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1. Obesity Is Associated with Attenuated Tissue Immunity in COVID-19

Author

Guo, Shuang A, Bowyer, Georgina S, Ferdinand, John R, Maes, Mailis, Tuong, Zewen K, Gillman, Eleanor, Liao, Mingfeng, Lindeboom, Rik GH, Yoshida, Masahiro, Worlock, Kaylee, Gopee, Hudaa, Stephenson, Emily, Gao, Catherine A, Lyons, Paul A, Smith, Kenneth GC, Haniffa, Muzlifah, Meyer, Kerstin B, Nikolić, Marko Z, Zhang, Zheng, Wunderink, Richard G, Misharin, Alexander V, Dougan, Gordon, Navapurkar, Vilas, Teichmann, Sarah A, Conway Morris, Andrew, Clatworthy, Menna R, Guo, Shuang A [0000-0002-1712-9180], Bowyer, Georgina S [0000-0002-2058-4045], Ferdinand, John R [0000-0003-0936-0128], Maes, Mailis [0000-0002-0266-6557], Tuong, Zewen K [0000-0002-6735-6808], Gillman, Eleanor [0000-0002-4221-7270], Lindeboom, Rik GH [0000-0002-3660-504X], Yoshida, Masahiro [0000-0002-3521-5322], Worlock, Kaylee [0000-0002-5656-7634], Gopee, Hudaa [0000-0001-8507-5682], Stephenson, Emily [0000-0002-4244-4019], Gao, Catherine A [0000-0001-5576-3943], Lyons, Paul A [0000-0001-7035-8997], Smith, Kenneth GC [0000-0003-3829-4326], Haniffa, Muzlifah [0000-0002-3927-2084], Meyer, Kerstin B [0000-0001-5906-1498], Nikolić, Marko Z [0000-0001-6304-6848], Zhang, Zheng [0000-0002-3544-1389], Wunderink, Richard G [0000-0002-8527-4195], Misharin, Alexander V [0000-0003-2879-3789], Dougan, Gordon [0000-0003-0022-965X], Navapurkar, Vilas [0000-0002-3610-3568], Teichmann, Sarah A [0000-0002-6294-6366], Conway Morris, Andrew [0000-0002-3211-3216], Clatworthy, Menna R [0000-0002-3340-9828], and Apollo - University of Cambridge Repository

Subjects
Adult, Pulmonary and Respiratory Medicine, obesity, Pediatric Obesity, SARS-CoV-2, COVID-19, Critical Care and Intensive Care Medicine, single-cell RNA sequencing, type-I interferon, Interferon Type I, Leukocytes, Mononuclear, bronchoalveolar lavage, Humans, Child, Lung
Abstract

Rationale: Obesity affects 40% of U.S. adults, is associated with a proinflammatory state, and presents a significant risk factor for the development of severe coronavirus disease (COVID-19). To date, there is limited information on how obesity might affect immune cell responses in severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection. Objectives: To determine the impact of obesity on respiratory tract immunity in COVID-19 across the human lifespan. Methods: We analyzed single-cell transcriptomes from BAL in three ventilated adult cohorts with (n = 24) or without (n = 9) COVID-19 from nasal immune cells in children with (n = 14) or without (n = 19) COVID-19, and from peripheral blood mononuclear cells in an independent adult COVID-19 cohort (n = 42), comparing obese and nonobese subjects. Measurements and Main Results: Surprisingly, we found that obese adult subjects had attenuated lung immune or inflammatory responses in SARS-CoV-2 infection, with decreased expression of IFN-α, IFN-γ, and TNF-α (tumor necrosis factor α) response gene signatures in almost all lung epithelial and immune cell subsets, and lower expression of IFNG and TNF in specific lung immune cells. Peripheral blood immune cells in an independent adult cohort showed a similar but less marked reduction in type-I IFN and IFNγ response genes, as well as decreased serum IFNα, in obese patients with SARS-CoV-2. Nasal immune cells from obese children with COVID-19 also showed reduced enrichment of IFN-α and IFN-γ response genes. Conclusions: These findings show blunted tissue immune responses in obese patients with COVID-19, with implications for treatment stratification, supporting the specific application of inhaled recombinant type-I IFNs in this vulnerable subset.

Published
2023

2. Reduced circulating BMP9 and pBMP10 in hospitalized COVID-19 patients

Author

Dunmore, Benjamin J, Upton, Paul D, Auckland, Kate, Samanta, Romit J, Lyons, Paul A, Smith, Kenneth G C, Gräf, Stefan, Summers, Charlotte, Morrell, Nicholas W, Smith, Kenneth G C [0000-0003-3829-4326], and Apollo - University of Cambridge Repository

Subjects
Endothelial Cell Dysfunction, Bmps, Viral Infections And Pathogenesis
Abstract

Similar to other causes of acute respiratory distress syndrome, coronavirus disease 2019 (COVID-19) is characterized by the aberrant expression of vascular injury biomarkers. We present the first report that circulating plasma bone morphogenetic proteins (BMPs), BMP9 and pBMP10, involved in vascular protection, are reduced in hospitalized patients with COVID-19.

Published
2023

3. Proteomic analysis of circulating immune cells identifies cellular phenotypes associated with COVID-19 severity

Author

Potts, Martin, Fletcher-Etherington, Alice, Nightingale, Katie, Mescia, Federica, Bergamaschi, Laura, Calero-Nieto, Fernando J, Antrobus, Robin, Williamson, James, Cambridge Institute Of Therapeutic Immunology And Infectious Disease-National Institute Of Health Research (CITIID-NIHR) COVID BioResource Collaboration, Parsons, Harriet, Huttlin, Edward L, Kingston, Nathalie, Göttgens, Berthold, Bradley, John R, Lehner, Paul J, Matheson, Nicholas J, Smith, Kenneth GC, Wills, Mark R, Lyons, Paul A, Weekes, Michael P, Weekes, Michael [0000-0003-3196-5545], and Apollo - University of Cambridge Repository

Subjects
CP: Immunology
Abstract

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

Published
2023

4. Identification of new risk loci shared across systemic vasculitides points towards potential target genes for drug repurposing

Author

Ortiz-Fernández, Lourdes, Carmona, Elio G, Kerick, Martin, Lyons, Paul, Carmona, Francisco David, López Mejías, Raquel, Khor, Chiea Chuen, Grayson, Peter C, Tombetti, Enrico, Jiang, Lindi, Direskeneli, Haner, Saruhan-Direskeneli, Guher, Callejas-Rubio, José-Luis, Vaglio, Augusto, Salvarani, Carlo, Hernández-Rodríguez, Jose, Cid, Maria Cinta, Morgan, Ann W, Merkel, Peter A, Burgner, David, Smith, Kenneth Gc, Gonzalez-Gay, Miguel Angel, Sawalha, Amr H, Martin, Javier, Marquez, Ana, Ortiz-Fernández, Lourdes [0000-0002-0247-4280], Carmona, Francisco David [0000-0002-1427-7639], Grayson, Peter C [0000-0002-8269-9438], Salvarani, Carlo [0000-0003-3708-3148], Hernández-Rodríguez, Jose [0000-0002-2357-2015], Cid, Maria Cinta [0000-0002-4730-0938], Gonzalez-Gay, Miguel Angel [0000-0002-7924-7406], Martin, Javier [0000-0002-2202-0622], Marquez, Ana [0000-0001-9913-7688], Apollo - University of Cambridge Repository, and Ortiz-Fernandez L., Carmona E. G., Kerick M., Lyons P., Carmona F. D., Mejias R. L., Khor C. C., Grayson P. C., Tombetti E., Jiang L., et al.

Subjects
Internal Diseases, Vasculitis, Immunology, Autoimmunity, SUSCEPTIBILITY, VARIANTS, Sağlık Bilimleri, İmmünoloji ve Romatoloji, İç Hastalıkları, Clinical Medicine (MED), General Biochemistry, Genetics and Molecular Biology, Immunology and Rheumatology, ACTIVATION, Genetic, Rheumatology, Health Sciences, Humans, Immunology and Allergy, Klinik Tıp (MED), CTLA-4 Antigen, Genetic Predisposition to Disease, Polymorphism, GENOME-WIDE ASSOCIATION, ROMATOLOJİ, Internal Medicine Sciences, Polymorphism, Genetic, Klinik Tıp, Systemic Vasculitis, Drug Repositioning, Dahili Tıp Bilimleri, CLINICAL MEDICINE, Tıp, Medicine, Romatoloji, Apoptosis Regulatory Proteins
Abstract

Objectives The number of susceptibility loci currently associated with vasculitis is lower than in other immune-mediated diseases due in part to small cohort sizes, a consequence of the low prevalence of vasculitides. This study aimed to identify new genetic risk loci for the main systemic vasculitides through a comprehensive analysis of their genetic overlap. Methods Genome-wide data from 8467 patients with any of the main forms of vasculitis and 29 795 healthy controls were meta-analysed using ASSET. Pleiotropic variants were functionally annotated and linked to their target genes. Prioritised genes were queried in DrugBank to identify potentially repositionable drugs for the treatment of vasculitis. Results Sixteen variants were independently associated with two or more vasculitides, 15 of them representing new shared risk loci. Two of these pleiotropic signals, located close to CTLA4 and CPLX1, emerged as novel genetic risk loci in vasculitis. Most of these polymorphisms appeared to affect vasculitis by regulating gene expression. In this regard, for some of these common signals, potential causal genes were prioritised based on functional annotation, including CTLA4, RNF145, IL12B, IL5, IRF1, IFNGR1, PTK2B, TRIM35, EGR2 and ETS2, each of which has key roles in inflammation. In addition, drug repositioning analysis showed that several drugs, including abatacept and ustekinumab, could be potentially repurposed in the management of the analysed vasculitides. Conclusions We identified new shared risk loci with functional impact in vasculitis and pinpointed potential causal genes, some of which could represent promising targets for the treatment of vasculitis., HELICAL Innovative Training Network, European Commission funded-under the Marie Sklodowska-Curie 813545, Cooperative Research Thematic Network programme RD16/0012/0013, Redes de Investigacion Cooperativa Orientadas a Resultados en Salud (RICORS) RD21/0002/0039, Instituto de Salud Carlos III PI18/00040, Juan de la Cierva Incorporacion fellowship IJC2019- 040746-I, United States Department of Health & Human Services, National Institutes of Health (NIH) - USA, NIH National Institute of Arthritis & Musculoskeletal & Skin Diseases (NIAMS) R01 AR070148, National Health and Medical Research Council (NHMRC) of Australia GTN1175744, Victorian Government's Operational Infrastructure Support Program, Rare Diseases Clinical Research Network (RDCRN), initiative of the Office of Rare Diseases Research (ORDR), NIH National Center for Advancing Translational Sciences (NCATS), NIH National Institute of Arthritis & Musculoskeletal & Skin Diseases (NIAMS) U54 AR057319, NIH National Center for Research Resources (NCRR) U54 RR019497

Published
2023

5. sj-docx-1-hpp-10.1177_15248399231162377 – Supplemental material for Program Factors Affecting Weight Loss and Mobility in Older Adults: Evidence From the Mobility and Vitality Lifestyle Program (MOVE UP)

Author

Liu, Xinran, Kieffer, Lori A., King, Jennifer, Boak, Brandi, Zgibor, Janice C., Smith, Kenneth J., Burke, Lora E., Jakicic, John M., Semler, Linda N., Danielson, Michelle E., Newman, Anne B., Venditti, Elizabeth M., and Albert, Steven M.

Subjects
Sociology, 111708 Health and Community Services, 111799 Public Health and Health Services not elsewhere classified, FOS: Health sciences, FOS: Sociology
Abstract

Supplemental material, sj-docx-1-hpp-10.1177_15248399231162377 for Program Factors Affecting Weight Loss and Mobility in Older Adults: Evidence From the Mobility and Vitality Lifestyle Program (MOVE UP) by Xinran Liu, Lori A. Kieffer, Jennifer King, Brandi Boak, Janice C. Zgibor, Kenneth J. Smith, Lora E. Burke, John M. Jakicic, Linda N. Semler, Michelle E. Danielson, Anne B. Newman, Elizabeth M. Venditti and Steven M. Albert in Health Promotion Practice

Published
2023
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6. Finding novel targets for the treatment and reversal of type 2 diabetes mellitus and obesity

Author

Ramzan, Imran, Taylor, Moira, Wilkinson, Dan, Smith, Kenneth, Atherton, Philip, and Idris, Iskandar

Subjects
Biomedical and clinical sciences, Medical biotechnology, FOS: Medical biotechnology
Abstract

Poster by Imran Ramzan, Moira Taylor, Kenneth Smith, Dan Wilkinson, Philip Atherton, and Iskandar Idris (University of Nottingham) Background: Recent studies have identified branched chain amino acids (BCAAs; isoleucine, leucine and valine) as potential biomarkers of, and being involved in, the pathogenesis of type 2 diabetes mellitus (T2DM), insulin resistance (IR) and obesity. Reducing circulatory BCAAs by dietary restriction was suggested to mitigate these risks in rodent models, but this is a challenging paradigm to deliver in humans. Objective: We aimed to design and assess the feasibility of a diet aimed at reducing circulating BCAA concentrations in humans, while maintaining energy balance and overall energy/protein intake. Methods: Twelve healthy individuals were assigned to either a 7-day BCAA-restricted diet or a 7-day control diet. Diets were iso-nitrogenous and iso-caloric, with only BCAA levels differing between the two. Results: The BCAA-restricted diet significantly reduced circulating BCAA concentrations by ~50% i.e., baseline 437 ± 60 to 217 ± 40 µmol/L (p < 0.005). Individually, both valine (245 ± 33 to 105 ± 23 µmol/L; p < 0.0001), and leucine (130 ± 20 to 75 ± 13 µmol/L; p < 0.05), decreased significantly in response to the BCAA-restricted diet. The BCAA-restricted diet marginally lowered Homeostatic Model Assessment of Insulin Resistance (HOMA-IR) levels: baseline 1.5 ± 0.2 to 1.0 ± 0.1; (p = 0.096). Conclusion: We successfully lowered circulating BCAAs by 50% while maintaining iso-nitrogenous, iso-caloric dietary intakes, and while meeting the recommended daily allowances (RDA) for protein requirements. The present pilot study represents a novel dietary means by which to reduce BCAA, and as such, provides a blueprint for a potential dietary therapeutic in obesity/diabetes.

Published
2023
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7. Evidence of previous SARS-CoV-2 infection in seronegative patients with long COVID

Author

Krishna, Benjamin A, Lim, Eleanor Y, Mactavous, Lenette, NIHR BioResource Team, Lyons, Paul A, Doffinger, Rainer, Bradley, John R, Smith, Kenneth GC, Sinclair, John, Matheson, Nicholas J, Lehner, Paul J, Wills, Mark R, Sithole, Nyaradzai, Krishna, Benjamin Anthony Cates [0000-0003-0919-2961], Bradley, John [0000-0002-7774-8805], Smith, Kenneth [0000-0003-3829-4326], Sinclair, John [0000-0002-2616-9571], Wills, Mark [0000-0001-8548-5729], Sithole, Nyarie [0000-0002-8020-223X], and Apollo - University of Cambridge Repository

Subjects
Long COVID, Post-Acute COVID-19 Syndrome, SARS-CoV-2, Immunity, Assay, T cell, COVID-19, Humans, Interleukin-2, Antibodies, Viral
Abstract

BACKGROUND: There is currently no consensus on the diagnosis, definition, symptoms, or duration of COVID-19 illness. The diagnostic complexity of Long COVID is compounded in many patients who were or might have been infected with SARS-CoV-2 but not tested during the acute illness and/or are SARS-CoV-2 antibody negative. METHODS: Given the diagnostic conundrum of Long COVID, we set out to investigate SARS-CoV-2-specific T cell responses in patients with confirmed SARS-CoV-2 infection and/or Long COVID from a cohort of mostly non-hospitalised patients. FINDINGS: We discovered that IL-2 release (but not IFN-γ release) from T cells in response to SARS-CoV-2 peptides is both sensitive (75% +/-13%) and specific (88%+/-7%) for previous SARS-CoV-2 infection >6 months after a positive PCR test. We identified that 42-53% of patients with Long COVID, but without detectable SARS-CoV-2 antibodies, nonetheless have detectable SARS-CoV-2 specific T cell responses. INTERPRETATION: Our study reveals evidence (detectable T cell mediated IL-2 release) of previous SARS-CoV-2 infection in seronegative patients with Long COVID. FUNDING: This work was funded by the Addenbrooke's Charitable Trust (900276 to NS), NIHR award (G112259 to NS) and supported by the NIHR Cambridge Biomedical Research Centre. NJM is supported by the MRC (TSF MR/T032413/1) and NHSBT (WPA15-02). PJL is supported by the Wellcome Trust (PRF 210688/Z/18/Z, 084957/Z/08/Z), a Medical Research Council research grant MR/V011561/1 and the United Kingdom Research and a Innovation COVID Immunology Consortium grant (MR/V028448/1).

Published
2022
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8. Measuring Inviting School Climate

Author

Okaya, Tom Mboya, Horne, Marj, Laming, Madeleine, and Smith, Kenneth H.

Abstract

The present study utilized the Inviting School Survey-Revised (ISS-R) (Smith, 2005b, 2013) based on Invitational Theory andPractice (Purkey & Novak, 2008) to examine the school climate of a public primary school in a low urban socio-economicsetting in Kenya. School climate was defined as the perceptions of primary school teachers and pupils in five areas: People,Places, Processes, Policies, and Programs, based on the Invitational theory and Practice paradigm. Results showed that theoverall school climate of Raduce primary school was inviting in many areas. The current study revealed that in spite of thechallenges facing a public school in an urban low socio-economic setting, it is possible with inviting policies, programs,processes, and people, to realize positive academic achievement with students.

Published
2022

9. Brain injury in COVID-19 is associated with dysregulated innate and adaptive immune responses

Author

Needham, Edward J, Ren, Alexander L, Digby, Richard J, Norton, Emma J, Ebrahimi, Soraya, Outtrim, Joanne G, Chatfield, Doris A, Manktelow, Anne E, Leibowitz, Maya M, Newcombe, Virginia FJ, Doffinger, Rainer, Barcenas-Morales, Gabriela, Fonseca, Claudia, Taussig, Michael J, Burnstein, Rowan M, Samanta, Romit J, Dunai, Cordelia, Sithole, Nyarie, Ashton, Nicholas J, Zetterberg, Henrik, Gisslén, Magnus, Edén, Arden, Marklund, Emelie, Openshaw, Peter JM, Dunning, Jake, Griffiths, Michael J, Cavanagh, Jonathan, Breen, Gerome, Irani, Sarosh R, Elmer, Anne, Kingston, Nathalie, Summers, Charlotte, Bradley, John R, Taams, Leonie S, Michael, Benedict D, Bullmore, Edward T, Smith, Kenneth GC, Lyons, Paul A, Coles, Alasdair J, Menon, David K, Cambridge NeuroCOVID Group, CITIID-NIHR COVID-19 BioResource Collaboration, Cambridge NIHR Clinical Research Facility, Needham, Edward J [0000-0001-7042-7462], Norton, Emma J [0000-0003-1877-2474], Newcombe, Virginia FJ [0000-0001-6044-9035], Zetterberg, Henrik [0000-0003-3930-4354], Irani, Sarosh R [0000-0002-7667-9748], Taams, Leonie S [0000-0002-9337-7194], Menon, David K [0000-0002-3228-9692], and Apollo - University of Cambridge Repository

Subjects
autoantibodies, Neurofilament Proteins, Brain Injuries, Influenza, Human, Immunity, COVID-19, Humans, brain injury, Biomarkers, neuroinflammation
Abstract

COVID-19 is associated with neurological complications including stroke, delirium and encephalitis. Furthermore, a post-viral syndrome dominated by neuropsychiatric symptoms is common, and is seemingly unrelated to COVID-19 severity. The true frequency and underlying mechanisms of neurological injury are unknown, but exaggerated host inflammatory responses appear to be a key driver of COVID-19 severity. We investigated the dynamics of, and relationship between, serum markers of brain injury [neurofilament light (NfL), glial fibrillary acidic protein (GFAP) and total tau] and markers of dysregulated host response (autoantibody production and cytokine profiles) in 175 patients admitted with COVID-19 and 45 patients with influenza. During hospitalization, sera from patients with COVID-19 demonstrated elevations of NfL and GFAP in a severity-dependent manner, with evidence of ongoing active brain injury at follow-up 4 months later. These biomarkers were associated with elevations of pro-inflammatory cytokines and the presence of autoantibodies to a large number of different antigens. Autoantibodies were commonly seen against lung surfactant proteins but also brain proteins such as myelin associated glycoprotein. Commensurate findings were seen in the influenza cohort. A distinct process characterized by elevation of serum total tau was seen in patients at follow-up, which appeared to be independent of initial disease severity and was not associated with dysregulated immune responses unlike NfL and GFAP. These results demonstrate that brain injury is a common consequence of both COVID-19 and influenza, and is therefore likely to be a feature of severe viral infection more broadly. The brain injury occurs in the context of dysregulation of both innate and adaptive immune responses, with no single pathogenic mechanism clearly responsible.

Published
2022

10. Soil carbon pools are affected by species identity and productivity in a tree common garden experiment

Author

Waring, Bonnie G., Smith, Kenneth R., Belluau, Michael, Khlifa, Rim, Messier, Christian, Munson, Alison, and Paquette, Alain

Subjects
Global and Planetary Change, Ecology, Forestry, Environmental Science (miscellaneous), Nature and Landscape Conservation
Abstract

The formation and turnover of soil organic carbon (C), the largest terrestrial C pool, is strongly impacted by the ultimate source of that C: leaves, wood, roots, and root exudates. The quantity and quality of these inputs is determined by the identity of the plants involved. Yet substantial uncertainty surrounds the complex relationships among plant traits and soil C, precluding efforts to maximize whole-ecosystem C uptake in nature-based climate mitigation scenarios. In this study, we leveraged a biodiversity-ecosystem function experiment with trees (IDENT) to explore the effects of interspecific variation in plant traits on soil C dynamics in the very early stages of stand development (9 years since planting). Mineral soil C stocks to 5 cm depth were quantified in monospecific plots of 19 tree species planted on a former agricultural field, and analyzed in relation to tree growth and functional traits. We found that tree species identity affected soil bulk density and, to a lesser extent, the carbon content of the topsoil, and thereby total C pools. Among species and across plots, mineral soil C stocks were positively correlated with rates of tree growth and were significantly larger beneath broadleaf trees with “fast” functional traits vs. conifers with more conservative leaf traits, when comparisons were made over equivalent soil depth increments. Thus, plant functional traits mediate interspecific differences in productivity, which in turn influence the magnitude of belowground C stocks. These results highlight important linkages between above- and belowground carbon cycles in the earliest stages of afforestation.

