zhang, J. Eunice, Flaherty, Lisa, Maziere, Nicole, Cass, Emily, Carracedo, Alejandra Doce, Carlucci, Nicola, Holmes, Anthony, Massey, Hannah, Murphy, Lee, McCafferty, Sarah, Clark, Richard, Fawkes, Angie, Morrice, Kirstie, Maclean, Alan, Wrobel, Nicola, Donnelly, Lorna, Coutts, Audrey, Hafezi, Katarzyna, MacGillivray, Louise, Gilchrist, Tammy, Adeniji, Kayode, Agranoff, Daniel, Agwuh, Ken, Ail, Dhiraj, Aldera, Erin L., Alegria, Ana, Allen, Sam, Angus, Brian, Ashish, Abdul, Atkinson, Dougal, Bari, Shahedal, Barlow, Gavin, Barnass, Stella, Barrett, Nicholas, Bassford, Christopher, Basude, Sneha, Baxter, David, Beadsworth, Michael, Bernatoniene, Jolanta, Berridge, John, Berry, Colin, Best, Nicola, Bothma, Pieter, Chadwick, David, Brittain-Long, Robin, Bulteel, Naomi, Burden, Tom, Burtenshaw, Andrew, Caruth, Vikki, Chambler, Duncan, Chee, Nigel, Child, Jenny, Chukkambotla, Srikanth, Clark, Tom, Collini, Paul, Cosgrove, Catherine, Cupitt, Jason, Cutino-Moguel, Maria-Teresa, Dark, Paul, Dawson, Chris, Dervisevic, Samir, Donnison, Phil, Douthwaite, Sam, Drummond, Andrew, DuRand, Ingrid, Dushianthan, Ahilanadan, Dyer, Tristan, Evans, Cariad, Eziefula, Chi, Fegan, Chrisopher, Finn, Adam, Fullerton, Duncan, Garg, Sanjeev, Garg, Atul, Gkrania-Klotsas, Effrossyni, Godden, Jo, Goldsmith, Arthur, Graham, Clive, Hardy, Elaine, Hartshorn, Stuart, Harvey, Daniel, Havalda, Peter, Hawcutt, Daniel B., Hobrok, Maria, Hodgson, Luke, Hormis, Anil, Jacobs, Michael, Jain, Susan, Jennings, Paul, Kaliappan, Agilan, Kasipandian, Vidya, Kegg, Stephen, Kelsey, Michael, Kendall, Jason, Kerrison, Caroline, Kerslake, Ian, Koch, Oliver, Koduri, Gouri, Koshy, George, Laha, Shondipon, Laird, Steven, Larkin, Susan, Leiner, Tamas, Lillie, Patrick, Limb, James, Linnett, Vanessa, Little, Jeff, Lyttle, Mark, MacMahon, Michael, MacNaughton, Emily, Mankregod, Ravish, Masson, Huw, Matovu, Elijah, McCullough, Katherine, McEwen, Ruth, Meda, Manjula, Mills, Gary, Minton, Jane, Mirfenderesky, Mariyam, Mohandas, Kavya, Mok, Quen, Moon, James, Moore, Elinoor, Morgan, Patrick, Morris, Craig, Mortimore, Katherine, Moses, Samuel, Mpenge, Mbiye, Mulla, Rohinton, Murphy, Michael, Nagel, Megan, Nagarajan, Thapas, Nelson, Mark, Norris, Lillian, O’Shea, Matthew K., Otahal, Igor, Ostermann, Marlies, Pais, Mark, Panchatsharam, Selva, Papakonstantinou, Danai, Paraiso, Hassan, Patel, Brij, Pattison, Natalie, Pepperell, Justin, Peters, Mark, Phull, Mandeep, Pintus, Stefania, Pooni, Jagtur Singh, Planche, Tim, Post, Frank, Price, David, Prout, Rachel, Rae, Nikolas, Reschreiter, Henrik, Reynolds, Tim, Richardson, Neil, Roberts, Mark, Roberts, Devender, Rose, Alistair, Rousseau, Guy, Ruge, Bobby, Ryan, Brendan, Saluja, Taranprit, Schmid, Matthias L., Shah, Aarti, Shanmuga, Prad, Sharma, Anil, Shawcross, Anna, Sizer, Jeremy, Shankar-Hari, Manu, Smith, Richard, Snelson, Catherine, Spittle, Nick, Staines, Nikki, Stambach, Tom, Stewart, Richard, Subudhi, Pradeep, Szakmany, Tamas, Tatham, Kate, Thomas, Jo, Thompson, Chris, Thompson, Robert, Tridente, Ascanio, Tupper-Carey, Darell, Twagira, Mary, Vallotton, Nick, Vancheeswaran, Rama, Vincent-Smith, Lisa, Visuvanathan, Shico, Vuylsteke, Alan, Waddy, Sam, Wake, Rachel, Walden, Andrew, Welters, Ingeborg, Whitehouse, Tony, Whittaker, Paul, Whittington, Ashley, Papineni, Padmasayee, Wijesinghe, Meme, Williams, Martin, Wilson, Lawrence, Winchester, Stephen, Wiselka, Martin, Wolverson, Adam, Wootton, Daniel G., Workman, Andrew, Yates, Bryan, Young, Peter, Dejnirattisai, Wanwisa, Huo, Jiandong, Zhou, Daming, Zahradník, Jiří, Supasa, Piyada, Liu, Chang, Duyvesteyn, Helen M.E., Ginn, Helen M., Tuekprakhon, Aekkachai, Nutalai, Rungtiwa, Wang, Beibei, Dijokaite, Aiste, Khan, Suman, Avinoam, Ori, Bahar, Mohammad, Skelly, Donal, Adele, Sandra, Johnson, Sile Ann, Amini, Ali, Ritter, Thomas G., Mason, Chris, Dold, Christina, Pan, Daniel, Assadi, Sara, Bellass, Adam, Omo-Dare, Nicola, Koeckerling, David, Flaxman, Amy, Jenkin, Daniel, Aley, Parvinder K., Voysey, Merryn, Costa Clemens, Sue Ann, Naveca, Felipe Gomes, Nascimento, Valdinete, Nascimento, Fernanda, Fernandes da Costa, Cristiano, Resende, Paola Cristina, Pauvolid-Correa, Alex, Siqueira, Marilda M., Baillie, Vicky, Serafin, Natali, Kwatra, Gaurav, Da Silva, Kelly, Madhi, Shabir A., Nunes, Marta C., Malik, Tariq, Openshaw, Peter J.M., Baillie, J. Kenneth, Townsend, Alain R., Huang, Kuan-Ying A., Tan, Tiong Kit, Carroll, Miles W., Barnes, Eleanor, Dunachie, Susanna J., Constantinides, Bede, Webster, Hermione, Crook, Derrick, Pollard, Andrew J., Lambe, Teresa, Paterson, Neil G., Williams, Mark A., Hall, David R., Fry, Elizabeth E., Mongkolsapaya, Juthathip, Ren, Jingshan, Schreiber, Gideon, Stuart, David I., and Screaton, Gavin R.

Published
2022
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21. The impact of viral mutations on recognition by SARS-CoV-2 specific T cells

Author

Aanensen, David M., Abudahab, Khalil, Adams, Helen, Adams, Alexander, Afifi, Safiah, Aggarwal, Dinesh, Ahmad, Shazaad S.Y., Aigrain, Louise, Alcolea-Medina, Adela, Alikhan, Nabil-Fareed, Allara, Elias, Amato, Roberto, Annett, Tara, Aplin, Stephen, Ariani, Cristina V., Asad, Hibo, Ash, Amy, Ashfield, Paula, Ashford, Fiona, Atkinson, Laura, Attwood, Stephen W., Auckland, Cressida, Aydin, Alp, Baker, David J., Baker, Paul, Balcazar, Carlos E., Ball, Jonathan, Barrett, Jeffrey C., Barrow, Magdalena, Barton, Edward, Bashton, Matthew, Bassett, Andrew R., Batra, Rahul, Baxter, Chris, Bayzid, Nadua, Beaver, Charlotte, Beckett, Angela H., Beckwith, Shaun M., Bedford, Luke, Beer, Robert, Beggs, Andrew, Bellis, Katherine L., Berry, Louise, Bertolusso, Beatrice, Best, Angus, Betteridge, Emma, Bibby, David, Bicknell, Kelly, Binns, Debbie, Birchley, Alec, Bird, Paul W., Bishop, Chloe, Blacow, Rachel, Blakey, Victoria, Blane, Beth, Bolt, Frances, Bonfield, James, Bonner, Stephen, Bonsall, David, Boswell, Tim, Bosworth, Andrew, Bourgeois, Yann, Boyd, Olivia, Bradley, Declan T., Breen, Cassie, Bresner, Catherine, Breuer, Judith, Bridgett, Stephen, Bronner, Iraad F., Brooks, Ellena, Broos, Alice, Brown, Julianne R., Bucca, Giselda, Buchan, Sarah L., Buck, David, Bull, Matthew, Burns, Phillipa J., Burton-Fanning, Shirelle, Byaruhanga, Timothy, Byott, Matthew, Campbell, Sharon, Carabelli, Alessandro M., Cargill, James S., Carlile, Matthew, Carvalho, Silvia F., Casey, Anna, Castigador, Anibolina, Catalan, Jana, Chalker, Vicki, Chaloner, Nicola J., Chand, Meera, Chappell, Joseph G., Charalampous, Themoula, Chatterton, Wendy, Chaudhry, Yasmin, Churcher, Carol M., Clark, Gemma, Clarke, Phillip, Cogger, Benjamin J., Cole, Kevin, Collins, Jennifer, Colquhoun, Rachel, Connor, Thomas R., Cook, Kate F., Coombes, Jason, Corden, Sally, Cormie, Claire, Cortes, Nicholas, Cotic, Marius, Cotton, Seb, Cottrell, Simon, Coupland, Lindsay, Cox, MacGregor, Cox, Alison, Craine, Noel, Crawford, Liam, Cross, Aidan, Crown, Matthew R., Crudgington, Dorian, Cumley, Nicola, Curran, Tanya, Curran, Martin D., da Silva Filipe, Ana, Dabrera, Gavin, Darby, Alistair C., Davidson, Rose K., Davies, Alisha, Davies, Robert M., Davis, Thomas, de Angelis, Daniela, De Lacy, Elen, de Oliveira Martins, Leonardo, Debebe, Johnny, Denton-Smith, Rebecca, Dervisevic, Samir, Dewar, Rebecca, Dey, Jayasree, Dias, Joana, Dobie, Donald, Dorman, Matthew J., Downing, Fatima, Driscoll, Megan, du Plessis, Louis, Duckworth, Nichola, Durham, Jillian, Eastick, Kirstine, Easton, Lisa J., Eccles, Richard, Edgeworth, Jonathan, Edwards, Sue, El Bouzidi, Kate, Eldirdiri, Sahar, Ellaby, Nicholas, Elliott, Scott, Eltringham, Gary, Ensell, Leah, Erkiert, Michelle J., Zamudio, Marina Escalera, Essex, Sarah, Evans, Johnathan M., Evans, Cariad, Everson, William, Fairley, Derek J., Fallon, Karlie, Fanaie, Arezou, Farr, Ben W., Fearn, Christopher, Feltwell, Theresa, Ferguson, Lynne, Fina, Laia, Flaviani, Flavia, Fleming, Vicki M., Forrest, Sally, Foster-Nyarko, Ebenezer, Foulkes, Benjamin H., Foulser, Luke, Fragakis, Mireille, Frampton, Dan, Francois, Sarah, Fraser, Christophe, Freeman, Timothy M., Fryer, Helen, Fuchs, Marc, Fuller, William, Gajee, Kavitha, Galai, Katerina, Gallagher, Abbie, Gallagher, Eileen, Gallagher, Michael D., Gallis, Marta, Gaskin, Amy, Gatica-Wilcox, Bree, Geidelberg, Lily, Gemmell, Matthew, Georgana, Iliana, George, Ryan P., Gifford, Laura, Gilbert, Lauren, Girgis, Sophia T., Glaysher, Sharon, Goldstein, Emily J., Golubchik, Tanya, Gomes, Andrea N., Gonçalves, Sónia, Goodfellow, Ian G., Goodwin, Scott, Goudarzi, Salman, Gourtovaia, Marina, Graham, Clive, Graham, Lee, Grant, Paul R., Green, Luke R., Green, Angie, Greenaway, Jane, Gregory, Richard, Guest, Martyn, Gunson, Rory N., Gupta, Ravi K., Gutierrez, Bernardo, Haldenby, Sam T., Hamilton, William L., Hansford, Samantha E., Haque, Tanzina, Harris, Kathryn A., Harrison, Ian, Harrison, Ewan M., Hart, Jennifer, Hartley, John A., Harvey, William T., Harvey, Matthew, Hassan-Ibrahim, Mohammed O., Heaney, Judith, Helmer, Thomas, Henderson, John H., Hesketh, Andrew R., Hey, Jessica, Heyburn, David, Higginson, Ellen E., Hill, Verity, Hill, Jack D., Hilson, Rachel A., Hilvers, Ember, Holden, Matthew T.G., Hollis, Amy, Holmes, Christopher W., Holmes, Nadine, Holmes, Alison H., Hopes, Richard, Hornsby, Hailey R., Hosmillo, Myra, Houlihan, Catherine, Howson-Wells, Hannah C., Hubb, Jonathan, Huckson, Hannah, Hughes, Warwick, Hughes, Joseph, Hughes, Margaret, Hutchings, Stephanie, Idle, Giles, Illingworth, Chris J., Impey, Robert, Irish-Tavares, Dianne, Iturriza-Gomara, Miren, Izuagbe, Rhys, Jackson, Chris, Jackson, Ben, Jackson, Leigh M., Jackson, Kathryn A., Jackson, David K., Jahun, Aminu S., James, Victoria, James, Keith, Jeanes, Christopher, Jeffries, Aaron R., Jeremiah, Sarah, Jermy, Andrew, John, Michaela, Johnson, Rob, Johnson, Kate, Johnston, Ian, Jones, Owen, Jones, Sophie, Jones, Hannah, Jones, Christopher R., Jones, Neil, Joseph, Amelia, Judges, Sarah, Kay, Gemma L., Kay, Sally, Keatley, Jon-Paul, Keeley, Alexander J., Kenyon, Anita, Kermack, Leanne M., Khakh, Manjinder, Kidd, Stephen P., Kimuli, Maimuna, Kirk, Stuart, Kitchen, Christine, Kitchman, Katie, Knight, Bridget A., Koshy, Cherian, Kraemer, Moritz U.G., Kumziene-Summerhayes, Sara, Kwiatkowski, Dominic, Lackenby, Angie, Laing, Kenneth G., Lampejo, Temi, Langford, Cordelia F., Lavin, Deborah, Lawton, Andrew I., Lee, Jack, Lee, David, Lensing, Stefanie V., Leonard, Steven, Levett, Lisa J., Le-Viet, Thanh, Lewis, Jonathan, Lewis, Kevin, Liddle, Jennifier, Liggett, Steven, Lillie, Patrick J., Lister, Michelle M., Livett, Rich, Lo, Stephanie, Loman, Nicholas