Published
2022

11. Altered TMPRSS2 usage by SARS-CoV-2 Omicron impacts infectivity and fusogenicity

Author

Meng, Bo, Abdullahi, Adam, Ferreira, Isabella ATM, Goonawardane, Niluka, Saito, Akatsuki, Kimura, Izumi, Yamasoba, Daichi, Gerber, Pehuén Pereyra, Fatihi, Saman, Rathore, Surabhi, Zepeda, Samantha K, Papa, Guido, Kemp, Steven, Ikeda, Terumasa, Toyoda, Mako, Tan, Toong Seng, Kuramochi, Jin, Mitsunaga, Shigeki, Ueno, Takamasa, Shirakawa, Kotaro, Takaori-Kondo, Akifumi, Brevini, Teresa, Mallery, Donna L, Charles, Oscar J, CITIID-NIHR BioResource COVID-19 Collaboration, Genotype To Phenotype Japan (G2P-Japan) Consortium, Ecuador-COVID19 Consortium, Bowen, John E, Joshi, Anshu, Walls, Alexandra C, Jackson, Laurelle, Martin, Darren, Smith, Kenneth, Bradley, John, Briggs, John AG, Choi, Jinwook, Madissoon, Elo, Meyer, Kerstin B, Mlcochova, Petra, Ceron-Gutierrez, Lourdes, Doffinger, Rainer, Teichmann, Sarah, Fisher, Andrew J, Pizzuto, Matteo S, De Marco, Anna, Corti, Davide, Hosmillo, Myra, Lee, Joo, James, Leo C, Thukral, Lipi, Veesler, David, Sigal, Alex, Sampaziotis, Fotios, Goodfellow, Ian G, Matheson, Nicholas J, Sato, Kei, Gupta, Ravindra, Gupta, Ravindra K [0000-0001-9751-1808], Apollo - University of Cambridge Repository, Kemp, Steven [0000-0001-7077-6793], Smith, Kenneth [0000-0003-3829-4326], Teichmann, Sarah [0000-0002-6294-6366], Hosmillo, Myra [0000-0002-3514-7681], Lee, Joo [0000-0002-7364-6422], Sampaziotis, Fotios [0000-0003-0812-7586], and Gupta, Ravindra [0000-0001-9751-1808]

Subjects
Adult, Male, COVID-19 Vaccines, Antibodies, Viral, Virus Replication, Membrane Fusion, Cell Line, Tissue Culture Techniques, Chlorocebus aethiops, Animals, Humans, Lung, Aged, Aged, 80 and over, Virulence, SARS-CoV-2, Immune Sera, Cell Membrane, Serine Endopeptidases, COVID-19, Convalescence, Middle Aged, Virus Internalization, Antibodies, Neutralizing, Intestines, Nasal Mucosa, Mutation, Spike Glycoprotein, Coronavirus, Female, Angiotensin-Converting Enzyme 2
Abstract

The SARS-CoV-2 Omicron BA.1 variant emerged in 20211 and has multiple mutations in its spike protein2. Here we show that the spike protein of Omicron has a higher affinity for ACE2 compared with Delta, and a marked change in its antigenicity increases Omicron's evasion of therapeutic monoclonal and vaccine-elicited polyclonal neutralizing antibodies after two doses. mRNA vaccination as a third vaccine dose rescues and broadens neutralization. Importantly, the antiviral drugs remdesivir and molnupiravir retain efficacy against Omicron BA.1. Replication was similar for Omicron and Delta virus isolates in human nasal epithelial cultures. However, in lung cells and gut cells, Omicron demonstrated lower replication. Omicron spike protein was less efficiently cleaved compared with Delta. The differences in replication were mapped to the entry efficiency of the virus on the basis of spike-pseudotyped virus assays. The defect in entry of Omicron pseudotyped virus to specific cell types effectively correlated with higher cellular RNA expression of TMPRSS2, and deletion of TMPRSS2 affected Delta entry to a greater extent than Omicron. Furthermore, drug inhibitors targeting specific entry pathways3 demonstrated that the Omicron spike inefficiently uses the cellular protease TMPRSS2, which promotes cell entry through plasma membrane fusion, with greater dependency on cell entry through the endocytic pathway. Consistent with suboptimal S1/S2 cleavage and inability to use TMPRSS2, syncytium formation by the Omicron spike was substantially impaired compared with the Delta spike. The less efficient spike cleavage of Omicron at S1/S2 is associated with a shift in cellular tropism away from TMPRSS2-expressing cells, with implications for altered pathogenesis.

Published
2022
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12. Coagulation factor V is a T-cell inhibitor expressed by leukocytes in COVID-19

Author

Wang, Jun, Kotagiri, Prasanti, Lyons, Paul, Al-Lamki, Rafia, Mescia, Federica, Bergamaschi, Laura, Turner, Lorinda, Morgan, Michael D, Calero-Nieto, Fernando J, Bach, Karsten, Mende, Nicole, Wilson, Nicola K, Watts, Emily R, Cambridge Institute Of Therapeutic Immunology And Infectious Disease-National Institute Of Health Research (CITIID-NIHR) Covid BioResource Collaboration, Maxwell, Patrick, Chinnery, Patrick F, Kingston, Nathalie, Papadia, Sofia, Stirrups, Kathleen, Walker, Neil, Gupta, Ravindra, Menon, David, Allinson, Kieren, Aitken, Sarah, Toshner, Mark, Weekes, Michael, Nathan, James, Walmsley, Sarah R, Ouwehand, Willem H, Kasanicki, Mary, Gottgens, Berthold, Marioni, John, Smith, Kenneth, Pober, Jordan S, Bradley, John, Wang, Jun [0000-0003-3667-3760], Lyons, Paul [0000-0001-7035-8997], Mende, Nicole [0000-0002-5078-2333], Maxwell, Patrick [0000-0002-0338-2679], Kingston, Nathalie [0000-0002-9190-2231], Johnson, Kathleen [0000-0002-6823-3252], Gupta, Ravindra [0000-0001-9751-1808], Menon, David [0000-0002-3228-9692], Aitken, Sarah [0000-0002-1897-4140], Toshner, Mark [0000-0002-3969-6143], Weekes, Michael [0000-0003-3196-5545], Nathan, James [0000-0002-0248-1632], Gottgens, Berthold [0000-0001-6302-5705], Marioni, John [0000-0001-9092-0852], Smith, Kenneth [0000-0003-3829-4326], Bradley, John [0000-0002-7774-8805], Apollo - University of Cambridge Repository, and Stirrups, Kathleen [0000-0002-6823-3252]

Subjects
FOS: Clinical medicine, FOS: Biological sciences, education, Immunology, Omics, Transcriptomics, Microbiology
Abstract

Funder: Royal Australasian College of Physicians, Funder: NIHR, Funder: UKRI, Funder: Chief Scientist Office, Clotting Factor V (FV) is primarily synthesized in the liver and when cleaved by thrombin forms pro-coagulant Factor Va (FVa). Using whole blood RNAseq and scRNAseq of peripheral blood mononuclear cells, we find that FV mRNA is expressed in leukocytes, and identify neutrophils, monocytes, and T regulatory cells as sources of increased FV in hospitalized patients with COVID-19. Proteomic analysis confirms increased FV in circulating neutrophils in severe COVID-19, and immunofluorescence microscopy identifies FV in lung-infiltrating leukocytes in COVID-19 lung disease. Increased leukocyte FV expression in severe disease correlates with T-cell lymphopenia. Both plasma-derived and a cleavage resistant recombinant FV, but not thrombin cleaved FVa, suppress T-cell proliferation in vitro. Anticoagulants that reduce FV conversion to FVa, including heparin, may have the unintended consequence of suppressing the adaptive immune system.

Published
2022

13. SARS-CoV-2 B.1.1.7 sensitivity to mRNA vaccine-elicited, convalescent and monoclonal antibodies

Author

Collier, Dami A, De Marco, Anna, Ferreira, Isabella ATM, Meng, Bo, Datir, Rawlings, Walls, Alexandra C, Kemp S, Steven A, Bassi, Jessica, Pinto, Dora, Fregni, Chiara Silacci, Bianchi, Siro, Tortorici, M Alejandra, Bowen, John, Culap, Katja, Jaconi, Stefano, Cameroni, Elisabetta, Snell, Gyorgy, Pizzuto, Matteo S, Pellanda, Alessandra Franzetti, Garzoni, Christian, Riva, Agostino, CITIID-NIHR BioResource COVID-19 Collaboration, Elmer, Anne, Kingston, Nathalie, Graves, Barbara, McCoy, Laura E, Smith, Kenneth Gc, Bradley, John R, Temperton, Nigel, Ceron-Gutierrez L, Lourdes, Barcenas-Morales, Gabriela, COVID-19 Genomics UK (COG-UK) Consortium, Harvey, William, Virgin, Herbert W, Lanzavecchia, Antonio, Piccoli, Luca, Doffinger, Rainer, Wills, Mark, Veesler, David, Corti, Davide, Gupta, Ravindra K, Datir, Rawlings [0000-0003-0521-2144], Smith, Kenneth [0000-0003-3829-4326], Bradley, John [0000-0002-7774-8805], Wills, Mark [0000-0001-8548-5729], and Apollo - University of Cambridge Repository

Subjects
The COVID-19 Genomics UK (COG-UK) consortium, The CITIID-NIHR BioResource COVID-19 Collaboration
Abstract

Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2) transmission is uncontrolled in many parts of the world, compounded in some areas by higher transmission potential of the B1.1.7 variant now seen in 50 countries. It is unclear whether responses to SARS-CoV-2 vaccines based on the prototypic strain will be impacted by mutations found in B.1.1.7. Here we assessed immune responses following vaccination with mRNA-based vaccine BNT162b2. We measured neutralising antibody responses following a single immunization using pseudoviruses expressing the wild-type Spike protein or the 8 amino acid mutations found in the B.1.1.7 spike protein. The vaccine sera exhibited a broad range of neutralising titres against the wild-type pseudoviruses that were modestly reduced against B.1.1.7 variant. This reduction was also evident in sera from some convalescent patients. Decreased B.1.1.7 neutralisation was also observed with monoclonal antibodies targeting the N-terminal domain (9 out of 10), the Receptor Binding Motif (RBM) (5 out of 31), but not in neutralising mAbs binding outside the RBM. Introduction of the E484K mutation in a B.1.1.7 background to reflect newly emerging viruses in the UK led to a more substantial loss of neutralising activity by vaccine-elicited antibodies and mAbs (19 out of 31) over that conferred by the B.1.1.7 mutations alone. E484K emergence on a B.1.1.7 background represents a threat to the vaccine BNT162b.

Published
2022
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14. The impact of hypoxia on B cells in COVID-19

Author

Kotagiri, Prasanti, Mescia, Federica, Hanson, Aimee L, Turner, Lorinda, Bergamaschi, Laura, Peñalver, Ana, Richoz, Nathan, Moore, Stephen D, Ortmann, Brian M, Dunmore, Benjamin J, Morgan, Michael D, Tuong, Zewen Kelvin, Cambridge Institute Of Therapeutic Immunology And Infectious Disease-National Institute Of Health Research (CITIID-NIHR) COVID BioResource Collaboration, Göttgens, Berthold, Toshner, Mark, Hess, Christoph, Maxwell, Patrick H, Clatworthy, Menna R, Nathan, James A, Bradley, John R, Lyons, Paul A, Burrows, Natalie, Smith, Kenneth GC, Hanson, Aimee [0000-0002-0231-8771], Tuong, Kelvin [0000-0002-6735-6808], Gottgens, Berthold [0000-0001-6302-5705], Toshner, Mark [0000-0002-3969-6143], Maxwell, Patrick [0000-0002-0338-2679], Clatworthy, Menna [0000-0002-3340-9828], Nathan, James [0000-0002-0248-1632], Bradley, John [0000-0002-7774-8805], Lyons, Paul [0000-0001-7035-8997], Smith, Kenneth [0000-0003-3829-4326], and Apollo - University of Cambridge Repository

Subjects
Oxygen, B cells, Mice, SARS-CoV-2, Lymphopenia, COVID-19, Animals, Humans, Pneumonia, Hypoxia
Abstract

Funder: Evelyn Trust, Funder: NHSBT, Funder: MRC, Funder: NIHR, Funder: Cambridge University Hospitals NHS Foundation Trust, BACKGROUND: Prominent early features of COVID-19 include severe, often clinically silent, hypoxia and a pronounced reduction in B cells, the latter important in defence against SARS-CoV-2. This presentation resembles the phenotype of mice with VHL-deficient B cells, in which Hypoxia-Inducible Factors are constitutively active, suggesting hypoxia might drive B cell abnormalities in COVID-19. METHODS: Detailed B cell phenotyping was undertaken by flow-cytometry on longitudinal samples from patients with COVID-19 across a range of severities (NIHR Cambridge BioResource). The impact of hypoxia on the transcriptome was assessed by single-cell and whole blood RNA sequencing analysis. The direct effect of hypoxia on B cells was determined through immunisation studies in genetically modified and hypoxia-exposed mice. FINDINGS: We demonstrate the breadth of early and persistent defects in B cell subsets in moderate/severe COVID-19, including reduced marginal zone-like, memory and transitional B cells, changes also observed in B cell VHL-deficient mice. These findings were associated with hypoxia-related transcriptional changes in COVID-19 patient B cells, and similar B cell abnormalities were seen in mice kept in hypoxic conditions. INTERPRETATION: Hypoxia may contribute to the pronounced and persistent B cell pathology observed in acute COVID-19 pneumonia. Assessment of the impact of early oxygen therapy on these immune defects should be considered, as their correction could contribute to improved outcomes. FUNDING: Evelyn Trust, Addenbrooke's Charitable Trust, UKRI/NIHR, Wellcome Trust.

Published
2022

15. B cell receptor repertoire kinetics after SARS-CoV-2 infection and vaccination

Author

Kotagiri, Prasanti, Mescia, Federica, Rae, William M, Bergamaschi, Laura, Tuong, Kelvin, Turner, Lorinda, Hunter, Kelvin, Gerber, Pehu��n P, Hosmillo, Myra, Cambridge Institute Of Therapeutic Immunology And Infectious Disease-National Institute Of Health Research (CITIID-NIHR) COVID BioResource Collaboration, Hess, Christoph, Clatworthy, Menna, Goodfellow, Ian G, Matheson, Nicholas, McKinney, Eoin F, Wills, Mark, Gupta, Ravindra, Bradley, John, Bashford-Rogers, Rachael JM, Lyons, Paul, Smith, Kenneth, Tuong, Kelvin [0000-0002-6735-6808], Hosmillo, Myra [0000-0002-3514-7681], Clatworthy, Menna [0000-0002-3340-9828], Matheson, Nicholas [0000-0002-3318-1851], Wills, Mark [0000-0001-8548-5729], Gupta, Ravindra [0000-0001-9751-1808], Bradley, John [0000-0002-7774-8805], Lyons, Paul [0000-0001-7035-8997], Smith, Kenneth [0000-0003-3829-4326], and Apollo - University of Cambridge Repository

Subjects
B cell receptor repertoire, SARS-CoV-2 vaccination, education, COVID-19, humanities, health care economics and organizations
Abstract

Funder: Medical Research Council, Funder: National Institute for Health Research (NIHR), B cells are important in immunity to both severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) infection and vaccination, but B cell receptor (BCR) repertoire development in these contexts has not been compared. We analyze serial samples from 171 SARS-CoV-2-infected individuals and 63 vaccine recipients and find the global BCR repertoire differs between them. Following infection, immunoglobulin (Ig)G1/3 and IgA1 BCRs increase, somatic hypermutation (SHM) decreases, and, in severe disease, IgM and IgA clones are expanded. In contrast, after vaccination, the proportion of IgD/M BCRs increase, SHM is unchanged, and expansion of IgG clones is prominent. VH1-24, which targets the N-terminal domain (NTD) and contributes to neutralization, is expanded post infection except in the most severe disease. Infection generates a broad distribution of SARS-CoV-2-specific clones predicted to target the spike protein, while a more focused response after vaccination mainly targets the spike's receptor-binding domain. Thus, the nature of SARS-CoV-2 exposure differentially affects BCR repertoire development, potentially informing vaccine strategies.

Published
2022

16. GWAS meta-analysis of intrahepatic cholestasis of pregnancy implicates multiple hepatic genes and regulatory elements

Author

Dixon, Peter H., Levine, Adam P., Cebola, Inês, Chan, Melanie M. Y., Amin, Aliya S., Aich, Anshul, Mozere, Monika, Maude, Hannah, Mitchell, Alice L., Zhang, Jun, Adlard, Julian, Ahmed, Munaza, Aitman, Tim, Alachkar, Hana, Allsup, David, Almeida-King, Jeff, Ancliff, Philip, Antrobus, Richard, Armstrong, Ruth, Arno, Gavin, Ashford, Sofie, Astle, William, Attwood, Anthony, Babbs, Chris, Bakchoul, Tamam, Bariana, Tadbir, Barwell, Julian, Bennett, David, Bentley, David, Bierzynska, Agnieszka, Biss, Tina, Bleda, Marta, Bogaard, Harm, Bourne, Christian, Boyce, Sara, Bradley, John, Breen, Gerome, Brennan, Paul, Brewer, Carole, Brown, Matthew, Browning, Michael, Buchan, Rachel, Buckland, Matthew, Bueser, Teofila, Burns, Siobhan, Burren, Oliver, Calleja, Paul, Carr-White, Gerald, Carss, Keren, Casey, Ruth, Caulfield, Mark, Chambers, John, Chambers, Jennifer, Cheng, Floria, Chinnery, Patrick F., Christian, Martin, Church, Colin, Brod, Naomi Clements, Coghlan, Gerry, Colby, Elizabeth, Cole, Trevor, Collins, Janine, Collins, Peter, Colombo, Camilla, Condliffe, Robin, Cook, Stuart, Cook, Terry, Cooper, Nichola, Corris, Paul, Crisp-Hihn, Abigail, Curry, Nicola, Danesino, Cesare, Daniels, Matthew, Daugherty, Louise, Davis, John, Deevi, Sri V. V., Dent, Timothy, Dewhurst, Eleanor, Dixon, Peter, Downes, Kate, Drazyk, Anna, Drewe, Elizabeth, Dutt, Tina, Edgar, David, Edwards, Karen, Egner, William, Erber, Wendy, Erwood, Marie, Estiu, Maria C., Evans, Gillian, Evans, Dafydd Gareth, Everington, Tamara, Eyries, Mélanie, Favier, Remi, Fletcher, Debra, Fox, James, Frary, Amy, French, Courtney, Freson, Kathleen, Frontini, Mattia, Gale, Daniel, Gall, Henning, Geoghegan, Claire, Gerighty, Terry, Ghio, Stefano, Ghofrani, Hossein-Ardeschir, Gibbs, Simon, Gilmour, Kimberley, Girerd, Barbara, Goddard, Sarah, Gomez, Keith, Gordins, Pavels, Gosal, David, Gräf, Stefan, Grassi, Luigi, Greene, Daniel, Greenhalgh, Lynn, Greinacher, Andreas, Gresele, Paolo, Griffiths, Philip, Grigoriadou, Sofia, Grocock, Russell, Grozeva, Detelina, Hackett, Scott, Hadinnapola, Charaka, Hague, William, Haimel, Matthias, Hall, Matthew, Hanson, Helen, Harkness, Kirsty, Harper, Andrew, Harris, Claire, Hart, Daniel, Hassan, Ahamad, Hayman, Grant, Henderson, Alex, Hoffmann, Jonathan, Horvath, Rita, Houweling, Arjan, Howard, Luke, Hu, Fengyuan, Hudson, Gavin, Hughes, Joseph, Huissoon, Aarnoud, Humbert, Marc, Humphray, Sean, Hunter, Sarah, Hurles, Matthew, Izatt, Louise, James, Roger, Johnson, Sally, Jolles, Stephen, Jolley, Jennifer, Jurkute, Neringa, Kasanicki, Mary, Kazkaz, Hanadi, Kazmi, Rashid, Kelleher, Peter, Kiely, David, Kingston, Nathalie, Klima, Robert, Kostadima, Myrto, Kovacs, Gabor, Koziell, Ania, Kreuzhuber, Roman, Kuijpers, Taco, Kumar, Ajith, Kumararatne, Dinakantha, Kuria, Manju, Laffa, Michael, Lalloo, Fiona, Lamber, Michele, Alle, Hana Lango, Lawrie, Allan, Layton, Mark, Lentaigne, Claire, Levine, Adam, Linger, Rachel, Longhurst, Hilary, Louka, Eleni, Ross, Robert MacKenzie, Madan, Bella, Maher, Eamonn, Maimaris, Jesmeen, Mangles, Sarah, Mapeta, Rutendo, Marchbank, Kevin, Marks, Stephen, Markus, Hugh S., Marshall, Andrew, Martin, Jennifer, Mathias, Mary, Matthews, Emma, Maxwell, Heather, McAlinden, Paul, McCarthy, Mark, Meacham, Stuart, Mead, Adam, Megy, Karyn, Mehta, Sarju, Michaelides, Michel, Millar, Carolyn, Moledina, Shahin, Montani, David, Moor, Tony, Morrell, Nicholas, Muir, Keith, Mumford, Andrew, Newnham, Michael, O'Sullivan, Jennifer, Obaji, Samya, Okoli, Steven, Olschewski, Andrea, Olschewski, Horst, Ong, Kai Ren, Ormondroy, Elizabeth, Ouwehan, Willem, Papadi, Sofia, Park, Soo-Mi, Parry, David, Paterson, Joan, Peacock, Andrew, Peden, John, Peerlinck, Kathelijne, Penkett, Christopher, Pepke-Zaba, Joanna, Petersen, Romina, Pyle, Angela, Rankin, Stuart, Rao, Anupama, Raymond, F. Lucy, Rayner-Matthew, Paula, Rees, Christine, Rendon, Augusto, Renton, Tara, Rice, Andrew, Richardson, Sylvia, Richter, Alex, Roberts, Irene, Roughley, Catherine, Roy, Noemi, Sadeghi-Alavijeh, Omid, Saleem, Moin, Samani, Nilesh, Sanchis-Juan, Alba, Sargur, Ravishankar, Satchell, Simon, Savic, Sinisa, Scelsi, Laura, Schulman, Sol, Scully, Marie, Searle, Claire, Seeger, Werner, Sewell, Carrock, Seyres, Denis, Shapiro, Susie, Sharmardina, Olga, Shtoyerman, Rakefet, Sibson, Keith, Side, Lucy, Simeoni, Ilenia, Simpson, Michael, Sivapalaratnam, Suthesh, Skytte, Anne-Bine, Smith, Katherine, Smith, Kenneth G. C., Snape, Katie, Soubrier, Florent, Staines, Simon, Staples, Emily, Stark, Hannah, Stephens, Jonathan, Stirrups, Kathleen, Stock, Sophie, Suntharalingam, Jay, Swietlik, Emilia, Tait, R. Campbell, Talks, Kate, Tan, Rhea, Thaventhiran, James, Themistocleous, Andreas, Thomas, Moira, Thomson, Kate, Thrasher, Adrian, Thys, Chantal, Tischkowitz, Marc, Titterton, Catherine, Toh, Cheng-Hock, Toshner, Mark, Traylor, Matthew, Treacy, Carmen, Trembath, Richard, Tuna, Salih, Turek, Wojciech, Turro, Ernest, Vale, Tom, Van Geet, Chris, Van Zuydam, Natalie, Vazquez-Lopez, Marta, von Ziegenweidt, Julie, Noordegraaf, Anton Vonk, Waisfisz, Quintin, Walker, Suellen, Ware, James, Watkins, Hugh, Watt, Christopher, Webster, Andrew, Wei, Wei, Welch, Steven, Wessels, Julie, Westbury, Sarah, Westwood, John-Paul, Wharton, John, Whitehorn, Deborah, Whitworth, James, Wilkins, Martin R., Wong, Edwin, Wood, Nicholas, Wood, Yvette, Woods, Geoff, Woodward, Emma, Wort, Stephen, Worth, Austen, Yates, Katherine, Yong, Patrick, Young, Tim, Yu, Ping, Yu-Wai-Man, Patrick, Ambrose, J. C., Arumugam, P., Bevers, R., Bleda, M., Boardman-Pretty, F., Boustred, C. R., Brittain, H., Brown, M. A., Caulfield, M. J., Chan, G. C., Fowler, T., Giess, A., Hamblin, A., Henderson, S., Hubbard, T. J. P., Jackson, R., Jones, L. J., Kasperaviciute, D., Kayikci, M., Kousathanas, A., Lahnstein, L., Leigh, S. E. A., Leong, I. U. S., Lopez, F. J., Maleady-Crowe, F., McEntagart, M., Minneci, F., Moutsianas, L., Mueller, M., Murugaesu, N., Need, A. C., O'Donovan, P., Odhams, C. A., Patch, C., Perez-Gil, D., Pereira, M. B., Pullinger, J., Rahim, T., Rendon, A., Rogers, T., Savage, K., Sawant, K., Scott, R. H., Siddiq, A., Sieghart, A., Smith, S. C., Sosinsky, A., Stuckey, A., Tanguy, M., Taylor Tavares, A. L., Thomas, E. R. A., Thompson, S. R., Tucci, A., Welland, M. J., Williams, E., Witkowska, K., Wood, S. M., Chambers, Jenny, Syngelaki, Argyro, Donnelly, Jennifer, Cooley, Sharon, Geary, Michael, Nicolaides, Kypros, Thorsell, Malin, Hague, William M., Estiu, Maria Cecilia, Marschall, Hanns-Ulrich, Gale, Daniel P., Williamson, Catherine, Pulmonary medicine, ACS - Pulmonary hypertension & thrombosis, Human genetics, ACS - Atherosclerosis & ischemic syndromes, Pediatrics, Foundation for the National Institutes of Health (FNIH), The Academy of Medical Sciences, British Heart Foundation, Imperial College Healthcare NHS Trust- BRC Funding, Paediatric Infectious Diseases / Rheumatology / Immunology, and ARD - Amsterdam Reproduction and Development