J., Loose, Matthew W., Louka, Stavroula F., Loveson, Katie F., Lowdon, Sarah, Lowe, Hannah, Lowe, Helen L., Lucaci, Anita O., Ludden, Catherine, Lynch, Jessica, Lyons, Ronan A., Lythgoe, Katrina, Machin, Nicholas W., MacIntyre-Cockett, George, Mack, Andrew, Macklin, Ben, Maclean, Alasdair, Macnaughton, Emily, Madona, Pinglawathee, Maes, Mailis, Maftei, Laurentiu, Mahanama, Adhyana I.K., Mahungu, Tabitha W., Mair, Daniel, Maksimovic, Joshua, Malone, Cassandra S., Maloney, Daniel, Manesis, Nikos, Manley, Robin, Mantzouratou, Anna, Marchbank, Angela, Mariappan, Arun, Martincorena, Inigo, Martinez Nunez, Rocio T., Mather, Alison E., Maxwell, Patrick, Mayhew, Megan, Mbisa, Tamyo, McCann, Clare M., McCarthy, Shane A., McCluggage, Kathryn, McClure, Patrick C., McCrone, J.T., McHugh, Martin P., McKenna, James P., McKerr, Caoimhe, McManus, Georgina M., McMurray, Claire L., McMurray, Claire, McNally, Alan, Meadows, Lizzie, Medd, Nathan, Megram, Oliver, Menegazzo, Mirko, Merrick, Ian, Michell, Stephen L., Michelsen, Michelle L., Mirfenderesky, Mariyam, Mirza, Jeremy, Miskelly, Julia, Moles-Garcia, Emma, Moll, Robin J., Molnar, Zoltan, Monahan, Irene M., Mondani, Matteo, Mookerjee, Siddharth, Moore, Christopher, Moore, Jonathan, Moore, Nathan, Moore, Catherine, Morcrette, Helen, Morgan, Sian, Morgan, Mari, Mori, Matilde, Morriss, Arthur, Moses, Samuel, Mower, Craig, Muir, Peter, Mukaddas, Afrida, Munemo, Florence, Munn, Robert, Murray, Abigail, Murray, Leanne J., Murray, Darren R., Mutingwende, Manasa, Myers, Richard, Nastouli, Eleni, Nebbia, Gaia, Nelson, Andrew, Nelson, Charlotte, Nicholls, Sam, Nichols, Jenna, Nicodemi, Roberto, Nomikou, Kyriaki, O’Grady, Justin, O'Brien, Sarah, Odedra, Mina, Ohemeng-Kumi, Natasha, Oliver, Karen, Orton, Richard J., Osman, Husam, xeine O'Toole, Pacchiarini, Nicole, Padgett, Debra, Page, Andrew J., Park, Emily J., Park, Naomi R., Parmar, Surendra, Partridge, David G., Pascall, David, Patel, Amita, Patel, Bindi, Paterson, Steve, Payne, Brendan A.I., Peacock, Sharon J., Pearson, Clare, Pelosi, Emanuela, Percival, Benita, Perkins, Jon, Perry, Malorie, Pinckert, Malte L., Platt, Steven, Podplomyk, Olga, Pohare, Manoj, Pond, Marcus, Pope, Cassie F., Poplawski, Radoslaw, Powell, Jessica, Poyner, Jennifer, Prestwood, Liam, Price, Anna, Price, James R., Prieto, Jacqui A., Pritchard, David T., Prosolek, Sophie J., Pugh, Georgia, Pusok, Monika, Pybus, Oliver G., Pymont, Hannah M., Quail, Michael A., Quick, Joshua, Radulescu, Clara, Raghwani, Jayna, Ragonnet-Cronin, Manon, Rainbow, Lucille, Rajan, Diana, Rajatileka, Shavanthi, Ramadan, Newara A., Rambaut, Andrew, Ramble, John, Randell, Paul A., Randell, Paul, Ratcliffe, Liz, Raviprakash, Veena, Raza, Mohammad, Redshaw, Nicholas M., Rey, Sara, Reynolds, Nicola, Richter, Alex, Robertson, David L., Robinson, Esther, Robson, Samuel C., Rogan, Fiona, Rooke, Stefan, Rowe, Will, Roy, Sunando, Rudder, Steven, Ruis, Chris, Rushton, Steven, Ryan, Felicity, Saeed, Kordo, Samaraweera, Buddhini, Sambles, Christine M., Sanderson, Roy, Sanderson, Theo, Sang, Fei, Sass, Thea, Scher, Emily, Scott, Garren, Scott, Carol, Sehmi, Jasveen, Shaaban, Sharif, Shah, Divya, Shaw, Jessica, Shelest, Ekaterina, Shepherd, James G., Sheridan, Liz A., Sheriff, Nicola, Shirley, Lesley, Sillitoe, John, Silviera, Siona, Simpson, David A., Singh, Aditi, Singleton, Dawn, Skvortsov, Timofey, Sloan, Tim J., Sluga, Graciela, Smith, Ken, Smith, Kim S., Smith, Perminder, Smith, Darren L., Smith, Louise, Smith, Colin P., Smith, Nikki, Smollett, Katherine L., Snell, Luke B., Somassa, Thomas, Southgate, Joel, Spellman, Karla, Spencer Chapman, Michael H., Spurgin, Lewis G., Spyer, Moira J., Stanley, Rachael, Stanley, William, Stanton, Thomas D., Starinskij, Igor, Stockton, Joanne, Stonehouse, Susanne, Storey, Nathaniel, Studholme, David J., Sudhanva, Malur, Swindells, Emma, Taha, Yusri, Tan, Ngee Keong, Tang, Julian W., Tang, Miao, Taylor, Ben E.W., Taylor, Joshua F., Taylor, Sarah, Temperton, Ben, Templeton, Kate E., Thomas, Claire, Thomson, Laura, Thomson, Emma C., Thornton, Alicia, Thurston, Scott A.J., Todd, John A., Tomb, Rachael, Tong, Lily, Tonkin-Hill, Gerry, Torok, M. Estee, Tovar-Corona, Jaime M., Trebes, Amy, Trotter, Alexander J., Tsatsani, Ioulia, Turnbull, Robyn, Twohig, Katherine A., Umpleby, Helen, Underwood, Anthony P., Vamos, Edith E., Vasylyeva, Tetyana I., Vattipally, Sreenu, Vernet, Gabrielle, Vipond, Barry B., Volz, Erik M., Walsh, Sarah, Wang, Dennis, Warne, Ben, Warwick-Dugdale, Joanna, Wastnedge, Elizabeth, Watkins, Joanne, Watson, Louisa K., Waugh, Sheila, Webster, Hermione J., Weldon, Danni, Westwick, Elaine, Whalley, Thomas, Wheeler, Helen, Whitehead, Mark, Whiteley, Max, Whitwham, Andrew, Wierzbicki, Claudia, Willford, Nicholas J., Williams, Lesley-Anne, Williams, Rebecca, Williams, Cheryl, Williams, Chris, Williams, Charlotte A., Williams, Rachel J., Williams, Thomas, Williams, Catryn, Williamson, Kathleen A., Wilson-Davies, Eleri, Witele, Eric, Withell, Karen T., Witney, Adam A., Wolverson, Paige, Wong, Nick, Workman, Trudy, Wright, Victoria, Wright, Derek W., Wyatt, Tim, Wyllie, Sarah, Xu-McCrae, Li, Yavus, Mehmet, Yaze, Geraldine, Yeats, Corin A., Yebra, Gonzalo, Yew, Wen C., Young, Gregory R., Young, Jamie, Zarebski, Alex E., Zhang, Peijun, Baillie, J. Kenneth, Semple, Malcolm G., Openshaw, Peter J.M., Carson, Gail, Alex, Beatrice, Andrikopoulos, Petros, Bach, Benjamin, Barclay, Wendy S., Bogaert, Debby, Chechi, Kanta, Cooke, Graham S., Docherty, Annemarie B., Correia, Gonçalo dos Santos, Dumas, Marc-Emmanuel, Dunning, Jake, Fletcher, Tom, Green, Christopher A., Greenhalf, William, Griffin, Julian L., Gupta, Rishi K., Harrison, Ewen M., Hiscox, Julian A., Wai Ho, Antonia Ying, Horby, Peter W., Ijaz, Samreen, Khoo, Saye, Klenerman, Paul, Law, Andrew, Lewis, Matthew