Subjects
VARIANT, LOCI, INTEGRATIVE ANALYSIS, General Physics and Astronomy, Cholestasis, Intrahepatic, TRIGLYCERIDE LEVELS, DISEASE, General Biochemistry, Genetics and Molecular Biology, Bile Acids and Salts, Pregnancy, Humans, MUTATION, Science & Technology, Multidisciplinary, Genomics England Research Consortium Collaborators, Infant, Newborn, NIHR BioResource, General Chemistry, GLUCOCORTICOID-RECEPTOR, Multidisciplinary Sciences, ALKALINE SPHINGOMYELINASE, Pregnancy Complications, INSIGHTS, Science & Technology - Other Topics, Premature Birth, Female, FASTING GLUCOSE, Genome-Wide Association Study
Abstract

Intrahepatic cholestasis of pregnancy (ICP) is a pregnancy-specific liver disorder affecting 0.5-2% of pregnancies. The majority of cases present in the third trimester with pruritus, elevated serum bile acids and abnormal serum liver tests. ICP is associated with an increased risk of adverse outcomes, including spontaneous preterm birth and stillbirth. Whilst rare mutations affecting hepatobiliary transporters contribute to the aetiology of ICP, the role of common genetic variation in ICP has not been systematically characterised to date. Here, we perform genome-wide association studies (GWAS) and meta-analyses for ICP across three studies including 1138 cases and 153,642 controls. Eleven loci achieve genome-wide significance and have been further investigated and fine-mapped using functional genomics approaches. Our results pinpoint common sequence variation in liver-enriched genes and liver-specific cis-regulatory elements as contributing mechanisms to ICP susceptibility. ispartof: NATURE COMMUNICATIONS vol:13 issue:1 ispartof: location:England status: published

Published
2022

17. SARS-CoV-2 spike N-terminal domain modulates TMPRSS2-dependent viral entry and fusogenicity

Author

Meng, Bo, Datir, Rawlings, Choi, Jinwook, CITIID-NIHR Bioresource COVID-19 Collaboration, Bradley, John R, Smith, Kenneth GC, Lee, Joo Hyeon, Gupta, Ravindra K, Lee, Joo [0000-0002-7364-6422], Gupta, Ravindra [0000-0001-9751-1808], and Apollo - University of Cambridge Repository

Subjects
Organoid, Omicron, SARS-CoV-2, Serine Endopeptidases, CP: Microbiology, COVID-19, spike, Virus Internalization, NTD, Delta, Spike Glycoprotein, Coronavirus, entry, Humans, fusogenicity, TMPRSS2
Abstract

The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) spike N-terminal domain (NTD) remains poorly characterized despite enrichment of mutations in this region across variants of concern (VOCs). Here, we examine the contribution of the NTD to infection and cell-cell fusion by constructing chimeric spikes bearing B.1.617 lineage (Delta and Kappa variants) NTDs and generating spike pseudotyped lentivirus. We find that the Delta NTD on a Kappa or wild-type (WT) background increases S1/S2 cleavage efficiency and virus entry, specifically in lung cells and airway organoids, through use of TMPRSS2. Delta exhibits increased cell-cell fusogenicity that could be conferred to WT and Kappa spikes by Delta NTD transfer. However, chimeras of Omicron BA.1 and BA.2 spikes with a Delta NTD do not show more efficient TMPRSS2 use or fusogenicity. We conclude that the NTD allosterically modulates S1/S2 cleavage and spike-mediated functions in a spike context-dependent manner, and allosteric interactions may be lost when combining regions from more distantly related VOCs.

Published
2022
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18. Single-cell multi-omics analysis of the immune response in COVID-19

Author

Stephenson, Emily, Reynolds, Gary, Botting, Rachel A., Calero-Nieto, Fernando J., Morgan, Michael D., Tuong, Zewen Kelvin, Bach, Karsten, Sungnak, Waradon, Worlock, Kaylee B., Yoshida, Masahiro, Kumasaka, Natsuhiko, Kania, Katarzyna, Engelbert, Justin, Olabi, Bayanne, Spegarova, Jarmila Stremenova, Wilson, Nicola K., Mende, Nicole, Jardine, Laura, Gardner, Louis C. S., Goh, Issac, Horsfall, Dave, McGrath, Jim, Webb, Simone, Mather, Michael W., Lindeboom, Rik G. H., Dann, Emma, Huang, Ni, Polanski, Krzysztof, Prigmore, Elena, Gothe, Florian, Scott, Jonathan, Payne, Rebecca P., Baker, Kenneth F., Hanrath, Aidan T., Schim van der Loeff, Ina C. D., Barr, Andrew S., Sanchez-Gonzalez, Amada, Bergamaschi, Laura, Mescia, Federica, Barnes, Josephine L., Kilich, Eliz, de Wilton, Angus, Saigal, Anita, Saleh, Aarash, Janes, Sam M., Smith, Claire M., Gopee, Nusayhah, Wilson, Caroline, Coupland, Paul, Coxhead, Jonathan M., Kiselev, Vladimir Yu, van Dongen, Stijn, Bacardit, Jaume, King, Hamish W., Rostron, Anthony J., Simpson, A. John, Hambleton, Sophie, Laurenti, Elisa, Lyons, Paul A., Meyer, Kerstin B., Nikolić, Marko Z., Duncan, Christopher J. A., Smith, Kenneth G. C., Teichmann, Sarah A., Clatworthy, Menna R., Marioni, John C., Göttgens, Berthold, and Haniffa, Muzlifah

Subjects
Proteome, COVID-19, Cross-Sectional Studies, Humans, Monocytes, Receptors, Antigen, B-Cell, Receptors, Antigen, T-Cell, SARS-CoV-2, Single-Cell Analysis, T-Lymphocytes, Transcriptome, CD34, Biology, Peripheral blood mononuclear cell, Article, General Biochemistry, Genetics and Molecular Biology, Immune system, Antigen, Receptors, Platelet activation, Progenitor cell, B-Cell, RNA sequencing, General Medicine, T-Cell, Haematopoiesis, Viral infection, Immunology, Infection, CD8
Abstract

Analysis of human blood immune cells provides insights into the coordinated response to viral infections such as severe acute respiratory syndrome coronavirus 2, which causes coronavirus disease 2019 (COVID-19). We performed single-cell transcriptome, surface proteome and T and B lymphocyte antigen receptor analyses of over 780,000 peripheral blood mononuclear cells from a cross-sectional cohort of 130 patients with varying severities of COVID-19. We identified expansion of nonclassical monocytes expressing complement transcripts (CD16+C1QA/B/C+) that sequester platelets and were predicted to replenish the alveolar macrophage pool in COVID-19. Early, uncommitted CD34+ hematopoietic stem/progenitor cells were primed toward megakaryopoiesis, accompanied by expanded megakaryocyte-committed progenitors and increased platelet activation. Clonally expanded CD8+ T cells and an increased ratio of CD8+ effector T cells to effector memory T cells characterized severe disease, while circulating follicular helper T cells accompanied mild disease. We observed a relative loss of IgA2 in symptomatic disease despite an overall expansion of plasmablasts and plasma cells. Our study highlights the coordinated immune response that contributes to COVID-19 pathogenesis and reveals discrete cellular components that can be targeted for therapy., Transcriptomic and proteomic profiling of blood samples from individuals with COVID-19 reveals immune cell and hematopoietic progenitor cell alterations that are differentially associated with disease severity.

Published
2021

19. The CMAC MicroFactory : mefenamic acid

Author

Chong, Magdalene, Brown, Cameron, Mustoe, Chantal, McGinty, John, Li, Wei, Pathan, Momina, Ottoboni, Sara, Prasad, Elke, Robertson, Murray, Mehta, Bhavik, McGowan, Mark, Siddique, Humera, Raval, Vishal, Pereira Diaz, Laura, Siddique, Mariam, Eales, William, Turner, Alice, Johnston, Blair, Robertson, John, Halbert, Gavin, Price, Chris, Benyahia, Brahim, Rielly, Chris, Sefcik, Jan, Nordon, Alison, McGlone, Thomas, Smith, Kenneth, Feilden, Helen, Houson, Ian, and Florence, Alastair

Subjects
RM
Published
2022

20. Age-related immune response heterogeneity to SARS-CoV-2 vaccine BNT162b2

Author

Collier, Dami A., Ferreira, Isabella A. T. M., Kotagiri, Prasanti, Datir, Rawlings P., Lim, Eleanor Y., Touizer, Emma, Meng, Bo, Abdullahi, Adam, Elmer, Anne, Kingston, Nathalie, Graves, Barbara, Le Gresley, Emma, Caputo, Daniela, Bergamaschi, Laura, Smith, Kenneth G. C., Bradley, John R., Ceron-Gutierrez, Lourdes, Cortes-Acevedo, Paulina, Barcenas-Morales, Gabriela, Linterman, Michelle A., McCoy, Laura E., Davis, Chris, Thomson, Emma, McKinney, Eoin, Doffinger, Rainer, Wills, Mark, Gupta, Ravindra K., Baker, Stephen, Dougan, Gordon, Hess, Christoph, Lehner, Paul J., Lyons, Paul A., Matheson, Nicholas J., Owehand, Willem H., Saunders, Caroline, Summers, Charlotte, Thaventhiran, James E. D., Toshner, Mark, Weekes, Michael P., Maxwell, Patrick, Shaw, Ashley, Bucke, Ashlea, Calder, Jo, Canna, Laura, Domingo, Jason, Fuller, Stewart, Harris, Julie, Hewitt, Sarah, Kennet, Jane, Jose, Sherly, Kourampa, Jenny, Meadows, Anne, O’Brien, Criona, Price, Jane, Publico, Cherry, Rastall, Rebecca, Ribeiro, Carla, Rowlands, Jane, Ruffolo, Valentina, Tordesillas, Hugo, Bullman, Ben, Dunmore, Benjamin J., Fawke, Stuart, Gräf, Stefan, Hodgson, Josh, Huang, Christopher, Hunter, Kelvin, Jones, Emma, Legchenko, Ekaterina, Matara, Cecilia, Martin, Jennifer, Mescia, Federica, O’Donnell, Ciara, Pointon, Linda, Pond, Nicole, Shih, Joy, Sutcliffe, Rachel, Tilly, Tobias, Treacy, Carmen, Tong, Zhen, Wood, Jennifer, Wylot, Marta, Betancourt, Ariana, Bower, Georgie, Cossetti, Chiara, De Sa, Aloka, Epping, Madeline, Gleadall, Nick, Grenfell, Richard, Hinch, Andrew, Huhn, Oisin, Jackson, Sarah, Jarvis, Isobel, Krishna, Ben, Lewis, Daniel, Marsden, Joe, Nice, Francesca, Okecha, Georgina, Omarjee, Ommar, Perera, Marianne, Potts, Martin, Richoz, Nathan, Romashova, Veronika, Yarkoni, Natalia Savinykh, Sharma, Rahul, Stefanucci, Luca, Stephens, Jonathan, Strezlecki, Mateusz, Turner, Lori, D. D. De Bie, Eckart M., Bunclark, Katherine, Josipovic, Masa, Mackay, Michael, Michael, Alice, Rossi, Sabrina, Selvan, Mayurun, Spencer, Sarah, Yong, Cissy, Ansaripour, Ali, Mwaura, Lucy, Patterson, Caroline, Polwarth, Gary, Polgarova, Petra, Di Stefano, Giovanni, Fahey, Codie, Michel, Rachel, Bong, Sze-How, Coudert, Jerome D., Holmes, Elaine, Allison, John, Butcher, Helen, Clapham-Riley, Debbie, Dewhurst, Eleanor, Furlong, Anita, Gray, Jennifer, Ivers, Tasmin, Kasanicki, Mary, Linger, Rachel, Meloy, Sarah, Muldoon, Francesca, Ovington, Nigel, Papadia, Sofia, Phelan, Isabel, Stark, Hannah, Stirrups, Kathleen E., Townsend, Paul, Walker, Neil, Webster, Jennifer, Collier, Dami A. [0000-0001-5446-4423], Datir, Rawlings P. [0000-0003-0521-2144], Smith, Kenneth G. C. [0000-0003-3829-4326], Linterman, Michelle A. [0000-0001-6047-1996], McCoy, Laura E. [0000-0001-9503-7946], Thomson, Emma [0000-0003-1482-0889], Lyons, Paul A. [0000-0001-7035-8997], Gupta, Ravindra K. [0000-0001-9751-1808], and Apollo - University of Cambridge Repository

Subjects
article, 13/106, 38/39, 631/250/2152/2153/1291, 631/326/596/4130, 38
Abstract

Although two-dose mRNA vaccination provides excellent protection against SARS-CoV-2, there is little information about vaccine efficacy against variants of concern (VOC) in individuals above eighty years of age1. Here we analysed immune responses following vaccination with the BNT162b2 mRNA vaccine2 in elderly participants and younger healthcare workers. Serum neutralization and levels of binding IgG or IgA after the first vaccine dose were lower in older individuals, with a marked drop in participants over eighty years old. Sera from participants above eighty showed lower neutralization potency against the B.1.1.7 (Alpha), B.1.351 (Beta) and P.1. (Gamma) VOC than against the wild-type virus and were more likely to lack any neutralization against VOC following the first dose. However, following the second dose, neutralization against VOC was detectable regardless of age. The frequency of SARS-CoV-2 spike-specific memory B cells was higher in elderly responders (whose serum showed neutralization activity) than in non-responders after the first dose. Elderly participants showed a clear reduction in somatic hypermutation of class-switched cells. The production of interferon-γ and interleukin-2 by SARS-CoV-2 spike-specific T cells was lower in older participants, and both cytokines were secreted primarily by CD4 T cells. We conclude that the elderly are a high-risk population and that specific measures to boost vaccine responses in this population are warranted, particularly where variants of concern are circulating.

Published
2021
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21. B cell receptor repertoire kinetics after SARS-CoV-2 infection and vaccination

Author

Kotagiri, Prasanti, Mescia, Federica, Rae, William M., Bergamaschi, Laura, Tuong, Zewen K., Turner, Lorinda, Hunter, Kevin, Gerber, Pehuén P., Hosmillo, Myra, Cambridge Institute of Therapeutic Immunology and Infectious Disease-National Institute of Health Research (CITIID-NIHR) COVID-19 BioResource Collaboration, Hess, Christoph, Clatworthy, Menna R., Goodfellow, Ian G., Matheson, Nicholas J., McKinney, Eoin F., Wills, Mark R., Gupta, Ravindra K., Bradley, John R., and Smith, Kenneth G.C.

Abstract

B cells are important in immunity to both severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) infection and vaccination, but B cell receptor (BCR) repertoire development in these contexts has not been compared. We analyze serial samples from 171 SARS-CoV-2-infected individuals and 63 vaccine recipients and find the global BCR repertoire differs between them. Following infection, immunoglobulin (Ig)G1/3 and IgA1 BCRs increase, somatic hypermutation (SHM) decreases, and, in severe disease, IgM and IgA clones are expanded. In contrast, after vaccination, the proportion of IgD/M BCRs increase, SHM is unchanged, and expansion of IgG clones is prominent. VH1-24, which targets the N-terminal domain (NTD) and contributes to neutralization, is expanded post infection except in the most severe disease. Infection generates a broad distribution of SARS-CoV-2-specific clones predicted to target the spike protein, while a more focused response after vaccination mainly targets the spike's receptor-binding domain. Thus, the nature of SARS-CoV-2 exposure differentially affects BCR repertoire development, potentially informing vaccine strategies., Cell Reports, 38 (7), ISSN:2666-3864, ISSN:2211-1247

Published
2022
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22. Longitudinal multi-omics analysis identifies early blood-based predictors of anti-TNF therapy response in inflammatory bowel disease

Author

Mishra, Neha, Aden, Konrad, Sørensen, Signe B, Overgaard, Silja H, Schulte, Berenice, Nikolaus, Susanna, Rey, Guillaume, Gasparoni, Gilles, Lyons, Paul A, Schultze, Joachim L, Walter, Jörn, Andersen, Vibeke, Blase, Johanna I, Consortium, SYSCID, Dermitzakis, Emmanouil T, Schreiber, Stefan, Rosenstiel, Philip, Banos, Aggelos, Bertsias, George, Beyer, Marc-Daniel, Boumpas, Dimitrios, Finckh, Axel, Franke, Andre, Baran, Nathan, Georges, Michel, Gu, Wei, Häsler, Robert, Jawhara, Mohamad, Kenyon, Amy, Kratsch, Christina, Krause, Roland, Lauc, Gordan, Mangino, Massimo, Natoli, Gioacchino, Bordoni, Dora, Ostaszewski, Marek, Pezer, Marija, Raes, Jeroen, Rahmouni, Souad, Ramos-Pamplona, Marilou, Reiz, Benedikt, Rosati, Elisa, Sanoudou, Despina, Satagopam, Venkata, Schneider, Reinhard, Tran, Florian, Schulte-Schrepping, Jonas, Sidiropoulos, Prodromos, Smith, Kenneth G C, Spector, Timothy, Vandeputte, Doris, Vieira-Silva, Sara, Vojta, Aleksandar, Warnat-Herresthal, Stefanie, Zoldoš, Vlatka, Conrad, Claudio, Avalos, Diana, Jaeckel, Charlot, and Scherer, Michael

Subjects
Tumor Necrosis Factor-alpha, genetics [Inflammatory Bowel Diseases], Intestinal inflammation, Therapy response, Biomarker, Biologics, Inflammatory Bowel Diseases, Personalized medicine, Infliximab, drug therapy [Inflammatory Bowel Diseases], therapeutic use [Interferons], Genetics, therapeutic use [Infliximab], Molecular Medicine, Humans, RNA, Tumor Necrosis Factor Inhibitors, ddc:610, Prospective Studies, Interferons, Molecular Biology, Genetics (clinical), Biomarkers
Abstract

Background and aims Treatment with tumor necrosis factor α (TNFα) antagonists in IBD patients suffers from primary non-response rates of up to 40%. Biomarkers for early prediction of therapy success are missing. We investigated the dynamics of gene expression and DNA methylation in blood samples of IBD patients treated with the TNF antagonist infliximab and analyzed the predictive potential regarding therapy outcome. Methods We performed a longitudinal, blood-based multi-omics study in two prospective IBD patient cohorts receiving first-time infliximab therapy (discovery: 14 patients, replication: 23 patients). Samples were collected at up to 7 time points (from baseline to 14 weeks after therapy induction). RNA-sequencing and genome-wide DNA methylation data were analyzed and correlated with clinical remission at week 14 as a primary endpoint. Results We found no consistent ex ante predictive signature across the two cohorts. Longitudinally upregulated transcripts in the non-remitter group comprised TH2- and eosinophil-related genes including ALOX15, FCER1A, and OLIG2. Network construction identified transcript modules that were coherently expressed at baseline and in non-remitting patients but were disrupted at early time points in remitting patients. These modules reflected processes such as interferon signaling, erythropoiesis, and platelet aggregation. DNA methylation analysis identified remission-specific temporal changes, which partially overlapped with transcriptomic signals. Machine learning approaches identified features from differentially expressed genes cis-linked to DNA methylation changes at week 2 as a robust predictor of therapy outcome at week 14, which was validated in a publicly available dataset of 20 infliximab-treated CD patients. Conclusions Integrative multi-omics analysis reveals early shifts of gene expression and DNA methylation as predictors for efficient response to anti-TNF treatment. Lack of such signatures might be used to identify patients with IBD unlikely to benefit from TNF antagonists at an early time point.

Published
2022

23. Single-cell multi-omics analysis of the immune response in COVID-19

Author

Stephenson, Emily, Reynolds, Gary, Botting, Rachel A., Calero-Nieto, Fernando J., Morgan, Michael D., Tuong, Zewen Kelvin, Bach, Karsten, Sungnak, Waradon, Worlock, Kaylee B., Yoshida, Masahiro, Kumasaka, Natsuhiko, Kania, Katarzyna, Engelbert, Justin, Olabi, Bayanne, Spegarova, Jarmila Stremenova, Wilson, Nicola K., Mende, Nicole, Jardine, Laura, Gardner, Louis C. S., Goh, Issac, Horsfall, Dave, McGrath, Jim, Webb, Simone, Mather, Michael W., Lindeboom, Rik G. H., Dann, Emma, Huang, Ni, Polanski, Krzysztof, Prigmore, Elena, Gothe, Florian, Scott, Jonathan, Payne, Rebecca P., Baker, Kenneth F., Hanrath, Aidan T., Schim Van Der Loeff, Ina C. D., Barr, Andrew S., Sanchez-Gonzalez, Amada, Bergamaschi, Laura, Mescia, Federica, Barnes, Josephine L., Kilich, Eliz, De Wilton, Angus, Saigal, Anita, Saleh, Aarash, Janes, Sam M., Smith, Claire M., Gopee, Nusayhah, Wilson, Caroline, Coupland, Paul, Coxhead, Jonathan M., Kiselev, Vladimir Yu, Van Dongen, Stijn, Bacardit, Jaume, King, Hamish W., Rostron, Anthony J., Simpson, A. John, Hambleton, Sophie, Laurenti, Elisa, Lyons, Paul A., Meyer, Kerstin B., Nikolić, Marko Z., Duncan, Christopher J. A., Teichmann, Sarah A., Clatworthy, Menna R., Marioni, John C., Göttgens, Berthold, Haniffa, Muzlifah, Baker, Stephen, Bradley, John R., Dougan, Gordon, Goodfellow, Ian G., Gupta, Ravindra K., Hess, Christoph, Kingston, Nathalie, Lehner, Paul J., Matheson, Nicholas J., Owehand, Willem H., Saunders, Caroline, Smith, Kenneth G. C., Summers, Charlotte, Thaventhiran, James E. D., Toshner, Mark, Weekes, Michael P., Bucke, Ashlea, Calder, Jo, Canna, Laura, Domingo, Jason, Elmer, Anne, Fuller, Stewart, Harris, Julie, Hewitt, Sarah, Kennet, Jane, Jose, Sherly, Kourampa, Jenny, Meadows, Anne, O’Brien, Criona, Price, Jane, Publico, Cherry, Rastall, Rebecca, Ribeiro, Carla, Rowlands, Jane, Ruffolo, Valentina, Tordesillas, Hugo, Bullman, Ben, Dunmore, Benjamin J., Fawke, Stuart, Gräf, Stefan, Hodgson, Josh, Huang, Christopher, Hunter, Kelvin, Jones, Emma, Legchenko, Ekaterina, Matara, Cecilia, Martin, Jennifer, O’Donnell, Ciara, Pointon, Linda, Pond, Nicole, Shih, Joy, Sutcliffe, Rachel, Tilly, Tobias, Treacy, Carmen, Tong, Zhen, Wood, Jennifer, Wylot, Marta, Betancourt, Ariana, Bower, Georgie, De Sa, Aloka, Epping, Madeline, Huhn, Oisin, Jackson, Sarah, Jarvis, Isobel, Marsden, Jimmy, Nice, Francesca, Okecha, Georgina, Omarjee, Ommar, Perera, Marianne, Richoz, Nathan, Sharma, Rahul, Turner, Lori, De Bie, Eckart M. D. D., Bunclark, Katherine, Josipovic, Masa, Mackay, Michael, Michael, Alice, Rossi, Sabrina, Selvan, Mayurun, Spencer, Sarah, Yong, Cissy, Ansaripour, Ali, Mwaura, Lucy, Patterson, Caroline, Polwarth, Gary, Polgarova, Petra, Stefano, Giovanni Di, Allison, John, Butcher, Helen, Caputo, Daniela, Clapham-Riley, Debbie, Dewhurst, Eleanor, Furlong, Anita, Graves, Barbara, Gray, Jennifer, Ivers, Tasmin, Kasanicki, Mary, Gresley, Emma Le, Linger, Rachel, Meloy, Sarah, Muldoon, Francesca, Ovington, Nigel, Papadia, Sofia, Phelan, Isabel, Stark, Hannah, Stirrups, Kathleen E., Townsend, Paul, Walker, Neil, Webster, Jennifer, Calero-Nieto, Fernando J. [0000-0003-3358-8253], Morgan, Michael D. [0000-0003-0757-0711], Tuong, Zewen Kelvin [0000-0002-6735-6808], Sungnak, Waradon [0000-0002-0136-4960], Yoshida, Masahiro [0000-0002-3521-5322], Kumasaka, Natsuhiko [0000-0002-3557-0375], Spegarova, Jarmila Stremenova [0000-0002-0710-9266], Wilson, Nicola K. [0000-0003-0865-7333], Mende, Nicole [0000-0002-5078-2333], Gardner, Louis C. S. [0000-0002-7200-978X], Goh, Issac [0000-0002-6397-3518], Horsfall, Dave [0000-0002-8086-812X], Webb, Simone [0000-0003-3058-8952], Mather, Michael W. [0000-0001-7972-7111], Lindeboom, Rik G. H. [0000-0002-3660-504X], Dann, Emma [0000-0002-7400-7438], Polanski, Krzysztof [0000-0002-2586-9576], Payne, Rebecca P. [0000-0002-9037-7367], Baker, Kenneth F. [0000-0002-6735-2911], Schim van der Loeff, Ina C. D. [0000-0003-1196-6196], Barr, Andrew S. [0000-0002-8084-7644], Mescia, Federica [0000-0002-2759-4027], Barnes, Josephine L. [0000-0001-9938-3176], Janes, Sam M. [0000-0002-6634-5939], Smith, Claire M. [0000-0002-8913-0009], Coupland, Paul [0000-0002-2871-3374], Bacardit, Jaume [0000-0002-2692-7205], King, Hamish W. [0000-0001-5972-8926], Rostron, Anthony J. [0000-0002-9336-1723], Simpson, A. John [0000-0003-4731-7294], Hambleton, Sophie [0000-0001-7954-3267], Laurenti, Elisa [0000-0002-9917-9092], Lyons, Paul A. [0000-0001-7035-8997], Meyer, Kerstin B. [0000-0001-5906-1498], Nikolić, Marko Z. [0000-0001-6304-6848], Smith, Kenneth G. C. [0000-0003-3829-4326], Teichmann, Sarah A. [0000-0002-6294-6366], Clatworthy, Menna R. [0000-0002-3340-9828], Marioni, John C. [0000-0001-9092-0852], Göttgens, Berthold [0000-0001-6302-5705], Haniffa, Muzlifah [0000-0002-3927-2084], and Apollo - University of Cambridge Repository

Subjects
692/699/255/2514, 631/208/514/1949, article, 631/250/232, 631/250/254, 631/326/596/4130
Abstract

Funder: Lister Institute of Preventive Medicine; doi: https://doi.org/10.13039/501100001255, Funder: University College London, Birkbeck MRC Doctoral Training Programme, Funder: The Jikei University School of Medicine, Funder: Action Medical Research (GN2779), Funder: NIHR Clinical Lectureship (CL-2017-01-004), Funder: NIHR (ACF-2018-01-004) and the BMA Foundation, Funder: Chan Zuckerberg Initiative (grant 2017-174169) and from Wellcome (WT211276/Z/18/Z and Sanger core grant WT206194), Funder: UKRI Innovation/Rutherford Fund Fellowship allocated by the MRC and the UK Regenerative Medicine Platform (MR/5005579/1 to M.Z.N.). M.Z.N. and K.B.M. have been funded by the Rosetrees Trust (M944), Funder: Barbour Foundation, Funder: ERC Consolidator and EU MRG-Grammar awards, Funder: Versus Arthritis Cure Challenge Research Grant (21777), and an NIHR Research Professorship (RP-2017-08-ST2-002), Funder: European Molecular Biology Laboratory (EMBL), Analysis of human blood immune cells provides insights into the coordinated response to viral infections such as severe acute respiratory syndrome coronavirus 2, which causes coronavirus disease 2019 (COVID-19). We performed single-cell transcriptome, surface proteome and T and B lymphocyte antigen receptor analyses of over 780,000 peripheral blood mononuclear cells from a cross-sectional cohort of 130 patients with varying severities of COVID-19. We identified expansion of nonclassical monocytes expressing complement transcripts (CD16+C1QA/B/C+) that sequester platelets and were predicted to replenish the alveolar macrophage pool in COVID-19. Early, uncommitted CD34+ hematopoietic stem/progenitor cells were primed toward megakaryopoiesis, accompanied by expanded megakaryocyte-committed progenitors and increased platelet activation. Clonally expanded CD8+ T cells and an increased ratio of CD8+ effector T cells to effector memory T cells characterized severe disease, while circulating follicular helper T cells accompanied mild disease. We observed a relative loss of IgA2 in symptomatic disease despite an overall expansion of plasmablasts and plasma cells. Our study highlights the coordinated immune response that contributes to COVID-19 pathogenesis and reveals discrete cellular components that can be targeted for therapy.

Published
2021
Full Text
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24. Single-cell multi-omics analysis of the immune response in COVID-19

Author

Stephenson, Emily, Reynolds, Gary, Botting, Rachel A, Calero-Nieto, Fernando J, Morgan, Michael D, Tuong, Zewen Kelvin, Bach, Karsten, Sungnak, Waradon, Worlock, Kaylee B, Yoshida, Masahiro, Kumasaka, Natsuhiko, Kania, Katarzyna, Engelbert, Justin, Olabi, Bayanne, Spegarova, Jarmila Stremenova, Wilson, Nicola K, Mende, Nicole, Jardine, Laura, Gardner, Louis CS, Goh, Issac, Horsfall, Dave, McGrath, Jim, Webb, Simone, Mather, Michael W, Lindeboom, Rik GH, Dann, Emma, Huang, Ni, Polanski, Krzysztof, Prigmore, Elena, Gothe, Florian, Scott, Jonathan, Payne, Rebecca P, Baker, Kenneth F, Hanrath, Aidan T, Schim Van Der Loeff, Ina CD, Barr, Andrew S, Sanchez-Gonzalez, Amada, Bergamaschi, Laura, Mescia, Federica, Barnes, Josephine L, Kilich, Eliz, De Wilton, Angus, Saigal, Anita, Saleh, Aarash, Janes, Sam M, Smith, Claire M, Gopee, Nusayhah, Wilson, Caroline, Coupland, Paul, Coxhead, Jonathan M, Kiselev, Vladimir Yu, Van Dongen, Stijn, Bacardit, Jaume, King, Hamish W, Cambridge Institute Of Therapeutic Immunology And Infectious Disease-National Institute Of Health Research (CITIID-NIHR) COVID-19 BioResource Collaboration, Rostron, Anthony J, Simpson, A John, Hambleton, Sophie, Laurenti, Elisa, Lyons, Paul A, Meyer, Kerstin B, Nikolić, Marko Z, Duncan, Christopher JA, Smith, Kenneth GC, Teichmann, Sarah A, Clatworthy, Menna R, Marioni, John C, Göttgens, Berthold, Haniffa, Muzlifah, Calero-Nieto, Fernando J [0000-0003-3358-8253], Morgan, Michael D [0000-0003-0757-0711], Tuong, Zewen Kelvin [0000-0002-6735-6808], Sungnak, Waradon [0000-0002-0136-4960], Yoshida, Masahiro [0000-0002-3521-5322], Kumasaka, Natsuhiko [0000-0002-3557-0375], Spegarova, Jarmila Stremenova [0000-0002-0710-9266], Wilson, Nicola K [0000-0003-0865-7333], Mende, Nicole [0000-0002-5078-2333], Gardner, Louis CS [0000-0002-7200-978X], Goh, Issac [0000-0002-6397-3518], Horsfall, Dave [0000-0002-8086-812X], Webb, Simone [0000-0003-3058-8952], Mather, Michael W [0000-0001-7972-7111], Lindeboom, Rik GH [0000-0002-3660-504X], Dann, Emma [0000-0002-7400-7438], Polanski, Krzysztof [0000-0002-2586-9576], Payne, Rebecca P [0000-0002-9037-7367], Baker, Kenneth F [0000-0002-6735-2911], Schim van der Loeff, Ina CD [0000-0003-1196-6196], Barr, Andrew S [0000-0002-8084-7644], Mescia, Federica [0000-0002-2759-4027], Barnes, Josephine L [0000-0001-9938-3176], Janes, Sam M [0000-0002-6634-5939], Smith, Claire M [0000-0002-8913-0009], Coupland, Paul [0000-0002-2871-3374], Bacardit, Jaume [0000-0002-2692-7205], King, Hamish W [0000-0001-5972-8926], Rostron, Anthony J [0000-0002-9336-1723], Simpson, A John [0000-0003-4731-7294], Hambleton, Sophie [0000-0001-7954-3267], Laurenti, Elisa [0000-0002-9917-9092], Lyons, Paul A [0000-0001-7035-8997], Meyer, Kerstin B [0000-0001-5906-1498], Nikolić, Marko Z [0000-0001-6304-6848], Smith, Kenneth GC [0000-0003-3829-4326], Teichmann, Sarah A [0000-0002-6294-6366], Clatworthy, Menna R [0000-0002-3340-9828], Marioni, John C [0000-0001-9092-0852], Göttgens, Berthold [0000-0001-6302-5705], Haniffa, Muzlifah [0000-0002-3927-2084], and Apollo - University of Cambridge Repository

Subjects
Cross-Sectional Studies, Proteome, SARS-CoV-2, T-Lymphocytes, Receptors, Antigen, T-Cell, COVID-19, Humans, Receptors, Antigen, B-Cell, Single-Cell Analysis, Transcriptome, Monocytes
Abstract

Analysis of human blood immune cells provides insights into the coordinated response to viral infections such as severe acute respiratory syndrome coronavirus 2, which causes coronavirus disease 2019 (COVID-19). We performed single-cell transcriptome, surface proteome and T and B lymphocyte antigen receptor analyses of over 780,000 peripheral blood mononuclear cells from a cross-sectional cohort of 130 patients with varying severities of COVID-19. We identified expansion of nonclassical monocytes expressing complement transcripts (CD16+C1QA/B/C+) that sequester platelets and were predicted to replenish the alveolar macrophage pool in COVID-19. Early, uncommitted CD34+ hematopoietic stem/progenitor cells were primed toward megakaryopoiesis, accompanied by expanded megakaryocyte-committed progenitors and increased platelet activation. Clonally expanded CD8+ T cells and an increased ratio of CD8+ effector T cells to effector memory T cells characterized severe disease, while circulating follicular helper T cells accompanied mild disease. We observed a relative loss of IgA2 in symptomatic disease despite an overall expansion of plasmablasts and plasma cells. Our study highlights the coordinated immune response that contributes to COVID-19 pathogenesis and reveals discrete cellular components that can be targeted for therapy.

Published
2021
Full Text
View/download PDF

25. Transcriptional networks in at-risk individuals identify signatures of type 1 diabetes progression

Author

Xhonneux, Louis-Pascal, Knight, Oliver, Lernmark, Åke, Bonifacio, Ezio, Hagopian, William A, Rewers, Marian J, She, Jin-Xiong, Toppari, Jorma, Parikh, Hemang, Smith, Kenneth GC, Ziegler, Anette-G, Akolkar, Beena, Krischer, Jeffrey P, McKinney, Eoin F, Xhonneux, Louis-Pascal [0000-0003-1990-4475], Knight, Oliver [0000-0002-0424-2379], Lernmark, Åke [0000-0003-1735-0499], Bonifacio, Ezio [0000-0002-8704-4713], Hagopian, William A [0000-0003-2979-0475], Rewers, Marian J [0000-0003-3829-9207], She, Jin-Xiong [0000-0002-0966-6381], Toppari, Jorma [0000-0003-2228-334X], Parikh, Hemang [0000-0002-9076-6709], Smith, Kenneth GC [0000-0003-3829-4326], Ziegler, Anette-G [0000-0002-6290-5548], Akolkar, Beena [0000-0002-2351-5942], McKinney, Eoin F [0000-0003-3516-3072], and Apollo - University of Cambridge Repository

Subjects
endocrine system, Islets of Langerhans, Diabetes Mellitus, Type 1, endocrine system diseases, Disease Progression, Humans, Autoimmunity, Bayes Theorem, Gene Regulatory Networks, Genetic Predisposition to Disease, Prospective Studies, Autoantibodies
Abstract

Type 1 diabetes (T1D) is a disease of insulin deficiency that results from autoimmune destruction of pancreatic islet β cells. The exact cause of T1D remains unknown, although asymptomatic islet autoimmunity lasting from weeks to years before diagnosis raises the possibility of intervention before the onset of clinical disease. The number, type, and titer of islet autoantibodies are associated with long-term disease risk but do not cause disease, and robust early predictors of individual progression to T1D onset remain elusive. The Environmental Determinants of Diabetes in the Young (TEDDY) consortium is a prospective cohort study aiming to determine genetic and environmental interactions causing T1D. Here, we analyzed longitudinal blood transcriptomes of 2013 samples from 400 individuals in the TEDDY study before both T1D and islet autoimmunity. We identified and interpreted age-associated gene expression changes in healthy infancy and age-independent changes tracking with progression to both T1D and islet autoimmunity, beginning before other evidence of islet autoimmunity was present. We combined multivariate longitudinal data in a Bayesian joint model to predict individual risk of T1D onset and validated the association of a natural killer cell signature with progression and the model's predictive performance on an additional 356 samples from 56 individuals in the independent Type 1 Diabetes Prediction and Prevention study. Together, our results indicate that T1D is characterized by early and longitudinal changes in gene expression, informing the immunopathology of disease progression and facilitating prediction of its course.

Published
2021

26. One Gene, Many Facets: Multiple Immune Pathway Dysregulation in SOCS1 Haploinsufficiency

Author

Körholz, Julia, Gabrielyan, Anastasia, Sowerby, John M, Boschann, Felix, Chen, Lan-Sun, Paul, Diana, Brandt, David, Kleymann, Janina, Kolditz, Martin, Toepfner, Nicole, Knöfler, Ralf, Jacobsen, Eva-Maria, Wolf, Christine, Conrad, Karsten, Röber, Nadja, Lee-Kirsch, Min Ae, Smith, Kenneth GC, Mundlos, Stefan, Berner, Reinhard, Dalpke, Alexander H, Schuetz, Catharina, Rae, William, Smith, Kenneth [0000-0003-3829-4326], Rae, William [0000-0003-0095-2514], and Apollo - University of Cambridge Repository

Subjects
Male, Pleiotropie, T-Lymphocytes, Immunology, genetic pleiotropy, Autoimmunity, Autoimmunität, Haploinsufficiency, Models, Biological, Immundefekt, Suppressor of Cytokine Signaling 1 Protein, SOCS1, Humans, ddc:610, Genetic pleiotropy, Child, Alleles, Original Research, inborn error of immunity (IEI), FOS: Clinical medicine, autoimmunity, Genetic Diseases, Inborn, Immunologic deficiency syndromes, Pedigree, Hyper-IgE syndrome, Case-Control Studies, Child, Preschool, Immune System, Job syndrome, Cytokines, Female, Job Syndrome, Biomarkers, Signal Transduction
Abstract

Background: Inborn errors of immunity (IEI) present with a large phenotypic spectrum of disease, which can pose diagnostic and therapeutic challenges. Suppressor of cytokine signaling 1 (SOCS1) is a key negative regulator of cytokine signaling, and has recently been associated with a novel IEI. Of patients described to date, it is apparent that SOCS1 haploinsufficiency has a pleiotropic effect in humans. Objective: We sought to investigate whether dysregulation of immune pathways, in addition to STAT1, play a role in the broad clinical manifestations of SOCS1 haploinsufficiency. Methods: We assessed impacts of reduced SOCS1 expression across multiple immune cell pathways utilizing patient cells and CRISPR/Cas9 edited primary human T cells. Results: SOCS1 haploinsufficiency phenotypes straddled across the International Union of Immunological Societies classifications of IEI. We found that reduced SOCS1 expression led to dysregulation of multiple intracellular pathways in immune cells. STAT1 phosphorylation is enhanced, comparably with STAT1 gain-of-function mutations, and STAT3 phosphorylation is similarly reduced with concurrent reduction of Th17 cells. Furthermore, reduced SOCS1 E3 ligase function was associated with increased FAK1 in immune cells, and increased AKT and p70 ribosomal protein S6 kinase phosphorylation. We also found Toll-like receptor responses are increased in SOCS1 haploinsufficiency patients. Conclusions: SOCS1 haploinsufficiency is a pleiotropic monogenic IEI. Dysregulation of multiple immune cell pathways may explain the variable clinical phenotype associated with this new condition. Knowledge of these additional dysregulated immune pathways is important when considering the optimum management for SOCS1 haploinsufficient patients.

Published
2021

27. Six weeks of high-intensity interval training enhances contractile activity induced vascular reactivity and skeletal muscle perfusion in older adults

Author

Herrod, Philip JJ, Atherton, Philip J, Smith, Kenneth, Williams, John P, Lund, Jonathan N, and Phillips, Bethan E

Subjects
Aging, Geriatrics and Gerontology
Abstract

Impairments in muscle microvascular function are associated with the pathogenesis of sarcopenia and cardiovascular disease. High-intensity interval training (HIIT) is an intervention by which a myriad of beneficial skeletal muscle/cardiovascular adaptations have been reported across age, including capillarisation and improved endothelial function. Herein, we hypothesised that HIIT would enhance muscle microvascular blood flow and vascular reactivity to acute contractile activity in older adults, reflecting HIIT-induced vascular remodelling. In a randomised controlled-trial, twenty-five healthy older adults aged 65–85years (mean BMI 27.0) were randomised to 6-week HIIT or a no-intervention control period of an equal duration. Measures of microvascular responses to a single bout of muscle contractions (i.e. knee extensions) were made in the m. vastus lateralis using contrast-enhanced ultrasound during a continuous intravenous infusion of Sonovue™ contrast agent, before and after the intervention period, with concomitant assessments of cardiorespiratory fitness and resting blood pressure. HIIT led to improvements in anaerobic threshold (13.2 ± 3.4 vs. 15.3 ± 3.8ml/kg/min, P < 0.001), dynamic exercise capacity (145 ± 60 vs. 159 ± 59W, P < 0.001) and resting (systolic) blood pressure (142 ± 15 vs. 133 ± 11mmHg, P < 0.01). Notably, HIIT elicited significant increases in microvascular blood flow responses to acute contractile activity (1.8 ± 0.63 vs. 2.3 ± 0.8 (arbitrary contrast units (AU), P < 0.01)), with no change in any of these parameters observed in the control group. Six weeks HIIT improves skeletal muscle microvascular responsiveness to acute contractile activity in the form of active hyperaemia-induced by a single bout of resistance exercise. These findings likely reflect reports of enhanced large vessel distensibility, improved endothelial function, and muscle capillarisation following HIIT. Moreover, our findings illustrate that HIIT may be effective in mitigating deleterious alterations in muscle microvascular mediated aspects of sarcopenia.