R., Liggi, Sonia, Lim, Wei Shen, Maslen, Lynn, Mentzer, Alexander J., Merson, Laura, Meynert, Alison M., Noursadeghi, Mahdad, Olanipekun, Michael, Osagie, Anthonia, Palmarini, Massimo, Palmieri, Carlo, Paxton, William A., Pollakis, Georgios, Price, Nicholas, Russell, Clark D., Sancho-Shimizu, Vanessa, Sands, Caroline J., Scott, Janet T., Sigfrid, Louise, Solomon, Tom, Sriskandan, Shiranee, Stuart, David, Summers, Charlotte, Swann, Olivia V., Takats, Zoltan, Takis, Panteleimon, Tedder, Richard S., Thompson, A.A. Roger, Thwaites, Ryan S., Zambon, Maria, Hardwick, Hayley, Donohue, Chloe, Griffiths, Fiona, Oosthuyzen, Wilna, Donegan, Cara, Spencer, Rebecca G., Dalton, Jo, Girvan, Michelle, Saviciute, Egle, Roberts, Stephanie, Harrison, Janet, Marsh, Laura, Connor, Marie, Halpin, Sophie, Jackson, Clare, Gamble, Carrol, Plotkin, Daniel, Lee, James, Leeming, Gary, Wham, Murray, Clohisey, Sara, Hendry, Ross, Scott-Brown, James, Shaw, Victoria, McDonald, Sarah E., Keating, Seán, Ahmed, Katie A., Armstrong, Jane A., Ashworth, Milton, Asiimwe, Innocent G., Bakshi, Siddharth, Barlow, Samantha L., Booth, Laura, Brennan, Benjamin, Bullock, Katie, Catterall, Benjamin W.A., Clark, Jordan J., Clarke, Emily A., Cole, Sarah, Cooper, Louise, Cox, Helen, Davis, Christopher, Dincarslan, Oslem, Dunn, Chris, Dyer, Philip, Elliott, Angela, Evans, Anthony, Finch, Lorna, Fisher, Lewis W.S., Foster, Terry, Garcia-Dorival, Isabel, Gunning, Philip, Hartley, Catherine, Jensen, Rebecca L., Jones, Christopher B., Jones, Trevor R., Khandaker, Shadia, King, Katharine, Kiy, Robyn T., Koukorava, Chrysa, Lake, Annette, Lant, Suzannah, Latawiec, Diane, Lavelle-Langham, Lara, Lefteri, Daniella, Lett, Lauren, Livoti, Lucia A., Mancini, Maria, McDonald, Sarah, McEvoy, Laurence, McLauchlan, John, Metelmann, Soeren, Miah, Nahida S., Middleton, Joanna, Mitchell, Joyce, Moore, Shona C., Murphy, Ellen G., Penrice-Randal, Rebekah, Pilgrim, Jack, Prince, Tessa, Reynolds, Will, Ridley, P. Matthew, Sales, Debby, Shaw, Victoria E., Shears, Rebecca K., Small, Benjamin, Subramaniam, Krishanthi S., Szemiel, Agnieska, Taggart, Aislynn, Tanianis-Hughes, Jolanta, Thomas, Jordan, Trochu, Erwan, van Tonder, Libby, Wilcock, Eve, Zhang, J. Eunice, Flaherty, Lisa, Maziere, Nicole, Cass, Emily, Carracedo, Alejandra Doce, Carlucci, Nicola, Holmes, Anthony, Massey, Hannah, Murphy, Lee, Wrobel, Nicola, McCafferty, Sarah, Morrice, Kirstie, MacLean, Alan, Adeniji, Kayode, Agranoff, Daniel, Agwuh, Ken, Ail, Dhiraj, Aldera, Erin L., Alegria, Ana, Allen, Sam, Angus, Brian, Ashish, Abdul, Atkinson, Dougal, Bari, Shahedal, Barlow, Gavin, Barnass, Stella, Barrett, Nicholas, Bassford, Christopher, Basude, Sneha, Baxter, David, Beadsworth, Michael, Bernatoniene, Jolanta, Berridge, John, Berry, Colin, Best, Nicola, Bothma, Pieter, Chadwick, David, Brittain-Long, Robin, Bulteel, Naomi, Burden, Tom, Burtenshaw, Andrew, Caruth, Vikki, Chambler, Duncan, Chee, Nigel, Child, Jenny, Chukkambotla, Srikanth, Clark, Tom, Collini, Paul, Cosgrove, Catherine, Cupitt, Jason, Cutino-Moguel, Maria-Teresa, Dark, Paul, Dawson, Chris, Donnison, Phil, Douthwaite, Sam, Drummond, Andrew, DuRand, Ingrid, Dushianthan, Ahilanadan, Dyer, Tristan, Eziefula, Chi, Fegan, Chrisopher, Finn, Adam, Fullerton, Duncan, Garg, Sanjeev, Garg, Atul, Gkrania-Klotsas, Effrossyni, Godden, Jo, Goldsmith, Arthur, Hardy, Elaine, Hartshorn, Stuart, Harvey, Daniel, Havalda, Peter, Hawcutt, Daniel B., Hobrok, Maria, Hodgson, Luke, Hormis, Anil, Jacobs, Michael, Jain, Susan, Jennings, Paul, Kaliappan, Agilan, Kasipandian, Vidya, Kegg, Stephen, Kelsey, Michael, Kendall, Jason, Kerrison, Caroline, Kerslake, Ian, Koch, Oliver, Koduri, Gouri, Koshy, George, Laha, Shondipon, Laird, Steven, Larkin, Susan, Leiner, Tamas, Lillie, Patrick, Limb, James, Linnett, Vanessa, Little, Jeff, Lyttle, Mark, MacMahon, Michael, MacNaughton, Emily, Mankregod, Ravish, Masson, Huw, Matovu, Elijah, McCullough, Katherine, McEwen, Ruth, Meda, Manjula, Mills, Gary, Minton, Jane, Mohandas, Kavya, Mok, Quen, Moon, James, Moore, Elinoor, Morgan, Patrick, Morris, Craig, Mortimore, Katherine, Mpenge, Mbiye, Mulla, Rohinton, Murphy, Michael, Nagel, Megan, Nagarajan, Thapas, Nelson, Mark, Norris, Lillian, O'Shea, Matthew K., Otahal, Igor, Ostermann, Marlies, Pais, Mark, Panchatsharam, Selva, Papakonstantinou, Danai, Paraiso, Hassan, Patel, Brij, Pattison, Natalie, Pepperell, Justin, Peters, Mark, Phull, Mandeep, Pintus, Stefania, Pooni, Jagtur Singh, Planche, Tim, Post, Frank, Price, David, Prout, Rachel, Rae, Nikolas, Reschreiter, Henrik, Reynolds, Tim, Richardson, Neil, Roberts, Mark, Roberts, Devender, Rose, Alistair, Rousseau, Guy, Ruge, Bobby, Ryan, Brendan, Saluja, Taranprit, Schmid, Matthias L., Shah, Aarti, Shanmuga, Prad, Sharma, Anil, Shawcross, Anna, Sizer, Jeremy, Shankar-Hari, Manu, Smith, Richard, Snelson, Catherine, Spittle, Nick, Staines, Nikki, Stambach, Tom, Stewart, Richard, Subudhi, Pradeep, Szakmany, Tamas, Tatham, Kate, Thomas, Jo, Thompson, Chris, Thompson, Robert, Tridente, Ascanio, Tupper-Carey, Darell, Twagira, Mary, Vallotton, Nick, Vancheeswaran, Rama, Vincent-Smith, Lisa, Visuvanathan, Shico, Vuylsteke, Alan, Waddy, Sam, Wake, Rachel, Walden, Andrew, Welters, Ingeborg, Whitehouse, Tony, Whittaker, Paul, Whittington, Ashley, Papineni, Padmasayee, Wijesinghe, Meme, Williams, Martin, Wilson, Lawrence, Winchester, Stephen, Wiselka, Martin, Wolverson, Adam, Wootton, Daniel G., Workman, Andrew, Yates, Bryan, Young, Peter, de Silva, Thushan I., Liu, Guihai, Lindsey, Benjamin B., Dong, Danning, Hsu, Nienyun Sharon, Shah, Dhruv, Wellington, Dannielle, Angyal, Adrienn, Brown, Rebecca, Parker, Matthew D., Ying, Zixi, Yao, Xuan, Turtle, Lance, Dunachie, Susanna, Maini, Mala K., Ogg, Graham, Knight, Julian C., Peng, Yanchun, Rowland-Jones, Sarah L., and Dong, Tao