Published
2021

28. Whole-genome sequencing of patients with rare diseases in a national health system

Author

Turro, Ernest, Astle, William J., Megy, Karyn, Gräf, Stefan, Greene, Daniel, Shamardina, Olga, Allen, Hana Lango, Sanchis-Juan, Alba, Frontini, Mattia, Thys, Chantal, Stephens, Jonathan, Mapeta, Rutendo, Burren, Oliver S., Downes, Kate, Haimel, Matthias, Tuna, Salih, Deevi, Sri V.V., Aitman, Timothy J., Bennett, David L., Calleja, Paul, Carss, Keren, Caulfield, Mark J., Chinnery, Patrick F., Dixon, Peter H., Gale, Daniel P., James, Roger, Koziell, Ania, Laffan, Michael A., Levine, Adam P., Maher, Eamonn R., Markus, Hugh S., Morales, Joannella, Morrell, Nicholas W., Mumford, Andrew D., Ormondroyd, Elizabeth, Rankin, Stuart, Rendon, Augusto, Richardson, Sylvia, Roberts, Irene, Roy, Noemi B.A., Saleem, Moin A., Smith, Kenneth G.C., Stark, Hannah, Tan, Rhea Y.Y., Themistocleous, Andreas C., Thrasher, Adrian J., Watkins, Hugh, Webster, Andrew R., Wilkins, Martin R., Williamson, Catherine, Whitworth, James, Humphray, Sean, Bentley, David R., Abbs, Stephen, Abulhoul, Lara, Adlard, Julian, Ahmed, Munaza, Alachkar, Hana, Allsup, David J., Almeida-King, Jeff, Ancliff, Philip, Antrobus, Richard, Armstrong, Ruth, Arno, Gavin, Ashford, Sofie, Attwood, Anthony, Aurora, Paul, Babbs, Christian, Bacchelli, Chiara, Bakchoul, Tamam, Banka, Siddharth, Bariana, Tadbir, Barwell, Julian, Batista, Joana, Baxendale, Helen E., Beales, Phil L., Bierzynska, Agnieszka, Biss, Tina, Bitner-Glindzicz, Maria A.K., Black, Graeme C., Bleda, Marta, Blesneac, Iulia, Bockenhauer, Detlef, Bogaard, Harm, Bourne, Christian J., Boyce, Sara, Bradley, John R., Bragin, Eugene, Breen, Gerome, Brennan, Paul, Brewer, Carole, Brown, Matthew, Browning, Andrew C., Browning, Michael J., Buchan, Rachel J., Buckland, Matthew S., Bueser, Teofila, Diz, Carmen Bugarin, Burn, John, Burns, Siobhan O., Burrows, Nigel, Campbell, Carolyn, Carr-White, Gerald, Casey, Ruth, Chambers, Jenny, Chambers, John, Chan, Melanie M.Y., Cheah, Calvin, Cheng, Floria, Chitre, Manali, Christian, Martin T., Church, Colin, Clayton-Smith, Jill, Cleary, Maureen, Brod, Naomi Clements, Coghlan, Gerry, Colby, Elizabeth, Cole, Trevor R.P., Collins, Janine, Collins, Peter W., Colombo, Camilla, Compton, Cecilia J., Condliffe, Robin, Cook, Stuart, Cook, H. Terence, Cooper, Nichola, Corris, Paul A A., Furnell, Abigail, Cunningham, Fiona, Curry, Nicola S., Cutler, Antony J., Daniels, Matthew J., Dattani, Mehul, Daugherty, Louise C., Davis, John, De Soyza, Anthony, Dent, Timothy, Deshpande, Charu, Dewhurst, Eleanor F., Douzgou, Sofia, Drazyk, Anna M., Drewe, Elizabeth, Duarte, Daniel, Dutt, Tina, Edgar, J. David M., Edwards, Karen, Egner, William, Ekani, Melanie N., Elliott, Perry, Erber, Wendy N., Erwood, Marie, Estiu, Maria C., Evans, Dafydd Gareth, Evans, Gillian, Everington, Tamara, Eyries, Mélanie, Fassihi, Hiva, Favier, Remi, Findhammer, Jack, Fletcher, Debra, Flinter, Frances A., Floto, R. Andres, Fowler, Tom, Fox, James, Frary, Amy J., French, Courtney E., Freson, Kathleen, Gall, Henning, Ganesan, Vijeya, Gattens, Michael, Geoghegan, Claire, Gerighty, Terence S.A., Gharavi, Ali G., Ghio, Stefano, Ghofrani, Hossein Ardeschir, Gibbs, J. Simon R., Gibson, Kate, Gilmour, Kimberly C., Girerd, Barbara, Gleadall, Nicholas S., Goddard, Sarah, Goldstein, David B., Gomez, Keith, Gordins, Pavels, Gosal, David, Graham, Jodie, Grassi, Luigi, Greenhalgh, Lynn, Greinacher, Andreas, Gresele, Paolo, Griffiths, Philip, Grigoriadou, Sofia, Grocock, Russell J., Grozeva, Detelina, Gurnell, Mark, Hackett, Scott, Hadinnapola, Charaka, Hague, William M., Hague, Rosie, Hall, Matthew, Hanson, Helen L., Haque, Eshika, Harkness, Kirsty, Harper, Andrew R., Harris, Claire L L., Hart, Daniel, Hassan, Ahamad, Hayman, Grant, Henderson, Alex, Herwadkar, Archana, Hoffman, Jonathan, Holden, Simon, Horvath, Rita, Houlden, Henry, Houweling, Arjan C C., Howard, Luke S., Hu, Fengyuan, Hudson, Gavin, Hughes, Joseph, Huissoon, Aarnoud P., Humbert, Marc, Hunter, Sarah, Hurles, Matthew, Irving, Melita, Izatt, Louise, Johnson, Sally A., Jolles, Stephen, Jolley, Jennifer, Josifova, Dragana, Jurkute, Neringa, Karten, Tim, Karten, Johannes, Kasanicki, Mary A., Kazkaz, Hanadi, Kazmi, Rashid, Kelleher, Peter, Kelly, Anne M., Kelsall, Wilf, Kempster, Carly, Kiely, David G., Kingston, Nathalie, Klima, Robert, Koelling, Nils, Kostadima, Myrto, Kovacs, Gabor, Kreuzhuber, Roman, Kuijpers, Taco W., Kumar, Ajith, Kumararatne, Dinakantha, Kurian, Manju A., Lalloo, Fiona, Lambert, Michele, Lawrie, Allan, Layton, D. Mark, Lench, Nick, Lentaigne, Claire, Lester, Tracy, Linger, Rachel, Longhurst, Hilary, Lorenzo, Lorena E., Louka, Eleni, Lyons, Paul A., Machado, Rajiv D., MacKenzie Ross, Robert V., Madan, Bella, Maimaris, Jesmeen, Malka, Samantha, Mangles, Sarah, Marchbank, Kevin J., Marks, Stephen, Marschall, Hanns Ulrich, Marshall, Andrew, Martin, Jennifer, Mathias, Mary, Matthews, Emma, Maxwell, Heather, McAlinden, Paul, McCarthy, Mark I., McKinney, Harriet, McMahon, Aoife, Meacham, Stuart, Mead, Adam J., Castello, Ignacio Medina, Mehta, Sarju G G., Michaelides, Michel, Millar, Carolyn, Mohammed, Shehla N., Moledina, Shahin, Montani, David, Moore, Anthony T., Mozere, Monika, Muir, Keith W., Nemeth, Andrea H., Newman, William G., Newnham, Michael, Noorani, Sadia, Nurden, Paquita, O’Sullivan, Jennifer, Obaji, Samya, Odhams, Chris, Okoli, Steven, Olschewski, Andrea, Olschewski, Horst, Ong, Kai Ren, Oram, S. Helen, Ouwehand, Willem H., Palles, Claire, Papadia, Sofia, Park, Soo Mi, Parry, David, Patel, Smita, Paterson, Joan, Peacock, Andrew, Pearce, Simon H H., Peden, John, Peerlinck, Kathelijne, Penkett, Christopher J., Pepke-Zaba, Joanna, Petersen, Romina, Pilkington, Clarissa, Poole, Kenneth E.S., Prathalingam, Radhika, Psaila, Bethan, Pyle, Angela, Quinton, Richard, Rahman, Shamima, Rao, Anupama, Raymond, F. Lucy, Rayner-Matthews, Paula J., Rees, Christine, Renton, Tara, Rhodes, Christopher J., Rice, Andrew S.C., Richter, Alex, Robert, Leema, Rogers, Anthony, Rose, Sarah J., Ross-Russell, Robert, Roughley, Catherine, Roy, Noemi B. A, Ruddy, Deborah M., Sadeghi-Alavijeh, Omid, Samani, Nilesh, Samarghitean, Crina, Sargur, Ravishankar B., Sarkany, Robert N., Satchell, Simon, Savic, Sinisa, Sayer, John A., Sayer, Genevieve, Scelsi, Laura, Schaefer, Andrew M., Schulman, Sol, Scott, Richard, Scully, Marie, Searle, Claire, Seeger, Werner, Sen, Arjune, Sewell, W. A.Carrock, Seyres, Denis, Shah, Neil, Shapiro, Susan E., Shaw, Adam C., Short, Patrick J., Sibson, Keith, Side, Lucy, Simeoni, Ilenia, Simpson, Michael A A., Sims, Matthew C., Sivapalaratnam, Suthesh, Smedley, Damian, Smith, Katherine R., Snape, Katie, Soranzo, Nicole, Soubrier, Florent, Southgate, Laura, Spasic-Boskovic, Olivera, Staines, Simon, Staples, Emily, Steward, Charles, Stirrups, Kathleen E., Stuckey, Alex, Suntharalingam, Jay, Swietlik, Emilia M., Syrris, Petros, Tait, R. Campbell, Talks, Kate, Tate, Katie, Taylor, John M., Taylor, Jenny C., Thaventhiran, James E., Thomas, Ellen, Thomas, David, Thomas, Moira J., Thomas, Patrick, Thomson, Kate, Threadgold, Glen, Tilly, Tobias, Tischkowitz, Marc, Titterton, Catherine, Todd, John A., Toh, Cheng Hock, Tolhuis, Bas, Tomlinson, Ian P., Toshner, Mark, Traylor, Matthew, Treacy, Carmen, Treadaway, Paul, Trembath, Richard, Turek, Wojciech, Twiss, Philip, Vale, Tom, Geet, Chris Van, Zuydam, Natalie van, Vandekuilen, Maarten, Vandersteen, Anthony M., Vazquez-Lopez, Marta, von Ziegenweidt, Julie, Vonk Noordegraaf, Anton, Wagner, Annette, Waisfisz, Quinten, Walker, Suellen M., Walker, Neil, Walter, Klaudia, Ware, James S., Watt, Christopher, Wedderburn, Lucy, Wei, Wei, Welch, Steven B., Wessels, Julie, Westbury, Sarah K., Westwood, John Paul, Wharton, John, Whitehorn, Deborah, Wilkie, Andrew O. M, Wilson, Brian T., Wong, Edwin K.S., Wood, Nicholas, Wood, Yvette, Woods, Christopher Geoffrey, Woodward, Emma R R., Wort, Stephen J., Worth, Austen, Wright, Michael, Yates, Katherine, Yong, Patrick F.K., Young, Timothy, Yu, Ping, Yu-Wai-Man, Patrick, Zlamalova, Eliska, University of Cambridge [UK] (CAM), John Wyeth & Brother Limited, Medical Research Council (MRC), Wellcome Trust, Pulmonary medicine, ACS - Pulmonary hypertension & thrombosis, Human genetics, ACS - Atherosclerosis & ischemic syndromes, Landsteiner Laboratory, Paediatric Infectious Diseases / Rheumatology / Immunology, ARD - Amsterdam Reproduction and Development, and Project, NIHR BioResource for the 100,000 Genomes

Subjects
0301 basic medicine, Erythrocytes, Internationality, Databases, Factual, National Health Programs, [SDV]Life Sciences [q-bio], Disease, VARIANTS, Genome, State Medicine, NIHR BioResource for the 100,000 Genomes Project, 0302 clinical medicine, Medicine, GATA1 Transcription Factor, Genetics, Multidisciplinary, Translational bioinformatics, ASSOCIATION, 3. Good health, Multidisciplinary Sciences, Phenotype, 030220 oncology & carcinogenesis, disease genetics, Medical genetics, Science & Technology - Other Topics, Receptors, Thrombopoietin, medicine.medical_specialty, General Science & Technology, Quantitative Trait Loci, Genomics, Computational biology, Biology, DIAGNOSIS, computational biology and bioinformatics, Actin-Related Protein 2-3 Complex, Article, LRBA, LINKS, 03 medical and health sciences, Rare Diseases, Humans, Alleles, Adaptor Proteins, Signal Transducing, Whole genome sequencing, National health, Science & Technology, Whole Genome Sequencing, MUTATIONS, business.industry, THROMBOCYTOPENIA, United Kingdom, MACROTHROMBOCYTOPENIA, genetics research, 030104 developmental biology, business, Rare disease
Abstract

Most patients with rare diseases do not receive a molecular diagnosis and the aetiological variants and causative genes for more than half such disorders remain to be discovered1. Here we used whole-genome sequencing (WGS) in a national health system to streamline diagnosis and to discover unknown aetiological variants in the coding and non-coding regions of the genome. We generated WGS data for 13,037 participants, of whom 9,802 had a rare disease, and provided a genetic diagnosis to 1,138 of the 7,065 extensively phenotyped participants. We identified 95 Mendelian associations between genes and rare diseases, of which 11 have been discovered since 2015 and at least 79 are confirmed to be aetiological. By generating WGS data of UK Biobank participants2, we found that rare alleles can explain the presence of some individuals in the tails of a quantitative trait for red blood cells. Finally, we identified four novel non-coding variants that cause disease through the disruption of transcription of ARPC1B, GATA1, LRBA and MPL. Our study demonstrates a synergy by using WGS for diagnosis and aetiological discovery in routine healthcare.

Published
2021

29. The physiological impact of high?intensity interval training in octogenarians with comorbidities

Author

Blackwell, James E.M., Gharahdaghi, Nima, Brook, Matthew S., Watanabe, Shinya, Boereboom, Catherine L., Doleman, Brett, Lund, Jonathan N., Wilkinson, Daniel J., Smith, Kenneth, Atherton, Philip J., Williams, John P., and Phillips, Bethan E.

Subjects
Physiology (medical), Orthopedics and Sports Medicine
Abstract

BackgroundDeclines in cardiorespiratory fitness (CRF) and fat-free mass (FFM) with age are linked to mortality, morbidity and poor quality of life. High-intensity interval training (HIIT) has been shown to improve CRF and FFM in many groups, but its efficacy in the very old, in whom comorbidities are present is undefined. We aimed to assess the efficacy of and physiological/metabolic responses to HIIT, in a cohort of octogenarians with comorbidities (e.g. hypertension and osteoarthritis).MethodsTwenty-eight volunteers (18 men, 10 women, 81.2 ± 0.6 years, 27.1 ± 0.6 kg·m−2) with American Society of Anaesthesiology (ASA) Grade 2–3 status each completed 4 weeks (12 sessions) HIIT after a control period of equal duration. Before and after each 4 week period, subjects underwent body composition assessments and cardiopulmonary exercise testing. Quadriceps muscle biopsies (m. vastus lateralis) were taken to quantify anabolic signalling, mitochondrial oxidative phosphorylation, and cumulative muscle protein synthesis (MPS) over 4-weeks.ResultsIn comorbid octogenarians, HIIT elicited improvements in CRF (anaerobic threshold: +1.2 ± 0.4 ml·kg−1·min−1, P = 0.001). HIIT also augmented total FFM (47.2 ± 1.4 to 47.6 ± 1.3 kg, P = 0.04), while decreasing total fat mass (24.8 ± 1.3 to 24 ± 1.2 kg, P = 0.0002) and body fat percentage (33.1 ± 1.5 to 32.1 ± 1.4%, P = 0.0008). Mechanistically, mitochondrial oxidative phosphorylation capacity increased after HIIT (i.e. citrate synthase activity: 52.4 ± 4 to 67.9 ± 5.1 nmol·min−1·mg−1, P = 0.005; membrane protein complexes (C): C-II, 1.4-fold increase, P = 0.002; C-III, 1.2-fold increase, P = 0.03), as did rates of MPS (1.3 ± 0.1 to 1.5 ± 0.1%·day−1, P = 0.03). The increase in MPS was supported by up-regulated phosphorylation of anabolic signalling proteins (e.g. AKT, p70S6K, and 4E-BP1; all P < 0.05). There were no changes in any of these parameters during the control period. No adverse events were reported throughout the study.ConclusionsThe HIIT enhances skeletal muscle mass and CRF in octogenarians with disease, with up-regulation of MPS and mitochondrial capacity likely underlying these improvements. HIIT can be safely delivered to octogenarians with disease and is an effective, time-efficient intervention to improve muscle mass and physical function in a short time frame.

Published
2021

30. SLAMF9 is found on select subsets of antigen-presenting cells and promotes resistance to Salmonella infection

Author

Wilson, Timothy J, Clare, Simon, Mikulin, Joseph, Johnson, Christopher M, Harcourt, Katherine, Lyons, Paul A, Dougan, Gordon, Smith, Kenneth GC, Lyons, Paul [0000-0001-7035-8997], Dougan, Gordon [0000-0003-0022-965X], Smith, Kenneth [0000-0003-3829-4326], and Apollo - University of Cambridge Repository

Subjects
Salmonella, inflammation, SLAMF9, dendritic cells, mononuclear phagocytes
Abstract

SLAMF9 is an orphan receptor of the CD2/SLAM family of leucocyte surface proteins. Examination of SLAMF9 expression and function indicates that SLAMF9 promotes inflammation by specialized subsets of antigen presenting cells. Within healthy liver and circulating mouse PBMCs, SLAMF9 is expressed on CD11b+, Ly6C-, CD11clow , F4/80low , MHC-II+, CX3 CR1+ mononuclear phagocytes as well as plasmacytoid dendritic cells. In addition, SLAMF9 can be found on peritoneal B1 cells and small (F4/80low ), but not large (F4/80high ), peritoneal macrophages. Upon systemic challenge with Salmonella enterica Typhimurium, Slamf9-/- mice were impaired in their ability to clear the infection from the liver. In humans, SLAMF9 is up-regulated upon differentiation of monocytes into macrophages, and LPS stimulation of PMA-differentiated, SLAMF9 knockdown THP-1 cells showed an essential role of SLAMF9 in production of GM-CSF, TNFα, and IL-1β. Taken together, these data implicate SLAMF9 in the initiation of inflammation and clearance of bacterial infection.