Published
2021
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22. Parkinson's disease and Parkinson's disease medications have distinct signatures of the gut microbiome

Author

Hill‐Burns, Erin M, Debelius, Justine W, Morton, James T, Wissemann, William T, Lewis, Matthew R, Wallen, Zachary D, Peddada, Shyamal D, Factor, Stewart A, Molho, Eric, Zabetian, Cyrus P, Knight, Rob, and Payami, Haydeh

Subjects
Biomedical and Clinical Sciences, Neurosciences, Clinical Sciences, Aging, Brain Disorders, Neurodegenerative, Nutrition, Parkinson's Disease, Microbiome, Genetics, 2.1 Biological and endogenous factors, Neurological, Oral and gastrointestinal, Age Factors, Antiparkinson Agents, Bifidobacterium, Carbidopa, Case-Control Studies, Catechol O-Methyltransferase Inhibitors, Cholinergic Antagonists, Confounding Factors, Epidemiologic, Diet, Drug Combinations, Dysbiosis, Female, Fruit, Gastrointestinal Microbiome, Humans, Lactobacillaceae, Levodopa, Male, Parkinson Disease, Pasteurellaceae, RNA, Ribosomal, 16S, Risk Factors, Sex Factors, United States, Vegetables, Verrucomicrobia, Parkinson's disease, medications, confounding, gut microbiome, functional pathways, Human Movement and Sports Sciences, Neurology & Neurosurgery, Clinical sciences
Abstract