Published
2020

31. Whole-genome sequencing of a sporadic primary immunodeficiency cohort

Author

Thaventhiran, James E.D., Lango Allen, Hana, Burren, Oliver S., Rae, William, Greene, Daniel, Staples, Emily, Zhang, Zinan, Farmery, James H.R., Simeoni, Ilenia, Rivers, Elizabeth, Maimaris, Jesmeen, Penkett, Christopher J., Stephens, Jonathan, Deevi, Sri V.V., Sanchis-Juan, Alba, Gleadall, Nicholas S., Thomas, Moira J., Sargur, Ravishankar B., Gordins, Pavels, Baxendale, Helen E., Brown, Matthew, Tuijnenburg, Paul, Worth, Austen, Hanson, Steven, Linger, Rachel J., Buckland, Matthew S., Rayner-Matthews, Paula J., Gilmour, Kimberly C., Samarghitean, Crina, Seneviratne, Suranjith L., Sansom, David M., Lynch, Andy G., Megy, Karyn, Ellinghaus, Eva, Ellinghaus, David, Jorgensen, Silje F., Karlsen, Tom H., Stirrups, Kathleen E., Cutler, Antony J., Kumararatne, Dinakantha S., Chandra, Anita, Edgar, J. David M., Herwadkar, Archana, Cooper, Nichola, Grigoriadou, Sofia, Huissoon, Aarnoud P., Goddard, Sarah, Jolles, Stephen, Schuetz, Catharina, Boschann, Felix, Abbs, Stephen, Adhya, Zoe, Adlard, Julian, Afzal, Maryam, Ahmed, Irshad, Ahmed, Munaza, Ahmed, Saeed, Aitman, Timothy J., Alachkar, Hana, Alamelu, Jayanthi, Alikhan, Raza, Allen, Carl E., Allen, Louise, Allsup, David J., Alvi, Arif, Ambegaonkar, Gautam, Anantharachagan, Ariharan, Ancliff, Philip, Anderson, Julie, Antrobus, Richard, Armstrong, Ruth, Arno, Gavin, Arumugakani, Gururaj, Arya, Rita, Ashford, Sofie, Astle, William J., Attwood, Anthony, Austin, Steve, Aydinok, Yesim, Ayub, Waqar, Babbs, Christian, Bacchelli, Chiara, Baglin, Trevor, Bakchoul, Tamam, Bariana, Tadbir K., Barratt, Jonathan, Barwell, Julian, Baski, John, Bates, Rachel W., Batista, Joana, Baynam, Gareth, Bennett, David L., Bethune, Claire, Bhatnagar, Neha, Bibi, Shahnaz, Bierzynska, Agnieszka, Biss, Tina, Bitner-Glindzicz, Maria A.K., Bleda, Marta, Blesneac, Iulia, Boardman, Barbara, Boddana, Preetham, Bogaard, Harm J., Booth, Claire, Boyce, Sara, Bradley, John R., Brady, Angela, Breen, Gerome, Brennan, Paul, Brewer, Carole, Briley, Annette, Brown, Richard, Browning, Michael J., Brownlie, Mary, Bryson, Christine J., Buchan, Rachel J., Buck, Jackie, Bueser, Teofila, Diz, Carmen Bugarin, Burns, Siobhan O., Calleja, Paul, Carmichael, Jenny, Carr-White, Gerald, Carss, Keren J., Casey, Ruth, Chalmers, Elizabeth, Chambers, Jenny, Chambers, John, Chan, Melanie M.Y., Chan, Melissa V., Cheng, Floria, Chinn, Ivan K., Chinnery, Patrick F., Chitre, Manali, Chong, Sam, Christian, Martin T., Church, Colin, Clement, Emma M., Brod, Naomi Clements, Clifford, Hayley, Clowes, Virginia E., Coghlan, Gerry, Colby, Elizabeth, Cole, Trevor R.P., Collins, Janine H., Collins, Peter W., Condliffe, Robin, Cook, H. Terence, Cook, Stuart, Cookson, Victoria, Corris, Paul A., Creaser-Myers, Amanda, Crisp-Hihn, Abigail, Curry, Nicola S., Da Costa, Rosa, Danesino, Cesare, Daniels, Matthew J., Darby, Damaris, Daugherty, Louise C., Davies, E. G., Davies, Sophie, Davis, John, de Bree, Godelieve J., Deacock, Sarah, Deegan, Patrick B., Dempster, John, Dent, Timothy, Deshpande, Charu, Devlin, Lisa A., Dewhurst, Eleanor F., Dixit, Anand K., Dixon, Peter H., Doffinger, Rainer, Dolling, Helen, Dormand, Natalie, Downes, Kate, Drazyk, Anna M., Drewe, Elizabeth, Duarte, Daniel, Dutt, Tina, Edwards, Karen E., Egner, William, Ekani, Melanie N., El-Shanawany, Tariq, Elkhalifa, Shuayb, Elston, Tony, Emmerson, Ingrid, Erber, Wendy N., Erwood, Marie, Estiu, Maria C., Evans, Dafydd Gareth, Evans, Gillian, Everington, Tamara, Eyries, Mélanie, Favier, Remi, Firth, Helen V., Fitzpatrick, Maggie M., Fletcher, Debra, Flinter, Frances A., Fox, James C., Frary, Amy J., French, Courtney E., Freson, Kathleen, Frontini, Mattia, Furie, Bruce, Gale, Daniel P., Gall, Henning J., Gardham, Alice, Gaspar, H. Bobby, Gattens, Michael, Ghali, Neeti, Ghataorhe, Pavandeep K., Ghio, Stefano, Ghofrani, Hossein Ardeschir, Ghurye, Rohit, Gibbs, J. Simon R., Gilbert, Rodney D., Girerd, Barbara, Girling, Joanna C., Gissen, Paul, Gorman, Kathleen M., Gosal, David, Graf, Stefan, Grassi, Luigi, Greenhalgh, Alan J., Greenhalgh, Lynn, Greinacher, Andreas, Gresele, Paolo, Griffiths, Philip G., Griffiths, Sian, Grozeva, Detelina, Hackett, Scott J., Hadden, Robert D.M., Hadinnapola, Charaka, Hague, Rosie, Hague, William M., Haimel, Matthias, Hall, Matthew, Halmagyi, Csaba, Hammerton, Tracey, Hanson, Helen L., Harkness, Kirsty, Harper, Andrew R., Harper, Lorraine, Harris, Claire, Harrison, Claire, Hart, Daniel, Hassan, Ahamad, Hayman, Grant, Heemskerk, Johan W.M., Hegde, Shivaram, Henderson, Alex, Henderson, Robert H., Hensiek, Anke, Henskens, Yvonne M.C., Hodgson, Joshua, Hoffman, Jonathan, Holden, Simon, Holder, Muriel, Horvath, Rita, Houlden, Henry, Houweling, Arjan C., Howard, Luke S., Hu, Fengyuan, Hudson, Gavin, Hughes, Sean, Hughes, Stephen, Huis in ‘t Veld, Anna E., Humbert, Marc, Hurles, Matthew E., Hurst, Jane A., Irvine, Val, Izatt, Louise, James, Roger, Jeevaratnam, Praveen, Johnson, Mark, Johnson, Sally A., Jolley, Jennifer D., Jones, Bryony, Jones, Julie, Josifova, Dragana, Jurkute, Neringa, Karim, Yousuf M., Karoshi, Mahantesh A., Kasanicki, Mary A., Kazkaz, Hanadi, Kazmi, Rashid, Keeling, David, Kelleher, Peter, Kelly, Anne M., Kempster, Carly, Kennedy, Fiona, Kiani, Sorena, Kiely, David G., Kingston, Nathalie, Kinsey, Sally, Klein, Nigel, Klima, Robert, Knox, Ellen, Kostadima, Myrto A., Kovacs, Gabor, Koziell, Ania B., Kreuzhuber, Roman, Krishnakumar, Deepa, Kuijpers, Taco W., Kumar, Ajith, Kurian, Manju A., Laffan, James, Laffan, Michael A., Lalloo, Fiona, Lambert, Michele P., Lawman, Sarah H.A., Lawrie, Allan, Layton, D. Mark, Lear, Sara E., Lees, Melissa M., Lentaigne, Claire, Levine, Adam P., Lewington, Andrew J.P., Li, Wei, Liesner, Ri, Liu, Bin, Longhurst, Hilary, Lorenzo, Lorena E., Louka, Eleni, Hadeler, Silvia Lucato, Lyons, Paul A., Macdougall, Malcolm, Machado, Rajiv D., MacKenzie Ross, Robert V., Mackillop, Lucy H., MacLaren, Robert, Madan, Bella, Magee, Laura, Mahdi-Rogers, Mohamed, Maher, Eamonn R., Makris, Mike, Mangles, Sarah, Manson, Ania, Manzur, Adnan, Mapeta, Rutendo, Marchbank, Kevin J., Mark, Patrick B., Marks, Stephen, Markus, Hugh S., Marschall, Hanns Ulrich, Marshall, Andrew, Martin, Jennifer M., Masati, Larahmie, Mathias, Mary, Matser, Vera, Matthews, Emma L., Maw, Anna, Maxwell, Heather, McAlinden, Paul, McCarthy, Mark I., McDermott, Elizabeth M., McGowan, Simon J., McJannet, Coleen, McKinney, Harriet, Meacham, Stuart, Mead, Adam J., Castello, Ignacio Medina, Meehan, Sharon, Mehta, Sarju, Mercer, Catherine L., Michaelides, Michel, Michell, Anna C., Milford, David, Millar, Carolyn M., Millar, Hazel, Mistry, Anoop, Moenen, Floor, Moledina, Shahin, Montani, David, Moore, Anthony T., Moore, Jason, Morrell, Nicholas W., Morrisson, Valerie, Mozere, Monika, Muir, Keith W., Mumford, Andrew D., Murng, Sai H.K., Nasir, Iman, Nejentsev, Sergey, Newnham, Michael, Ng, Joanne, Ngoh, Adeline, Noorani, Sadia, Noori, Muna, Nurden, Paquita, O’Sullivan, Jennifer M., Obaji, Samya, Okoli, Steven, Oksenhendler, Eric, Olschewski, Andrea, Olschewski, Horst, Ong, Albert C.M., Ong, Kai Ren, Oram, Helen, Ormondroyd, Elizabeth, Othman, Shokri, Ouwehand, Willem H., Pantazis, Antonis, Papadia, Sofia, Papandreou, Apostolos, Park, Soo Mi, Parker, Alasdair P.J., Parry, David, Parsons, Georgina, Pasi, K. John, Paterson, Joan, Payne, Jeanette H., Peacock, Andrew J., Peerlinck, Kathelijne, Pepke-Zaba, Joanna, Perry, David, Petersen, Romina, Piechowski-Jozwiak, Bartlomiej, Pinto, Fernando, Polwarth, Gary J., Ponsford, Mark J., Prasad, Sanjay, Prokopenko, Inga, Psaila, Beth, Pyle, Angela, Qasim, Waseem, Quinn, Ellen, Quinti, Isabella, Raina, Sanjay, Ranganathan, Lavanya, Rankin, Julia, Rankin, Stuart, Rao, Anupama, Raymond, F. Lucy, Rehnstrom, Karola, Reid, Evan, Reilly, Mary M., Renton, Tara, Revel-Vilk, Shoshana, Rhodes, Christopher J., Rice, Andrew S.C., Richards, Emma E., Richards, Mike, Richardson, Sylvia, Richter, Alex, Robert, Leema, Roberts, Irene, Rondina, Matthew T., Rosser, Elisabeth, Rothwell, Peter, Roughley, Catherine, Roy, Noemi B., Rue-Albrecht, Kevin, Sadeghi-Alavijeh, Omid, Saleem, Moin A., Salmon, Richard M., Samani, Nilesh J., Sambrook, Jennifer G., Sandford, Richard, Santra, Saikat, Satchell, Simon C., Savic, Sinisa, Scelsi, Laura, Schotte, Gwen, Schulman, Sol, Schulze, Harald, Scott, Richard, Scully, Marie, Searle, Claire, Seeger, Werner, Sewell, W. A.Carrock, Seyres, Denis, Shackley, Fiona, Shamardina, Olga, Shapiro, Susan E., Sharma, Pankaj, Shehata, Hassan A., Shipley, Deborah, Shtoyerman, Rakefet, Sibson, Keith, Side, Lucy, Simpson, Michael, Sims, Matthew C., Sinha, Manish D., Sivapalaratnam, Suthesh, Skytte, Anne Bine, Smith, Kenneth G.C., Snape, Katie, Sneddon, Linda, Sohal, Aman, Soubrier, Florent, Southgate, Laura, Southwood, Mark, Splitt, Miranda, Staines, Simon, Stark, Hannah, Stauss, Hans, Steele, Cathal L., Stein, Daniel, Stein, Penelope E., Stock, Sophie, Stubbs, Matthew J., Suntharalingam, Jay, Swietlik, Emilia M., Symington, Emily, Tait, R. Campbell, Talks, Kate, Tan, Rhea Y.Y., Taylor, Gordon B., Thachil, Jecko, Themistocleous, Andreas C., Thomas, David C., Thomas, Ellen, Thomas, Patrick, Thompson, Dorothy A., Thomson, Kate, Thrasher, Adrian J., Thys, Chantal, Tilly, Tobias, Tischkowitz, Marc, Titterton, Catherine, Todd, John A., Toh, Cheng Hock, Tool, Anton T.J., Toshner, Mark R., Traylor, Matthew, Treacy, Carmen M., Treadaway, Paul, Trembath, Richard C., Trippier, Sarah, Tuna, Salih, Turek, Wojciech, Turro, Ernest, Upton, Paul D., Urniaz, Rafal, Vale, Tom, Van Geet, Chris, van Zuydam, Natalie, Vandersteen, Anthony M., Vazquez-Lopez, Marta, Veltman, Marijcke W.M., Vogt, Julie, von Ziegenweidt, Julie, Noordegraaf, Anton Vonk, Vora, Ajay, Vries, Minka J.A., Wakeling, Emma L., Walker, Neil, Walker, Suellen M., Walsh, Roddy, Wanjiku, Ivy, Ware, James S., Warner, Timothy Q., Wassmer, Evangeline, Watkins, Hugh, Watson, Henry G., Watt, Christopher, Waugh, Dean, Webb, Nick, Webster, Andrew R., Wei, Wei, Welch, Angela, Welch, Steven B., Werring, David, Wessels, Julie, Westbury, Sarah K., Westwood, John Paul W., Wharton, John, Whitehorn, Deborah, Whitworth, James, Wilkins, Martin R., Willcocks, Lisa, Williams, David J., Williamson, Catherine, Wong, Edwin K.S., Wood, Nicholas, Wood, Yvette, Woods, Christopher Geoffrey, Woodward, Emma R., Workman, Sarita, Wort, Stephen J., Yates, Katherine, Yeatman, Nigel, Yong, Patrick F.K., Young, Timothy, Yu, Ping, Yu-Wai-Man, Patrick, Zlamalova, Eliska, Wellcome Trust, Thaventhiran, James [0000-0001-8616-074X], Lango Allen, Hana [0000-0002-7803-8688], Burren, Oliver [0000-0002-3388-5760], Rae, William [0000-0003-0095-2514], Zhang, Zinan [0000-0003-3831-2272], Megy, Karyn [0000-0002-2826-3879], Johnson, Kathleen [0000-0002-6823-3252], Smith, Kenneth [0000-0003-3829-4326], Apollo - University of Cambridge Repository, University of St Andrews. School of Medicine, University of St Andrews. Statistics, University of St Andrews. Sir James Mackenzie Institute for Early Diagnosis, University of St Andrews. Cellular Medicine Division, Ege Üniversitesi, Experimental Immunology, Graduate School, AII - Inflammatory diseases, Infectious diseases, APH - Aging & Later Life, APH - Global Health, Paediatric Infectious Diseases / Rheumatology / Immunology, ARD - Amsterdam Reproduction and Development, Pulmonary medicine, ACS - Pulmonary hypertension & thrombosis, Human genetics, APH - Quality of Care, ACS - Atherosclerosis & ischemic syndromes, Biochemie, RS: Carim - B03 Cell biochemistry of thrombosis and haemostasis, Faculteit FHML Centraal, MUMC+: DA CDL Algemeen (9), RS: GROW - R3 - Innovative Cancer Diagnostics & Therapy, MUMC+: MA Hematologie (9), Interne Geneeskunde, and Promovendi CD

Subjects
0301 basic medicine, Male, Protein Tyrosine Phosphatase, Non-Receptor Type 2/genetics, Genome-wide association study, VARIANTS, Regulatory Sequences, Nucleic Acid, medicine.disease_cause, Genome, Cohort Studies, 0302 clinical medicine, RARE, QR180 Immunology, Primary Immunodeficiency Consortium for the NIHR Bioresource, Genetics, Protein Tyrosine Phosphatase, Non-Receptor Type 2, Multidisciplinary, Suppressor of Cytokine Signaling 1 Protein/genetics, GENETIC-VARIATION, RNA-Binding Proteins, Primary Immunodeficiency Diseases/diagnosis, ASSOCIATION, Penetrance, Multidisciplinary Sciences, DEFICIENCY, QR180, Science & Technology - Other Topics, Female, General Science & Technology, Primary Immunodeficiency Diseases, Transcription Factors/genetics, Genomics, COMMON VARIABLE IMMUNODEFICIENCY, QH426 Genetics, Biology, Article, Actin-Related Protein 2-3 Complex, 03 medical and health sciences, Suppressor of Cytokine Signaling 1 Protein, SDG 3 - Good Health and Well-being, SUPPRESSOR, Actin-Related Protein 2-3 Complex/genetics, medicine, Humans, QH426, Whole genome sequencing, Science & Technology, Whole Genome Sequencing, Common variable immunodeficiency, DAS, Bayes Theorem, Immune dysregulation, Regulatory Sequences, Nucleic Acid/genetics, medicine.disease, RNA-Binding Proteins/genetics, STAT1 MUTATIONS, 030104 developmental biology, Primary immunodeficiency, IUIS PHENOTYPIC CLASSIFICATION, GAIN, 030215 immunology, Genome-Wide Association Study, Transcription Factors
Abstract

Primary immunodeficiency (PID) is characterized by recurrent and often life-threatening infections, autoimmunity and cancer, and it poses major diagnostic and therapeutic challenges. Although the most severe forms of PID are identified in early childhood, most patients present in adulthood, typically with no apparent family history and a variable clinical phenotype of widespread immune dysregulation: about 25% of patients have autoimmune disease, allergy is prevalent and up to 10% develop lymphoid malignancies1–3. Consequently, in sporadic (or non-familial) PID genetic diagnosis is difficult and the role of genetics is not well defined. Here we address these challenges by performing whole-genome sequencing in a large PID cohort of 1,318 participants. An analysis of the coding regions of the genome in 886 index cases of PID found that disease-causing mutations in known genes that are implicated in monogenic PID occurred in 10.3% of these patients, and a Bayesian approach (BeviMed4) identified multiple new candidate PID-associated genes, including IVNS1ABP. We also examined the noncoding genome, and found deletions in regulatory regions that contribute to disease causation. In addition, we used a genome-wide association study to identify loci that are associated with PID, and found evidence for the colocalization of—and interplay between—novel high-penetrance monogenic variants and common variants (at the PTPN2 and SOCS1 loci). This begins to explain the contribution of common variants to the variable penetrance and phenotypic complexity that are observed in PID. Thus, using a cohort-based whole-genome-sequencing approach in the diagnosis of PID can increase diagnostic yield and further our understanding of the key pathways that influence immune responsiveness in humans. © 2020, The Author(s), under exclusive licence to Springer Nature Limited., Wellcome Trust, WT: 104807/Z/14/Z University College London, UCL: 100140/Z/12/Z, 107212/Z/15/Z, MR/L019027, 203141/Z/16/Z, 091157/Z/10/Z Bundesministerium für Bildung und Forschung, BMBF: 01ZX1306A University of Cambridge 201250/Z/16/Z 01ZX1709 Seventh Framework Programme, FP7 NIHR Bristol Biomedical Research Centre Deutsche Forschungsgemeinschaft, DFG Deutsche Forschungsgemeinschaft, DFG: EXC 2167-390884018 Juvenile Diabetes Research Foundation United Kingdom, JDRF: 9-2011-253, 5-SRA-2015-130-A-N National Institute for Health Research, NIHR: RG65966 Medical Research Council, MRC: RG95376, MR/L006197/1 Great Ormond Street Hospital for Children, GOSH, Acknowledgements The NBR-RD PID Consortium is part of the NIHR BioResource, for which funding was provided by the NIHR (NIHR, grant number RG65966). We acknowledge the participation of all NIHR BioResource volunteers, and thank the NIHR BioResource centre and staff for their contribution. J.E.D.T. is supported by the Medical Research Council (MRC) (RG95376 and MR/L006197/1); A.J.T. is supported by the Wellcome Trust (104807/Z/14/Z) and the NIHR Biomedical Research Centre at Great Ormond Street Hospital for Children NHS Foundation Trust and University College London; K.G.C.S. is supported by the MRC (programme grant MR/L019027) and is a Wellcome Investigator; A.J.C. was supported by the Wellcome Trust (091157/Z/10/Z, 107212/Z/15/Z, 100140/Z/12/Z, 203141/Z/16/Z), JDRF (9-2011-253, 5-SRA-2015-130-A-N), NIHR Oxford Biomedical Research Centre and NIHR Cambridge Biomedical Research Centre; E.E. has received funding from the European Union Seventh Framework Programme (FP7-PEOPLE-2013-COFUND) under grant agreement number 609020-Scientia Fellows; E.R. is supported by the Wellcome Trust (201250/Z/16/Z); D.E. is supported by the German Federal Ministry of Education and Research (BMBF) within the framework of the e:Med research and funding concept (SysInflame grant 01ZX1306A; GB-XMAP grant 01ZX1709) and funded by the Deutsche Forschungsgemeinschaft (DFG; German Research Foundation) under Germany’s Excellence Strategy (EXC 2167-390884018). The NIHR Cambridge Biomedical Research Centre (BRC) is a partnership between Cambridge University Hospitals NHS Foundation Trust and the University of Cambridge, funded by the NIHR. This research was co-funded by the support listed above and the NIHR Cambridge BRC.

Published
2020

33. Single-dose BNT162b2 vaccine protects against asymptomatic SARS-CoV-2 infection

Author

Jones, Nick K, Rivett, Lucy, Seaman, Shaun, Samworth, Richard J, Warne, Ben, Workman, Chris, Ferris, Mark, Wright, Jo, Quinnell, Natalie, Shaw, Ashley, Cambridge COVID-19 Collaboration, Goodfellow, Ian G, Lehner, Paul J, Howes, Rob, Wright, Giles, Matheson, Nicholas J, Weekes, Michael P, Amory, Amy, Baker, Stephen, Bateman, Emma, Begum, Aklima, Begum, Moushima, Bradley, John, Brennan, Michael, Burn, Helen, Crofts, Caroline, Chaudhry, Afzal, Chaudhry, Yasmin, Cooper, Daniel J, Dawson, Sharon, Dougan, Gordon, Feather, Renny, Free, Louise, Friel, Katie, Gildea, Claire, Georgana, Iliana, Grimwade, Lizz, Gupta, Ravi, Hall, Susan, Hannan, Sophie, Hayes, James, Hosaja, Aleksandra, Hosmillo, Myra, Izuagbe, Rhys, Jahun, Aminu, James, Lidia, Jardin, Jill, Kingston, Nathalie, Lear, Sara, Lyons, Paul A, Maxwell, Patrick H, Mott, Sue, Mugavin, Sarah, Mwiya, Joyce, Peacock, Sharon, Nallattil, Ravi Prakash, Oloyede, Kazeem, Ouwehand, Willem H, Page, Elle, Perez, Marina, Raine, Tim, Routledge, Matthew, Saunders, Caroline, Smith, Kenneth GC, Sparkes, Dominic, Stafford, Maria, Summers, Charlotte, Tatsi, Despiona, Thaventhiran, James ED, Thomas Johnson, Sharon, Török, M Estée, Toshner, Mark, Turner, Lesley, Wall, Kate, Watson, Karis, Jones, Nick K [0000-0003-4475-7761], Rivett, Lucy [0000-0002-2781-9345], Goodfellow, Ian G [0000-0002-9483-510X], Lehner, Paul J [0000-0001-9383-1054], Matheson, Nicholas J [0000-0002-3318-1851], Weekes, Michael P [0000-0003-3196-5545], and Apollo - University of Cambridge Repository

Subjects
Microbiology and Infectious Disease, Epidemiology and Global Health, SARS-CoV-2, COVID-19, asymptomatic, BNT162b2, Pfizer-BioNTech, Research Advance, vaccination, Human
Abstract

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

Published
2021
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34. The acute transcriptional response to resistance exercise: impact of age and contraction mode

Author

Deane, Colleen S., Ames, Ryan M., Phillips, Bethan E., Weedon, Michael N., Willis, Craig R.G., Boereboom, Catherine, Abdulla, Haitham, Bukhari, Syed S.I., Lund, Jonathan N., Williams, John P., Wilkinson, Daniel J., Smith, Kenneth, Gallagher, Iain J., Kadi, Fawzi, Szewczyk, Nathaniel J., Atherton, Philip J., and Etheridge, Timothy

Subjects
Male, Aging, genetic structures, Down-Regulation, Resistance Training, Healthy Volunteers, Up-Regulation, sarcopenia, Young Adult, Gene Ontology, eccentric, Humans, sense organs, RNA-Seq, Muscle, Skeletal, Transcriptome, concentric, Research Paper, Aged, Muscle Contraction
Abstract

Optimization of resistance exercise (RE) remains a hotbed of research for muscle building and maintenance. However, the interactions between the contractile components of RE (i.e. concentric (CON) and eccentric (ECC)) and age, are poorly defined. We used transcriptomics to compare age-related molecular responses to acute CON and ECC exercise. Eight young (21±1 y) and eight older (70±1 y) exercise-naïve male volunteers had vastus lateralis biopsies collected at baseline and 5 h post unilateral CON and contralateral ECC exercise. RNA was subjected to next-generation sequencing and differentially expressed (DE) genes tested for pathway enrichment using Gene Ontology (GO). The young transcriptional response to CON and ECC was highly similar and older adults displayed moderate contraction-specific profiles, with no GO enrichment. Age-specific responses to ECC revealed 104 DE genes unique to young, and 170 DE genes in older muscle, with no GO enrichment. Following CON, 15 DE genes were young muscle-specific, whereas older muscle uniquely expressed 147 up-regulated genes enriched for cell adhesion and blood vessel development, and 28 down-regulated genes involved in mitochondrial respiration, amino acid and lipid metabolism. Thus, older age is associated with contraction-specific regulation often without clear functional relevance, perhaps reflecting a degree of stochastic age-related dysregulation.

Published
2019

35. Phenylbutyrate, a branched-chain amino acid keto dehydrogenase activator, promotes branched-chain amino acid metabolism and induces muscle catabolism in C2C12 cells

Author

Crossland, Hannah, Smith, Kenneth, Idris, Iskandar, Phillips, Bethan E, Atherton, Philip J, and Wilkinson, Daniel J

Subjects
Physiology
Abstract

New Findings: What is the central question of this study? The compound sodium phenylbutyrate (PB) has been shown to promote branched-chain amino acid (BCAA) catabolism, and as such has been proposed as a treatment for disorders with enhanced BCAA levels: does PB induce muscle protein catabolism by forcing BCAA degradation away from muscle protein synthesis and mechanistic target of rapamycin (mTOR) inhibition? What is the main finding and its importance? Accelerated BCAA catabolism using PB resulted in adverse effects related to mTOR signalling and muscle protein metabolism in skeletal muscle cells, which may limit its application in conditions where muscle wasting is a risk. Abstract: The compound sodium phenylbutyrate (PB) has been used for reducing ammonia in patients with urea cycle disorders and proposed as a treatment for disorders with enhanced branched-chain amino acid (BCAA) levels, due to its effects on promoting BCAA catabolism. In skeletal muscle cells, we hypothesised that PB would induce muscle protein catabolism due to forcing BCAA degradation away from muscle protein synthesis and downregulating mechanistic target of rapamycin (mTOR). PB reduced medium BCAA and branched-chain keto acid (BCKA) concentrations, while total cell protein (?21%; P

Published
2021

36. Complex Fault Geometry of the 2020 MWW6.5 Monte Cristo Range, Nevada Earthquake Sequence

Author

Ruhl, Christine J., Morton, Emily A., Bormann, Jayne M., Hatch-Ibarra, Rachel, Ichinose, Gene, and Smith, Kenneth D.

Subjects
Physics - Geophysics, FOS: Physical sciences, Geophysics (physics.geo-ph)
Abstract

On 15 May 2020 an MWW 6.5 earthquake occurred beneath the Monte Cristo Range in the Mina Deflection region of western Nevada. Rapid deployment of eight temporary seismic stations enables detailed analysis of its productive and slowly decaying aftershock sequence (p=0.8) which included ~18,000 autodetected events in 3.5 months. Double-difference, waveform-based relative relocation of 16,714 earthquakes reveals a complex network of faults, many of which cross the inferred 35-km long east-northeast-striking, left-lateral mainshock rupture. Seismicity aligns with left-lateral, right-lateral, and normal mechanism moment tensors of 128 of the largest earthquakes. The mainshock occurred near the middle of the aftershock zone at the intersection of two distinct zones of seismicity. In the western section, numerous subparallel, shallow, north-northeast-striking faults form a broad flower-structure-like fault mesh that coalesces at depth into a near-vertical, left-lateral fault. We infer the near-vertical fault to be a region of significant slip in the mainshock and an eastward extension of the left-lateral Candelaria fault. Near the mainshock hypocenter, seismicity occurs on a northeast-striking, west-dipping structure which extends north from the Eastern Columbus Salt Marsh normal fault. Together, these two intersecting structures bound the Columbus Salt Marsh tectonic basin. East of this intersection and the mainshock hypocenter, seismicity occurs in a narrow, near-vertical, east-northeast-striking fault zone through to its eastern terminus. At the eastern end, the aftershock zone broadens and extends northwest towards the southern extension of the northwest-striking, right-lateral Petrified Springs fault system. The eastern section hosts significantly fewer aftershocks than the western section, but has more moment release.

Published
2021
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37. Combined Point-of-Care Nucleic Acid and Antibody Testing for SARS-CoV-2 following Emergence of D614G Spike Variant

Author

Mlcochova, Petra, Collier, Dami, Ritchie, Allyson, Assennato, Sonny M, Hosmillo, Myra, Goel, Neha, Meng, Bo, Chatterjee, Krishna, Mendoza, Vivien, Temperton, Nigel, Kiss, Leo, James, Leo C, Ciazynska, Katarzyna A, Xiong, Xiaoli, Briggs, John AG, Nathan, James A, Mescia, Federica, Bergamaschi, Laura, Zhang, Hongyi, Barmpounakis, Petros, Demeris, Nikos, Skells, Richard, Lyons, Paul A, Bradley, John, Baker, Steven, Allain, Jean Pierre, Smith, Kenneth GC, Bousfield, Rachel, Wilson, Michael, Sparkes, Dominic, Amoroso, Glenn, Gkrania-Klotsas, Effrosyni, Hardwick, Susie, Boyle, Adrian, Goodfellow, Ian, Gupta, Ravindra K, Cambridge Institute Of Therapeutic Immunology And Infectious Disease-National Institute Of Health Research (CITIID-NIHR) COVID BioResource Collaboration, Mlcochova, Petra [0000-0001-6908-9363], Hosmillo, Myra [0000-0002-3514-7681], Chatterjee, Krishna [0000-0002-2654-8854], Kiss, Leo [0000-0001-8735-1118], Nathan, James [0000-0002-0248-1632], Mescia, Federica [0000-0002-2759-4027], Lyons, Paul [0000-0001-7035-8997], Bradley, John [0000-0002-7774-8805], Baker, Stephen [0000-0003-1308-5755], Gkrania-Klotsas, Effrossyni [0000-0002-0930-8330], Gupta, Ravindra [0000-0001-9751-1808], and Apollo - University of Cambridge Repository

Subjects
Aged, 80 and over, Immunoassay, Male, point of care testing, SARS-CoV-2, COVID-19, Middle Aged, D614G, Antibodies, Viral, Sensitivity and Specificity, COVID-19 Testing, rapid diagnoses, Neutralization Tests, Point-of-Care Testing, Spike Glycoprotein, Coronavirus, Humans, Female, Nucleic Acid Amplification Techniques, Aged
Abstract

Rapid COVID-19 diagnosis in the hospital is essential, although this is complicated by 30%-50% of nose/throat swabs being negative by SARS-CoV-2 nucleic acid amplification testing (NAAT). Furthermore, the D614G spike mutant dominates the pandemic and it is unclear how serological tests designed to detect anti-spike antibodies perform against this variant. We assess the diagnostic accuracy of combined rapid antibody point of care (POC) and nucleic acid assays for suspected COVID-19 disease due to either wild-type or the D614G spike mutant SARS-CoV-2. The overall detection rate for COVID-19 is 79.2% (95% CI 57.8-92.9) by rapid NAAT alone. The combined point of care antibody test and rapid NAAT is not affected by D614G and results in very high sensitivity for COVID-19 diagnosis with very high specificity.

Published
2020

38. How Do Stressors Influence Accountants' Performance?: A Meta-analytical Structural Equation Modelling Analysis

Author

Bonache, Adrien, J Smith, Kenneth, Centre de Recherche en Gestion des Organisations [Dijon] (CREGO), Université Bourgogne Franche-Comté [COMUE] (UBFC)-Université de Haute-Alsace (UHA) Mulhouse - Colmar (Université de Haute-Alsace (UHA))-Université de Bourgogne (UB)-Université de Franche-Comté (UFC), Université Bourgogne Franche-Comté [COMUE] (UBFC), Salisbury University, University of Maryland System, Centre de Recherche en Gestion des Organisations - CREGO - UR7317 (CREGO), Université de Haute-Alsace (UHA) Mulhouse - Colmar (Université de Haute-Alsace (UHA))-Université de Bourgogne (UB)-Université de Franche-Comté (UFC), Université Bourgogne Franche-Comté [COMUE] (UBFC)-Université Bourgogne Franche-Comté [COMUE] (UBFC), université de Bourgogne, CREGO, Centre de Recherche en Gestion des Organisations (EA 7317) (CREGO), Université de Franche-Comté (UFC), and Université Bourgogne Franche-Comté [COMUE] (UBFC)-Université Bourgogne Franche-Comté [COMUE] (UBFC)-Université de Bourgogne (UB)-Université de Haute-Alsace (UHA) Mulhouse - Colmar (Université de Haute-Alsace (UHA))-Université Bourgogne Franche-Comté [COMUE] (UBFC)

Subjects
[SHS.GESTION]Humanities and Social Sciences/Business administration, [SHS.GESTION] Humanities and Social Sciences/Business administration, ComputingMilieux_MISCELLANEOUS, [SHS]Humanities and Social Sciences
Abstract

International audience

Published
2020

39. Publisher Correction:Whole-genome sequencing of a sporadic primary immunodeficiency cohort (Nature, (2020), 583, 7814, (90-95), 10.1038/s41586-020-2265-1)

Author

Thaventhiran, James E.D., Lango Allen, Hana, Burren, Oliver S., Rae, William, Greene, Daniel, Staples, Emily, Zhang, Zinan, Farmery, James H.R., Simeoni, Ilenia, Rivers, Elizabeth, Maimaris, Jesmeen, Penkett, Christopher J., Stephens, Jonathan, Deevi, Sri V.V., Sanchis-Juan, Alba, Gleadall, Nicholas S., Thomas, Moira J., Sargur, Ravishankar B., Gordins, Pavels, Baxendale, Helen E., Brown, Matthew, Tuijnenburg, Paul, Worth, Austen, Hanson, Steven, Linger, Rachel J., Buckland, Matthew S., Rayner-Matthews, Paula J., Gilmour, Kimberly C., Samarghitean, Crina, Seneviratne, Suranjith L., Sansom, David M., Lynch, Andy G., Megy, Karyn, Ellinghaus, Eva, Ellinghaus, David, Jorgensen, Silje F., Karlsen, Tom H., Stirrups, Kathleen E., Cutler, Antony J., Kumararatne, Dinakantha S., Chandra, Anita, Edgar, J. David M., Herwadkar, Archana, Cooper, Nichola, Grigoriadou, Sofia, Huissoon, Aarnoud P., Goddard, Sarah, Jolles, Stephen, Schuetz, Catharina, Boschann, Felix, Abbs, Stephen, Adhya, Zoe, Adlard, Julian, Afzal, Maryam, Ahmed, Irshad, Ahmed, Munaza, Ahmed, Saeed, Aitman, Timothy J., Alachkar, Hana, Alamelu, Jayanthi, Alikhan, Raza, Allen, Carl E., Allen, Louise, Allsup, David J., Alvi, Arif, Ambegaonkar, Gautam, Anantharachagan, Ariharan, Ancliff, Philip, Anderson, Julie, Antrobus, Richard, Armstrong, Ruth, Arno, Gavin, Arumugakani, Gururaj, Arya, Rita, Ashford, Sofie, Astle, William J., Attwood, Anthony, Austin, Steve, Aydinok, Yesim, Ayub, Waqar, Babbs, Christian, Bacchelli, Chiara, Baglin, Trevor, Bakchoul, Tamam, Bariana, Tadbir K., Barratt, Jonathan, Barwell, Julian, Baski, John, Bates, Rachel W., Batista, Joana, Baynam, Gareth, Bennett, David L., Bethune, Claire, Bhatnagar, Neha, Bibi, Shahnaz, Bierzynska, Agnieszka, Biss, Tina, Bitner-Glindzicz, Maria A.K., Bleda, Marta, Blesneac, Iulia, Boardman, Barbara, Boddana, Preetham, Bogaard, Harm J., Booth, Claire, Boyce, Sara, Bradley, John R., Brady, Angela, Breen, Gerome, Brennan, Paul, Brewer, Carole, Briley, Annette, Brown, Richard, Browning, Michael J., Brownlie, Mary, Bryson, Christine J., Buchan, Rachel J., Buck, Jackie, Bueser, Teofila, Diz, Carmen Bugarin, Burns, Siobhan O., Calleja, Paul, Carmichael, Jenny, Carr-White, Gerald, Carss, Keren J., Casey, Ruth, Chalmers, Elizabeth, Chambers, Jenny, Chambers, John, Chan, Melanie M.Y., Chan, Melissa V., Cheng, Floria, Chinn, Ivan K., Chinnery, Patrick F., Chitre, Manali, Chong, Sam, Christian, Martin T., Church, Colin, Clement, Emma M., Brod, Naomi Clements, Clifford, Hayley, Clowes, Virginia E., Coghlan, Gerry, Colby, Elizabeth, Cole, Trevor R.P., Collins, Janine H., Collins, Peter W., Condliffe, Robin, Cook, H. Terence, Cook, Stuart, Cookson, Victoria, Corris, Paul A., Creaser-Myers, Amanda, Crisp-Hihn, Abigail, Curry, Nicola S., Da Costa, Rosa, Danesino, Cesare, Daniels, Matthew J., Darby, Damaris, Daugherty, Louise C., Davies, E. G., Davies, Sophie, Davis, John, de Bree, Godelieve J., Deacock, Sarah, Deegan, Patrick B., Dempster, John, Dent, Timothy, Deshpande, Charu, Devlin, Lisa A., Dewhurst, Eleanor F., Dixit, Anand K., Dixon, Peter H., Doffinger, Rainer, Dolling, Helen, Dormand, Natalie, Downes, Kate, Drazyk, Anna M., Drewe, Elizabeth, Duarte, Daniel, Dutt, Tina, Edwards, Karen E., Egner, William, Ekani, Melanie N., El-Shanawany, Tariq, Elkhalifa, Shuayb, Elston, Tony, Emmerson, Ingrid, Erber, Wendy N., Erwood, Marie, Estiu, Maria C., Evans, Dafydd Gareth, Evans, Gillian, Everington, Tamara, Eyries, Mélanie, Favier, Remi, Firth, Helen V., Fitzpatrick, Maggie M., Fletcher, Debra, Flinter, Frances A., Fox, James C., Frary, Amy J., French, Courtney E., Freson, Kathleen, Frontini, Mattia, Furie, Bruce, Gale, Daniel P., Gall, Henning J., Gardham, Alice, Gaspar, H. Bobby, Gattens, Michael, Ghali, Neeti, Ghataorhe, Pavandeep K., Ghio, Stefano, Ghofrani, Hossein Ardeschir, Ghurye, Rohit, Gibbs, J. Simon R., Gilbert, Rodney D., Girerd, Barbara, Girling, Joanna C., Gissen, Paul, Gorman, Kathleen M., Gosal, David, Graf, Stefan, Grassi, Luigi, Greenhalgh, Alan J., Greenhalgh, Lynn, Greinacher, Andreas, Gresele, Paolo, Griffiths, Philip G., Griffiths, Sian, Grozeva, Detelina, Hackett, Scott J., Hadden, Robert D.M., Hadinnapola, Charaka, Hague, Rosie, Hague, William M., Haimel, Matthias, Hall, Matthew, Halmagyi, Csaba, Hammerton, Tracey, Hanson, Helen L., Harkness, Kirsty, Harper, Andrew R., Harper, Lorraine, Harris, Claire, Harrison, Claire, Hart, Daniel, Hassan, Ahamad, Hayman, Grant, Heemskerk, Johan W.M., Hegde, Shivaram, Henderson, Alex, Henderson, Robert H., Hensiek, Anke, Henskens, Yvonne M.C., Hodgson, Joshua, Hoffman, Jonathan, Holden, Simon, Holder, Muriel, Horvath, Rita, Houlden, Henry, Houweling, Arjan C., Howard, Luke S., Hu, Fengyuan, Hudson, Gavin, Hughes, Sean, Hughes, Stephen, Huis in ‘t Veld, Anna E., Humbert, Marc, Hurles, Matthew E., Hurst, Jane A., Irvine, Val, Izatt, Louise, James, Roger, Jeevaratnam, Praveen, Johnson, Mark, Johnson, Sally A., Jolley, Jennifer D., Jones, Bryony, Jones, Julie, Josifova, Dragana, Jurkute, Neringa, Karim, Yousuf M., Karoshi, Mahantesh A., Kasanicki, Mary A., Kazkaz, Hanadi, Kazmi, Rashid, Keeling, David, Kelleher, Peter, Kelly, Anne M., Kempster, Carly, Kennedy, Fiona, Kiani, Sorena, Kiely, David G., Kingston, Nathalie, Kinsey, Sally, Klein, Nigel, Klima, Robert, Knox, Ellen, Kostadima, Myrto A., Kovacs, Gabor, Koziell, Ania B., Kreuzhuber, Roman, Krishnakumar, Deepa, Kuijpers, Taco W., Kumar, Ajith, Kurian, Manju A., Laffan, James, Laffan, Michael A., Lalloo, Fiona, Lambert, Michele P., Lawman, Sarah H.A., Lawrie, Allan, Layton, D. Mark, Lear, Sara E., Lees, Melissa M., Lentaigne, Claire, Levine, Adam P., Lewington, Andrew J.P., Li, Wei, Liesner, Ri, Liu, Bin, Longhurst, Hilary, Lorenzo, Lorena E., Louka, Eleni, Hadeler, Silvia Lucato, Lyons, Paul A., Macdougall, Malcolm, Machado, Rajiv D., MacKenzie Ross, Robert V., Mackillop, Lucy H., MacLaren, Robert, Madan, Bella, Magee, Laura, Mahdi-Rogers, Mohamed, Maher, Eamonn R., Makris, Mike, Mangles, Sarah, Manson, Ania, Manzur, Adnan, Mapeta, Rutendo, Marchbank, Kevin J., Mark, Patrick B., Marks, Stephen, Markus, Hugh S., Marschall, Hanns Ulrich, Marshall, Andrew, Martin, Jennifer M., Masati, Larahmie, Mathias, Mary, Matser, Vera, Matthews, Emma L., Maw, Anna, Maxwell, Heather, McAlinden, Paul, McCarthy, Mark I., McDermott, Elizabeth M., McGowan, Simon J., McJannet, Coleen, McKinney, Harriet, Meacham, Stuart, Mead, Adam J., Castello, Ignacio Medina, Meehan, Sharon, Mehta, Sarju, Mercer, Catherine L., Michaelides, Michel, Michell, Anna C., Milford, David, Millar, Carolyn M., Millar, Hazel, Mistry, Anoop, Moenen, Floor, Moledina, Shahin, Montani, David, Moore, Anthony T., Moore, Jason, Morrell, Nicholas W., Morrisson, Valerie, Mozere, Monika, Muir, Keith W., Mumford, Andrew D., Murng, Sai H.K., Nasir, Iman, Nejentsev, Sergey, Newnham, Michael, Ng, Joanne, Ngoh, Adeline, Noorani, Sadia, Noori, Muna, Nurden, Paquita, O’Sullivan, Jennifer M., Obaji, Samya, Okoli, Steven, Oksenhendler, Eric, Olschewski, Andrea, Olschewski, Horst, Ong, Albert C.M., Ong, Kai Ren, Oram, Helen, Ormondroyd, Elizabeth, Othman, Shokri, Ouwehand, Willem H., Pantazis, Antonis, Papadia, Sofia, Papandreou, Apostolos, Park, Soo Mi, Parker, Alasdair P.J., Parry, David, Parsons, Georgina, Pasi, K. John, Paterson, Joan, Payne, Jeanette H., Peacock, Andrew J., Peerlinck, Kathelijne, Pepke-Zaba, Joanna, Perry, David, Petersen, Romina, Piechowski-Jozwiak, Bartlomiej, Pinto, Fernando, Polwarth, Gary J., Ponsford, Mark J., Prasad, Sanjay, Prokopenko, Inga, Psaila, Beth, Pyle, Angela, Qasim, Waseem, Quinn, Ellen, Quinti, Isabella, Raina, Sanjay, Ranganathan, Lavanya, Rankin, Julia, Rankin, Stuart, Rao, Anupama, Raymond, F. Lucy, Rehnstrom, Karola, Reid, Evan, Reilly, Mary M., Renton, Tara, Revel-Vilk, Shoshana, Rhodes, Christopher J., Rice, Andrew S.C., Richards, Emma E., Richards, Mike, Richardson, Sylvia, Richter, Alex, Robert, Leema, Roberts, Irene, Rondina, Matthew T., Rosser, Elisabeth, Rothwell, Peter, Roughley, Catherine, Roy, Noemi B., Rue-Albrecht, Kevin, Sadeghi-Alavijeh, Omid, Saleem, Moin A., Salmon, Richard M., Samani, Nilesh J., Sambrook, Jennifer G., Sandford, Richard, Santra, Saikat, Satchell, Simon C., Savic, Sinisa, Scelsi, Laura, Schotte, Gwen, Schulman, Sol, Schulze, Harald, Scott, Richard, Scully, Marie, Searle, Claire, Seeger, Werner, Sewell, W. A.Carrock, Seyres, Denis, Shackley, Fiona, Shamardina, Olga, Shapiro, Susan E., Sharma, Pankaj, Shehata, Hassan A., Shipley, Deborah, Shtoyerman, Rakefet, Sibson, Keith, Side, Lucy, Simpson, Michael, Sims, Matthew C., Sinha, Manish D., Sivapalaratnam, Suthesh, Skytte, Anne Bine, Smith, Kenneth G.C., Snape, Katie, Sneddon, Linda, Sohal, Aman, Soubrier, Florent, Southgate, Laura, Southwood, Mark, Splitt, Miranda, Staines, Simon, Stark, Hannah, Stauss, Hans, Steele, Cathal L., Stein, Daniel, Stein, Penelope E., Stock, Sophie, Stubbs, Matthew J., Suntharalingam, Jay, Swietlik, Emilia M., Symington, Emily, Tait, R. Campbell, Talks, Kate, Tan, Rhea Y.Y., Taylor, Gordon B., Thachil, Jecko, Themistocleous, Andreas C., Thomas, David C., Thomas, Ellen, Thomas, Patrick, Thompson, Dorothy A., Thomson, Kate, Thrasher, Adrian J., Thys, Chantal, Tilly, Tobias, Tischkowitz, Marc, Titterton, Catherine, Todd, John A., Toh, Cheng Hock, Tool, Anton T.J., Toshner, Mark R., Traylor, Matthew, Treacy, Carmen M., Treadaway, Paul, Trembath, Richard C., Trippier, Sarah, Tuna, Salih, Turek, Wojciech, Turro, Ernest, Upton, Paul D., Urniaz, Rafal, Vale, Tom, Van Geet, Chris, van Zuydam, Natalie, Vandersteen, Anthony M., Vazquez-Lopez, Marta, Veltman, Marijcke W.M., Vogt, Julie, von Ziegenweidt, Julie, Noordegraaf, Anton Vonk, Vora, Ajay, Vries, Minka J.A., Wakeling, Emma L., Walker, Neil, Walker, Suellen M., Walsh, Roddy, Wanjiku, Ivy, Ware, James S., Warner, Timothy Q., Wassmer, Evangeline, Watkins, Hugh, Watson, Henry G., Watt, Christopher, Waugh, Dean, Webb, Nick, Webster, Andrew R., Wei, Wei, Welch, Angela, Welch, Steven B., Werring, David, Wessels, Julie, Westbury, Sarah K., Westwood, John Paul W., Wharton, John, Whitehorn, Deborah, Whitworth, James, Wilkins, Martin R., Willcocks, Lisa, Williams, David J., Williamson, Catherine, Wong, Edwin K.S., Wood, Nicholas, Wood, Yvette, Woods, Christopher Geoffrey, Woodward, Emma R., Workman, Sarita, Wort, Stephen J., Yates, Katherine, Yeatman, Nigel, Yong, Patrick F.K., Young, Timothy, Yu, Ping, Yu-Wai-Man, Patrick, Zlamalova, Eliska, Pulmonary medicine, ACS - Pulmonary hypertension & thrombosis, and ACS - Atherosclerosis & ischemic syndromes

Abstract

An amendment to this paper has been published and can be accessed via a link at the top of the paper.