BackgroundThere is mounting evidence for a connection between the gut and Parkinson's disease (PD). Dysbiosis of gut microbiota could explain several features of PD.ObjectiveThe objective of this study was to determine if PD involves dysbiosis of gut microbiome, disentangle effects of confounders, and identify candidate taxa and functional pathways to guide research.MethodsA total of 197 PD cases and 130 controls were studied. Microbial composition was determined by 16S rRNA gene sequencing of DNA extracted from stool. Metadata were collected on 39 potential confounders including medications, diet, gastrointestinal symptoms, and demographics. Statistical analyses were conducted while controlling for potential confounders and correcting for multiple testing. We tested differences in the overall microbial composition, taxa abundance, and functional pathways.ResultsIndependent microbial signatures were detected for PD (P = 4E-5), participants' region of residence within the United States (P = 3E-3), age (P = 0.03), sex (P = 1E-3), and dietary fruits/vegetables (P = 0.01). Among patients, independent signals were detected for catechol-O-methyltransferase-inhibitors (P = 4E-4), anticholinergics (P = 5E-3), and possibly carbidopa/levodopa (P = 0.05). We found significantly altered abundances of the Bifidobacteriaceae, Christensenellaceae, [Tissierellaceae], Lachnospiraceae, Lactobacillaceae, Pasteurellaceae, and Verrucomicrobiaceae families. Functional predictions revealed changes in numerous pathways, including the metabolism of plant-derived compounds and xenobiotics degradation.ConclusionPD is accompanied by dysbiosis of gut microbiome. Results coalesce divergent findings of prior studies, reveal altered abundance of several taxa, nominate functional pathways, and demonstrate independent effects of PD medications on the microbiome. The findings provide new leads and testable hypotheses on the pathophysiology and treatment of PD. © 2017 International Parkinson and Movement Disorder Society.

Published
2017

23. Statistical analysis in metabolic phenotyping

Author

Blaise, Benjamin J., Correia, Gonçalo D. S., Haggart, Gordon A., Surowiec, Izabella, Sands, Caroline, Lewis, Matthew R., Pearce, Jake T. M., Trygg, Johan, Nicholson, Jeremy K., Holmes, Elaine, and Ebbels, Timothy M. D.

Published
2021
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25. Reference materials for MS-based untargeted metabolomics and lipidomics: a review by the metabolomics quality assurance and quality control consortium (mQACC)

Author

Lippa, Katrice A., Aristizabal-Henao, Juan J., Beger, Richard D., Bowden, John A., Broeckling, Corey, Beecher, Chris, Clay Davis, W., Dunn, Warwick B., Flores, Roberto, Goodacre, Royston, Gouveia, Gonçalo J., Harms, Amy C., Hartung, Thomas, Jones, Christina M., Lewis, Matthew R., Ntai, Ioanna, Percy, Andrew J., Raftery, Dan, Schock, Tracey B., Sun, Jinchun, Theodoridis, Georgios, Tayyari, Fariba, Torta, Federico, Ulmer, Candice Z., Wilson, Ian, and Ubhi, Baljit K.

Published
2022
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26. Roux-en-Y gastric bypass-induced bacterial perturbation contributes to altered host-bacterial co-metabolic phenotype

Author

Li, Jia V., Ashrafian, Hutan, Sarafian, Magali, Homola, Daniel, Rushton, Laura, Barker, Grace, Cabrera, Paula Momo, Lewis, Matthew R., Darzi, Ara, Lin, Edward, Gletsu-Miller, Nana Adwoa, Atkin, Stephen L., Sathyapalan, Thozhukat, Gooderham, Nigel J., Nicholson, Jeremy K., Marchesi, Julian R., Athanasiou, Thanos, and Holmes, Elaine

Published
2021
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32. Complete Genome Sequence and Comparative Genomic Analysis of an Emerging Human Pathogen, Serotype V Streptococcus agalactiae

Author

Tettelin, Hervé, Masignani, Vega, Cieslewicz, Michael J., Eisen, Jonathan A., Peterson, Scott, Wessels, Michael R., Paulsen, Ian T., Nelson, Karen E., Margarit, Immaculada, Read, Timothy D., Madoff, Lawrence C., Wolf, Alex M., Beanan, Maureen J., Brinkac, Lauren M., Daugherty, Sean C., DeBoy, Robert T., Durkin, A. Scott, Kolonay, James F., Madupu, Ramana, Lewis, Matthew R., Radune, Diana, Fedorova, Nadezhda B., Scanlan, David, Khouri, Hoda, Mulligan, Stephanie, Carty, Heather A., Cline, Robin T., Van Aken, Susan E., Gill, John, Scarselli, Maria, Mora, Marirosa, Iacobini, Emilia T., Brettoni, Cecilia, Galli, Giuliano, Mariani, Massimo, Vegni, Filippo, Maione, Domenico, Rinaudo, Daniela, Rappuoli, Rino, Telford, John L., Kasper, Dennis L., Grandi, Guido, and Fraser, Claire M.

Published
2002

33. Urinary metabolic phenotyping for Alzheimer’s disease

Author

Kurbatova, Natalja, Garg, Manik, Whiley, Luke, Chekmeneva, Elena, Jiménez, Beatriz, Gómez-Romero, María, Pearce, Jake, Kimhofer, Torben, D’Hondt, Ellie, Soininen, Hilkka, Kłoszewska, Iwona, Mecocci, Patrizia, Tsolaki, Magda, Vellas, Bruno, Aarsland, Dag, Nevado-Holgado, Alejo, Liu, Benjamine, Snowden, Stuart, Proitsi, Petroula, Ashton, Nicholas J., Hye, Abdul, Legido-Quigley, Cristina, Lewis, Matthew R., Nicholson, Jeremy K., Holmes, Elaine, Brazma, Alvis, and Lovestone, Simon

Published
2020
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35. Complete Genome Sequence of a Virulent Isolate of Streptococcus pneumoniae

Author

Tettelin, Hervé, Nelson, Karen E., Paulsen, Ian T., Eisen, Jonathan A., Read, Timothy D., Peterson, Scott, Heidelberg, John, DeBoy, Robert T., Haft, Daniel H., Dodson, Robert J., Durkin, A. Scott, Gwinn, Michelle, Kolonay, James F., Nelson, William C., Peterson, Jeremy D., Umayam, Lowell A., White, Owen, Salzberg, Steven L., Lewis, Matthew R., Radune, Diana, Holtzapple, Erik, Khouri, Hoda, Wolf, Alex M., Utterback, Terry R., Hansen, Cheryl L., McDonald, Lisa A., Feldblyum, Tamara V., Angiuoli, Samuel, Dickinson, Tanja, Hickey, Erin K., Holt, Ingeborg E., Loftus, Brendan J., Yang, Fan, Smith, Hamilton O., Venter, J. Craig, Dougherty, Brian A., Morrison, Donald A., Hollingshead, Susan K., and Fraser, Claire M.

Published
2001

39. Multivariate metabotyping of plasma predicts survival in patients with decompensated cirrhosis

Author

McPhail, Mark J.W., Shawcross, Debbie L., Lewis, Matthew R., Coltart, Iona, Want, Elizabeth J., Antoniades, Charalambos G., Veselkov, Kiril, Triantafyllou, Evangelos, Patel, Vishal, Pop, Oltin, Gomez-Romero, Maria, Kyriakides, Michael, Zia, Rabiya, Abeles, Robin D., Crossey, Mary M.E., Jassem, Wayel, O’Grady, John, Heaton, Nigel, Auzinger, Georg, Bernal, William, Quaglia, Alberto, Coen, Muireann, Nicholson, Jeremy K., Wendon, Julia A., Holmes, Elaine, and Taylor-Robinson, Simon D.

Published
2016
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42. Contributors

Author

Alexander, James L., primary, Barbas, Coral, additional, Bonner, Frank W., additional, Brennan, Lorraine, additional, Fussell, Julia C., additional, Cameron, Simon J., additional, Castagné, Raphaële, additional, Chadeau-Hyam, Marc, additional, Climaco Pinto, Rui, additional, Deda, Olga, additional, Dehghan, Abbas, additional, Dunn, Warwick B., additional, Ebbels, Timothy M.D., additional, Elliott, Paul, additional, Evangelou, Evangelos, additional, Everett, Jeremy R., additional, Galea, Dieter, additional, Gao, Jianliang, additional, García, Antonia, additional, Gika, Helen, additional, Glen, Robert C., additional, Godzien, Joanna, additional, Holmes, Elaine, additional, Hoyles, Lesley, additional, Kelly, Frank J., additional, Karaman, Ibrahim, additional, Kinross, James M., additional, Laponogov, Ivan, additional, Lewis, Matthew R., additional, Lindon, John C., additional, López-Gonzálvez, Ángeles, additional, Maslen, Lynn, additional, Nicholson, Jeremy K., additional, O’Neill, Kevin S., additional, Parkinson, John A., additional, Pearce, Jake T.M., additional, Plumb, Robert S., additional, Posma, Joram M., additional, Raikos, Nikolaos, additional, Sadawi, Noureddin, additional, Salek, Reza M., additional, Swann, Jonathan, additional, Takats, Zoltan, additional, Theodoridis, Georgios, additional, Tzoulaki, Ioanna, additional, Vaqas, Babar, additional, Veselkov, Kirill, additional, and Wilson, Ian D., additional

Published
2019
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43. Small Intestinal Permeability and Metabolomic Profiles in Feces and Plasma Associate With Clinical Response in Patients With Active Psoriatic Arthritis Participating in a Fecal Microbiota Transplantation Trial: Exploratory Findings From the FLORA Trial.

Author

Kragsnaes, Maja Skov, Miguens Blanco, Jesus, Mullish, Benjamin H., Serrano‐Contreras, Jose Ivan, Kjeldsen, Jens, Horn, Hans Christian, Pedersen, Jens Kristian, Munk, Heidi Lausten, Nilsson, Anna Christine, Salam, Ash, Lewis, Matthew R., Chekmeneva, Elena, Kristiansen, Karsten, Marchesi, Julian R., and Ellingsen, Torkell

Subjects
FECAL analysis, PSORIATIC arthritis, METABOLOMICS, BLOOD plasma, SMALL intestine, QUESTIONNAIRES, DESCRIPTIVE statistics, RESEARCH funding, FECAL microbiota transplantation, STATISTICAL sampling, GASTROSCOPY
Abstract

Objective: We investigated intestinal permeability and fecal, plasma, and urine metabolomic profiles in methotrexate‐treated active psoriatic arthritis (PsA) and how this related to clinical response following one sham or fecal microbiota transplantation (FMT). Methods: This exploratory study is based on the FLORA trial cohort, in which 31 patients with moderate‐to‐high peripheral PsA disease activity, despite at least 3 months of methotrexate‐treatment, were included in a 26‐week, double‐blind, 1:1 randomized, sham‐controlled trial. Participants were randomly allocated to receive either one healthy donor FMT (n = 15) or sham (n = 16) via gastroscopy. The primary trial end point was the proportion of treatment failures through 26 weeks. We performed a lactulose‐to‐mannitol ratio (LMR) test at baseline (n = 31) and at week 26 (n = 26) to assess small intestinal permeability. Metabolomic profiles in fecal, plasma, and urine samples collected at baseline, weeks 4, 12, and 26 were measured using 1H Nuclear Magnetic Resonance. Results: Trial failures (n = 7) had significantly higher LMR compared with responders (n = 19) at week 26 (0.027 [0.017‐0.33]) vs. 0.012 [0‐0.064], P = 0.013), indicating increased intestinal permeability. Multivariate analysis revealed a significant model for responders (n = 19) versus failures (n = 12) at all time points based on their fecal (P < 0.0001) and plasma (P = 0.005) metabolomic profiles, whereas urine metabolomic profiles did not differ between groups (P = 1). Fecal N‐acetyl glycoprotein GlycA correlated with Health Assessment Questionnaire Disability Index (coefficient = 0.50; P = 0.03) and fecal propionate correlated with American College of Rheumatology 20 response at week 26 (coefficient = 27, P = 0.02). Conclusion: Intestinal permeability and fecal and plasma metabolomic profiles of patients with PsA were associated with the primary clinical trial end point, failure versus responder. [ABSTRACT FROM AUTHOR]

Published
2023
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44. Commentary on “The road to reliable peptide assays is paved with good guidelines”

Author

Kowalka, Anna M., primary, Alexiadou, Kleopatra, additional, Cuenco, Joyceline, additional, Clarke, Rosemary E., additional, Camuzeaux, Stephane, additional, Minnion, James, additional, Williams, Emma L., additional, Bech, Paul, additional, Purkayastha, Sanjay, additional, Ahmed, Ahmed R., additional, Takats, Zoltan, additional, Khoo, Bernard, additional, Whitwell, Harry J., additional, Romero, Maria G., additional, Bloom, Stephen R., additional, Lewis, Matthew R., additional, and Tan, Tricia M.‐M., additional

Published
2023
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45. Alabama Bass Alter Reservoir Black Bass Species Assemblages When Introduced Outside Their Native Range

Author

Sammons, Steven M., primary, Dorsey, Lawrence G., additional, Loftis, C. Scott, additional, Chrisman, Preston, additional, Scott, Mark, additional, Hammonds, John, additional, Jolley, Michael, additional, Hatcher, Hunter, additional, Odenkirk, John, additional, Damer, John, additional, Lewis, Matthew R., additional, and Peatman, Eric J., additional

Published
2023
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47. Monkeypox virus isolation from longitudinal samples in 11 hospitalised patients

Author

Carson, Gail, Openshaw, Peter, Merson, Laura, Russell, Clark D, Zambon, Maria, Chand, Meera, Tedder, Richard, Khoo, Saye, Horby, Peter, Turtle, Lance CW, Solomon, Tom, Ijaz, Samreen, Fletcher, Tom, Palmarini, Massimo, Ho, Antonia, Price, Nicholas, Alex, Beatrice, Andrikopoulos, Petros, Black, Benjamin, Barclay, Wendy S, Bogaert, Debby, Chechi, Kanta, Da Silva Filipe, Ana, De Silva, Thushan, Docherty, Annemarie B, Dos Santos Correia, Gonçalo, Dumas, Marc-Emmanuel, Green, Christopher A, Greenhalf, William, Griffin, Julian L, Gupta, Rishi, Harrison, Ewen M, Holden, Karl, Klenerman, Paul, Law, Andrew, Lewis, Matthew R, Liggi, Sonia, Lim, Wei Shen, Maslen, Lynn, Mentzer, Alexander J, Meynert, Alison, Moore, Shona, Noursadeghi, Mahdad, Olanipekun, Michael, Osagie, Antonia, Palmieri, Carlo, Paxton, William A, Pollakis, Georgios, Rambaut, Andrew, Robertson, David, Sancho-Shimizu, Vanessa, Sands, Caroline J, Scott, Janet T, Sigfrid, Louise, Sriskandan, Shiranee, Stuart, David, Summers, Charlotte, Swann, Olivia V, Takats, Zoltan, Takis, Panteleimon, Thompson, AA Roger, Thomson, Emma C, Thwaites, Ryan S, Hardwick, Hayley, Oosthuyzen, Wilna, Ostermann, Mariles, Callaby, Helen, Olver, Janie, Emery, Kirsty, Richards, Kevin S, Killip, Marian, Groves, Natalie, Beadsworth, Mike B J, Price, D Ashley, Cooke, Graham S, Collini, Paul, Cole, Joby, Dunning, Jake, Semple, Malcolm G, Baillie, J Kenneth, Rampling, Tommy, and Houlihan, Catherine F

Published
2025
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48. Additional file 1 of Pathobionts in the tumour microbiota predict survival following resection for colorectal cancer

Author

Alexander, James L., Posma, Joram M., Scott, Alasdair, Poynter, Liam, Mason, Sam E., Doria, M. Luisa, Herendi, Lili, Roberts, Lauren, McDonald, Julie A. K., Cameron, Simon, Hughes, David J., Liska, Vaclav, Susova, Simona, Soucek, Pavel, der Sluis, Verena Horneffer-van, Gomez-Romero, Maria, Lewis, Matthew R., Hoyles, Lesley, Woolston, Andrew, Cunningham, David, Darzi, Ara, Gerlinger, Marco, Goldin, Robert, Takats, Zoltan, Marchesi, Julian R., Teare, Julian, and Kinross, James

Abstract

Additional file 1: Table S1. Total number of sequencing reads before and after QC filtering and coverage after QC filtering. Median DNA yield per sample: 4.76 µg/ml (interquartile range 2.53 µg/ml – 11.50 µg/ml). Table S2. Czech cohort demographics. Table S3. Cox proportional hazards analysis showing univariable associations of variables with outcome (death or recurrence of CRC) in 127 UK patients. Table S4. Demographics of patients included in full tumour exome sequencing. Fig. S1. Czech data set. Y-axis labels are species, or higher taxonomic rank if species data is not known, X-axis labels show the taxonomic order. Clustering from UK data is applied. Fig. S2. Scatter plots of matched 16S rRNA amplicon sequencing read counts with bacteria-specific qPCR for four target bacteria (a) Ruminococcus gnavus, (b) Faecalibacterium prausnitzii, (c) Fusobacterium nucleatum, (d) Granulicatella adiacens. r and p values derived from Spearman correlation. Fig. S3. Czech data set for metabolites with clustering from UK data applied. Fig. S4. Network analysis linking bacterial taxa with metabolites based on identification of metabolites which are involved in enzymatic reactions encoded by genes present in the microbial clusters, with reference to the KEGG database. 13 Green circle: the microbe is found in the list of organisms with enzymatic link(s) to the metabolite. Magenta cross: the microbe is not be found in the list of organisms with enzymatic link(s) to the metabolite. Fig. S5. Results of full exome sequencing on 9 tumour samples. Each sample is denoted by its dominant microbiota (micro) and metabolomic (met) cluster subtypes. Mutation loads are shown. Mutations to key driver genes are listed within sub-groups. The type of mutation is shown adjacent (right side) of each gene. FS: frameshift deletion; NS: non synonymous mutation; SS: splice site; PS: premature stop; non-FS del: non-frameshift deletion.

Published
2023
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49. The postprandial secretion of peptide YY 1‐36 and 3‐36 in obesity is differentially increased after gastric bypass versus sleeve gastrectomy

Author

Kowalka, Anna M., primary, Alexiadou, Kleopatra, additional, Cuenco, Joyceline, additional, Clarke, Rosemary E., additional, Minnion, James, additional, Williams, Emma L., additional, Bech, Paul, additional, Purkayastha, Sanjay, additional, Ahmed, Ahmed R., additional, Takats, Zoltan, additional, Whitwell, Harry J., additional, Romero, Maria Gomez, additional, Bloom, Stephen R., additional, Camuzeaux, Stephane, additional, Lewis, Matthew R., additional, Khoo, Bernard, additional, and Tan, Tricia M.‐M., additional

Published
2022
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50. Improved quantitation of short-chain carboxylic acids in human biofluids using 3-nitrophenylhydrazine derivatization and liquid chromatography with tandem mass spectrometry (LC-MS/MS)

Author

Valdivia-Garcia, Maria A., primary, Chappell, Katie E., additional, Camuzeaux, Stephane, additional, Olmo-García, Lucía, additional, van der Sluis, Verena Horneffer, additional, Radhakrishnan, Shiva T., additional, Stephens, Hannah, additional, Bouri, Sonia, additional, de Campos Braz, Lucia M., additional, Williams, Horace T., additional, Lewis, Matthew R., additional, Frost, Gary, additional, and Li, Jia V., additional

Published
2022
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