Published
2020

40. Whole-genome sequencing of a sporadic primary immunodeficiency cohort

Author

Thaventhiran, James E. D., Lango Allen, Hana, Burren, Oliver S., Rae, William, Greene, Daniel, Staples, Emily, Zhang, Zinan, Farmery, James H. R., Simeoni, Ilenia, Rivers, Elizabeth, Maimaris, Jesmeen, Penkett, Christopher J., Stephens, Jonathan, Deevi, Sri V. V., Sanchis-Juan, Alba, Gleadall, Nicholas S., Thomas, Moira J., Sargur, Ravishankar B., Gordins, Pavels, Baxendale, Helen E., Brown, Matthew, Tuijnenburg, Paul, Worth, Austen, Hanson, Steven, Linger, Rachel J., Buckland, Matthew S., Rayner-Matthews, Paula J., Gilmour, Kimberly C., Samarghitean, Crina, Seneviratne, Suranjith L., Sansom, David M., Lynch, Andy G., Megy, Karyn, Ellinghaus, Eva, Ellinghaus, David, Jorgensen, Silje F., Karlsen, Tom H., Stirrups, Kathleen E., Cutler, Antony J., Kumararatne, Dinakantha S., Chandra, Anita, Edgar, J. David M., Herwadkar, Archana, Cooper, Nichola, Grigoriadou, Sofia, Huissoon, Aarnoud P., Goddard, Sarah, Jolles, Stephen, Schuetz, Catharina, Boschann, Felix, Lyons, Paul A., Hurles, Matthew E., Savic, Sinisa, Burns, Siobhan O., Kuijpers, Taco W., Turro, Ernest, Ouwehand, Willem H., Thrasher, Adrian J., Smith, Kenneth G. C., Tait, R. Campbell, Chalmers, Elizabeth, Hague, Rosie, Maxwell, Heather, Peacock, Andrew J., Mark, Patrick B., and Muir, Keith W.

Abstract

Primary immunodeficiency (PID) is characterized by recurrent and often life-threatening infections, autoimmunity and cancer, and it poses major diagnostic and therapeutic challenges. Although the most severe forms of PID are identified in early childhood, most patients present in adulthood, typically with no apparent family history and a variable clinical phenotype of widespread immune dysregulation: about 25% of patients have autoimmune disease, allergy is prevalent and up to 10% develop lymphoid malignancies1,2,3. Consequently, in sporadic (or non-familial) PID genetic diagnosis is difficult and the role of genetics is not well defined. Here we address these challenges by performing whole-genome sequencing in a large PID cohort of 1,318 participants. An analysis of the coding regions of the genome in 886 index cases of PID found that disease-causing mutations in known genes that are implicated in monogenic PID occurred in 10.3% of these patients, and a Bayesian approach (BeviMed4) identified multiple new candidate PID-associated genes, including IVNS1ABP. We also examined the noncoding genome, and found deletions in regulatory regions that contribute to disease causation. In addition, we used a genome-wide association study to identify loci that are associated with PID, and found evidence for the colocalization of—and interplay between—novel high-penetrance monogenic variants and common variants (at the PTPN2 and SOCS1 loci). This begins to explain the contribution of common variants to the variable penetrance and phenotypic complexity that are observed in PID. Thus, using a cohort-based whole-genome-sequencing approach in the diagnosis of PID can increase diagnostic yield and further our understanding of the key pathways that influence immune responsiveness in humans.

Published
2020

41. Whole-genome sequencing of patients with rare diseases in a national health system

Author

Turro, Ernest, Astle, William J., Megy, Karyn, Gräf, Stefan, Greene, Daniel, Shamardina, Olga, Allen, Hana Lango, Sanchis-Juan, Alba, Frontini, Mattia, Thys, Chantal, Stephens, Jonathan, Mapeta, Rutendo, Burren, Oliver S., Downes, Kate, Haimel, Matthias, Tuna, Salih, Deevi, Sri V. V., Aitman, Timothy J., Bennett, David L., Calleja, Paul, Carss, Keren, Caulfield, Mark J., Chinnery, Patrick F., Dixon, Peter H., Gale, Daniel P., James, Roger, Koziell, Ania, Laffan, Michael A., Levine, Adam P., Maher, Eamonn R., Markus, Hugh S., Morales, Joannella, Morrell, Nicholas W., Mumford, Andrew D., Ormondroyd, Elizabeth, Rankin, Stuart, Rendon, Augusto, Richardson, Sylvia, Roberts, Irene, Roy, Noemi B. A., Saleem, Moin A., Smith, Kenneth G. C., Stark, Hannah, Tan, Rhea Y. Y., Themistocleous, Andreas C., Thrasher, Adrian J., Watkins, Hugh, Webster, Andrew R., Wilkins, Martin R., Williamson, Catherine, Whitworth, James, Humphray, Sean, Bentley, David R., Kingston, Nathalie, Walker, Neil, Bradley, John R., Ashford, Sofie, Penkett, Christopher J., Freson, Kathleen, Stirrups, Kathleen E., Raymond, F. Lucy, Ouwehand, Willem H., Peacock, Andrew, Hague, Rosie, Maxwell, Heather, Muir, Keith W., Tait, R. Campbell, and Thomas, Moira J.

Abstract

Most patients with rare diseases do not receive a molecular diagnosis and the aetiological variants and causative genes for more than half such disorders remain to be discovered1. Here we used whole-genome sequencing (WGS) in a national health system to streamline diagnosis and to discover unknown aetiological variants in the coding and non-coding regions of the genome. We generated WGS data for 13,037 participants, of whom 9,802 had a rare disease, and provided a genetic diagnosis to 1,138 of the 7,065 extensively phenotyped participants. We identified 95 Mendelian associations between genes and rare diseases, of which 11 have been discovered since 2015 and at least 79 are confirmed to be aetiological. By generating WGS data of UK Biobank participants2, we found that rare alleles can explain the presence of some individuals in the tails of a quantitative trait for red blood cells. Finally, we identified four novel non-coding variants that cause disease through the disruption of transcription of ARPC1B, GATA1, LRBA and MPL. Our study demonstrates a synergy by using WGS for diagnosis and aetiological discovery in routine healthcare.

Published
2020

42. Whole-genome sequencing of patients with rare diseases in a national health system

Author

Turro, Ernest, Astle, William J, Megy, Karyn, Gräf, Stefan, Greene, Daniel, Shamardina, Olga, Allen, Hana Lango, Sanchis-Juan, Alba, Frontini, Mattia, Thys, Chantal, Stephens, Jonathan, Mapeta, Rutendo, Burren, Oliver S, Downes, Kate, Haimel, Matthias, Tuna, Salih, Deevi, Sri, Aitman, Timothy J, Bennett, David L, Calleja, Paul, Carss, Keren, Caulfield, Mark J, Chinnery, Patrick F, Dixon, Peter H, Gale, Daniel P, James, Roger, Koziell, Ania, Laffan, Michael A, Levine, Adam P, Maher, Eamonn R, Markus, Hugh S, Morales, Joannella, Morrell, Nicholas W, Mumford, Andrew D, Ormondroyd, Elizabeth, Rankin, Stuart, Rendon, Augusto, Richardson, Sylvia, Roberts, Irene, Roy, Noemi BA, Saleem, Moin A, Smith, Kenneth GC, Stark, Hannah, Tan, Rhea YY, Themistocleous, Andreas C, Thrasher, Adrian J, Watkins, Hugh, Webster, Andrew R, Wilkins, Martin R, Williamson, Catherine, Whitworth, James, Humphray, Sean, Bentley, David R, NIHR BioResource For The 100,000 Genomes Project, Kingston, Nathalie, Walker, Neil, Bradley, John R, Ashford, Sofie, Penkett, Christopher J, Freson, Kathleen, Stirrups, Kathleen E, Raymond, F Lucy, Ouwehand, Willem H, Ouwehand, Willem H [0000-0002-7744-1790], and Apollo - University of Cambridge Repository

Subjects
Erythrocytes, Internationality, Databases, Factual, National Health Programs, Whole Genome Sequencing, Quantitative Trait Loci, Actin-Related Protein 2-3 Complex, State Medicine, United Kingdom, Phenotype, Rare Diseases, Humans, GATA1 Transcription Factor, Receptors, Thrombopoietin, Alleles, Adaptor Proteins, Signal Transducing
Abstract

Most patients with rare diseases do not receive a molecular diagnosis and the aetiological variants and causative genes for more than half such disorders remain to be discovered1. Here we used whole-genome sequencing (WGS) in a national health system to streamline diagnosis and to discover unknown aetiological variants in the coding and non-coding regions of the genome. We generated WGS data for 13,037 participants, of whom 9,802 had a rare disease, and provided a genetic diagnosis to 1,138 of the 7,065 extensively phenotyped participants. We identified 95 Mendelian associations between genes and rare diseases, of which 11 have been discovered since 2015 and at least 79 are confirmed to be aetiological. By generating WGS data of UK Biobank participants2, we found that rare alleles can explain the presence of some individuals in the tails of a quantitative trait for red blood cells. Finally, we identified four novel non-coding variants that cause disease through the disruption of transcription of ARPC1B, GATA1, LRBA and MPL. Our study demonstrates a synergy by using WGS for diagnosis and aetiological discovery in routine healthcare.

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

Author

Rivett, Lucy, Sridhar, Sushmita, Sparkes, Dominic, Routledge, Matthew, Jones, Nick K, Forrest, Sally, Young, Jamie, Pereira-Dias, Joana, Hamilton, William L, Ferris, Mark, Torok, M Estee, Meredith, Luke, Collaboration, The CITIID-NIHR COVID-19 BioResource, Curran, Martin D, Fuller, Stewart, Chaudhry, Afzal, Shaw, Ashley, Samworth, Richard J, Bradley, John R, Dougan, Gordon, Smith, Kenneth GC, Lehner, Paul J, Matheson, Nicholas J, Wright, Giles, Goodfellow, Ian G, Baker, Stephen, Weekes, Michael P, Gupta, Ravi, Lyons, Paul A, Toshner, Mark, Warne, Ben, Bartholdson Scott, Josefin, Cormie, Claire, Gill, Harmeet, Kean, Iain, Maes, Mailis, Reynolds, Nicola, Wantoch, Michelle, Caddy, Sarah, Caller, Laura, Feltwell, Theresa, Hall, Grant, Hosmillo, Myra, Houldcroft, Charlotte, Jahun, Aminu, Khokhar, Fahad, Yakovleva, Anna, Butcher, Helen, Caputo, Daniela, Clapham-Riley, Debra, Dolling, Helen, Furlong, Anita, Graves, Barbara, Gresley, Emma Le, Kingston, Nathalie, Papadia, Sofia, Stark, Hannah, Stirrups, Kathleen E, Webster, Jennifer, Calder, Joanna, Harris, Julie, Hewitt, Sarah, Kennet, Jane, Meadows, Anne, Rastall, Rebecca, Brien, Criona O, Price, Jo, Publico, Cherry, Rowlands, Jane, Ruffolo, Valentina, Tordesillas, Hugo, Brookes, Karen, Canna, Laura, Cruz, Isabel, Dempsey, Katie, Elmer, Anne, Escoffery, Naidine, Jones, Heather, Ribeiro, Carla, Saunders, Caroline, Wright, Angela, Nyagumbo, Rutendo, Roberts, Anne, Bucke, Ashlea, Hargreaves, Simone, Johnson, Danielle, Narcorda, Aileen, Read, Debbie, Sparke, Christian, Warboys, Lucy, Lagadu, Kirsty, Mactavous, Lenette, Gould, Tim, Raine, Tim, Mather, Claire, Ramenatte, Nicola, Vallier, Anne-Laure, Kasanicki, Mary, Eames, Penelope-Jane, McNicholas, Chris, Thake, Lisa, Bartholomew, Neil, Brown, Nick, Parmar, Surendra, Zhang, Hongyi, Bowring, Ailsa, Martell, Geraldine, Quinnell, Natalie, Wright, Jo, Murphy, Helen, Dunmore, Benjamin J, Legchenko, Ekaterina, Gräf, Stefan, Huang, Christopher, Hodgson, Josh, Hunter, Kelvin, Martin, Jennifer, Mescia, Federica, O'Donnell, Ciara, Pointon, Linda, Shih, Joy, Sutcliffe, Rachel, Tilly, Tobias, Tong, Zhen, Treacy, Carmen, Wood, Jennifer, Bergamaschi, Laura, Betancourt, Ariana, Bowyer, Georgie, De Sa, Aloka, Epping, Maddie, Hinch, Andrew, Huhn, Oisin, Jarvis, Isobel, Lewis, Daniel, Marsden, Joe, McCallum, Simon, Nice, Francescsa, Rivett, Lucy [0000-0002-2781-9345], Lehner, Paul J [0000-0001-9383-1054], Matheson, Nicholas J [0000-0002-3318-1851], Goodfellow, Ian G [0000-0002-9483-510X], Weekes, Michael P [0000-0003-3196-5545], and Apollo - University of Cambridge Repository

Subjects
Epidemiology and Global Health, SARS-CoV-2, infectious disease, education, occupational health, virus diseases, COVID-19, Human Biology and Medicine, Research Article, virology, emerging pathogens, Human, Virus
Abstract

Funder: Addenbrooke's Charitable Trust, Cambridge University Hospitals; FundRef: http://dx.doi.org/10.13039/501100002927, Significant differences exist in the availability of healthcare worker (HCW) SARS-CoV-2 testing between countries, and existing programmes focus on screening symptomatic rather than asymptomatic staff. Over a 3 week period (April 2020), 1032 asymptomatic HCWs were screened for SARS-CoV-2 in a large UK teaching hospital. Symptomatic staff and symptomatic household contacts were additionally tested. Real-time RT-PCR was used to detect viral RNA from a throat+nose self-swab. 3% of HCWs in the asymptomatic screening group tested positive for SARS-CoV-2. 17/30 (57%) were truly asymptomatic/pauci-symptomatic. 12/30 (40%) had experienced symptoms compatible with coronavirus disease 2019 (COVID-19)>7 days prior to testing, most self-isolating, returning well. Clusters of HCW infection were discovered on two independent wards. Viral genome sequencing showed that the majority of HCWs had the dominant lineage B∙1. Our data demonstrates the utility of comprehensive screening of HCWs with minimal or no symptoms. This approach will be critical for protecting patients and hospital staff.

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

Author

Jones, Nick K, Rivett, Lucy, Sparkes, Dominic, Forrest, Sally, Sridhar, Sushmita, Young, Jamie, Pereira-Dias, Joana, Cormie, Claire, Gill, Harmeet, Reynolds, Nicola, Wantoch, Michelle, Routledge, Matthew, Warne, Ben, Levy, Jack, Córdova Jiménez, William David, Samad, Fathima Nisha Begum, McNicholas, Chris, Ferris, Mark, Gray, Jane, Gill, Michael, Collaboration, The CITIID-NIHR COVID-19 BioResource, Curran, Martin D, Fuller, Stewart, Chaudhry, Afzal, Shaw, Ashley, Bradley, John R, Hannon, Gregory J, Goodfellow, Ian G, Dougan, Gordon, Smith, Kenneth GC, Wright, Giles, Baker, Stephen, Weekes, Michael P, Bradley, John, Goodfellow, Ian, Gupta, Ravi, Lehner, Paul J, Lyons, Paul A, Matheson, Nicholas J, Torok, M Estee, Toshner, Mark, Jones, Nick K [0000-0003-4475-7761], Sridhar, Sushmita [0000-0001-7453-7482], Hannon, Gregory J [0000-0003-4021-3898], Goodfellow, Ian G [0000-0002-9483-510X], Lehner, Paul J [0000-0001-9383-1054], Matheson, Nicholas J [0000-0002-3318-1851], Weekes, Michael P [0000-0003-3196-5545], and Apollo - University of Cambridge Repository

Subjects
Epidemiology and Global Health, SARS-CoV-2, infectious disease, occupational health, virus diseases, COVID-19, Research Advance, Human Biology and Medicine, virology, emerging pathogens, Human
Abstract

Funder: Addenbrooke's Charitable Trust, Cambridge University Hospitals; FundRef: http://dx.doi.org/10.13039/501100002927, Funder: National Institute for Health Research; FundRef: http://dx.doi.org/10.13039/501100000272, Previously, we showed that 3% (31/1032)of asymptomatic healthcare workers (HCWs) from a large teaching hospital in Cambridge, UK, tested positive for SARS-CoV-2 in April 2020. About 15% (26/169) HCWs with symptoms of coronavirus disease 2019 (COVID-19) also tested positive for SARS-CoV-2 (Rivett et al., 2020). Here, we show that the proportion of both asymptomatic and symptomatic HCWs testing positive for SARS-CoV-2 rapidly declined to near-zero between 25th April and 24th May 2020, corresponding to a decline in patient admissions with COVID-19 during the ongoing UK ‘lockdown’. These data demonstrate how infection prevention and control measures including staff testing may help prevent hospitals from becoming independent ‘hubs’ of SARS-CoV-2 transmission, and illustrate how, with appropriate precautions, organizations in other sectors may be able to resume on-site work safely.

Published
2020

46. Additional file 3 of Genetic feature engineering enables characterisation of shared risk factors in immune-mediated diseases

Author

Burren, Oliver S., Reales, Guillermo, Limy Wong, Bowes, John, Lee, James C., Barton, Anne, Lyons, Paul A., Smith, Kenneth G. C., Thomson, Wendy, Kirk, Paul D. W., and Wallace, Chris

Abstract

Additional file 3: Fig. S1-S21. Distribution of SNPs across the basis components, reconstruction plot error, hierarchical clustering of basis diseases and their basis counterparts using different thresholds, delta plots for the 13 principal components in the IMD basis, test for consistency across trait groups, comparison of projections across different ancestries, distribution of entries in the rotation matrix for each component in the basis, and QQ plots of p-values for driver SNPs on trait-significant components.

Published
2020
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47. Additional file 4 of Genetic feature engineering enables characterisation of shared risk factors in immune-mediated diseases

Author

Burren, Oliver S., Reales, Guillermo, Limy Wong, Bowes, John, Lee, James C., Barton, Anne, Lyons, Paul A., Smith, Kenneth G. C., Thomson, Wendy, Kirk, Paul D. W., and Wallace, Chris

Subjects
musculoskeletal diseases, genetic structures, immune system diseases, skin and connective tissue diseases, urologic and male genital diseases
Abstract

Additional file 4. Methods for GWAS analysis of individual level datasets: vasculitis, JIA and PsA.

Published
2020
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48. A thermostable, closed SARS-CoV-2 spike protein trimer

Author

Xiong, Xiaoli, Qu, Kun, Ciazynska, Katarzyna A., Hosmillo, Myra, Carter, Andrew P., Ebrahimi, Soraya, Ke, Zunlong, Scheres, Sjors H. W., Bergamaschi, Laura, Grice, Guinevere L., Zhang, Ying, Bradley, John, Lyons, Paul A., Smith, Kenneth G. C., Toshner, Mark, Elmer, Anne, Ribeiro, Carla, Kourampa, Jenny, Jose, Sherly, Kennet, Jane, Rowlands, Jane, Meadows, Anne, O’Brien, Criona, Rastall, Rebecca, Crucusio, Cherry, Hewitt, Sarah, Price, Jane, Calder, Jo, Canna, Laura, Bucke, Ashlea, Tordesillas, Hugo, Harris, Julie, Ruffolo, Valentina, Domingo, Jason, Graves, Barbara, Butcher, Helen, Caputo, Daniela, Le Gresley, Emma, Dunmore, Benjamin J., Martin, Jennifer, Legchenko, Ekaterina, Treacy, Carmen, Huang, Christopher, Wood, Jennifer, Sutcliffe, Rachel, Hodgson, Josh, Shih, Joy, Graf, Stefan, Tong, Zhen, Mescia, Federica, Tilly, Tobias, O’Donnell, Ciara, Hunter, Kelvin, Pointon, Linda, Pond, Nicole, Wylot, Marta, Jones, Emma, Fawke, Stuart, Bullman, Ben, Turner, Lori, Jarvis, Isobel, Omarjee, Ommar, De Sa, Aloka, Marsden, Joe, Betancourt, Ariana, Perera, Marianne, Epping, Maddie, Richoz, Nathan, Bower, Georgie, Sharma, Rahul, Nice, Francesca, Huhn, Oisin, Stark, Hannah, Walker, Neil, Stirrups, Kathy, Ovington, Nigel, Dewhust, Eleanor, Li, Emily, Papadia, Sofia, Nathan, James A., Baker, Stephen, James, Leo C., Baxendale, Helen E., Goodfellow, Ian, Doffinger, Rainer, Briggs, John A. G., Hosmillo, Myra [0000-0002-3514-7681], Nathan, James [0000-0002-0248-1632], Baker, Stephen [0000-0003-1308-5755], Goodfellow, Ian [0000-0002-9483-510X], and Apollo - University of Cambridge Repository

Subjects
Models, Molecular, Immunogen, Protein Conformation, Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), Trimer, Enzyme-Linked Immunosorbent Assay, Receptor binding site, medicine.disease_cause, Protein Engineering, Article, 03 medical and health sciences, Betacoronavirus, 0302 clinical medicine, Protein structure, COVID-19 Testing, Models, Structural Biology, medicine, Humans, Disulfides, Molecular Biology, 030304 developmental biology, Cell entry, 0303 health sciences, Mutation, Clinical Laboratory Techniques, Protein Stability, SARS-CoV-2, Cryoelectron Microscopy, Temperature, Spike Protein, Molecular, Coronavirus Infections, Flow Cytometry, Immunoglobulin G, Protein Multimerization, Spike Glycoprotein, Coronavirus, Spike Glycoprotein, 3. Good health, Coronavirus, Membrane, Biophysics, 030217 neurology & neurosurgery
Abstract

The spike (S) protein of SARS-CoV-2 mediates receptor binding and cell entry and is the dominant target of the immune system. S exhibits substantial conformational flexibility. It transitions from closed to open conformations to expose its receptor binding site, and subsequently from prefusion to postfusion conformations to mediate fusion of viral and cellular membranes. S protein derivatives are components of vaccine candidates and diagnostic assays, as well as tools for research into the biology and immunology of SARS-CoV-2. Here we have designed mutations in S which allow production of thermostable, crosslinked, S protein trimers that are trapped in the closed, pre-fusion, state. We have determined the structures of crosslinked and non-crosslinked proteins, identifying two distinct closed conformations of the S trimer. We demonstrate that the designed, thermostable, closed S trimer can be used in serological assays. This protein has potential applications as a reagent for serology, virology and as an immunogen.

Published
2020
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50. Additional file 3 of Genetic feature engineering enables characterisation of shared risk factors in immune-mediated diseases

Author

Burren, Oliver S., Reales, Guillermo, Limy Wong, Bowes, John, Lee, James C., Barton, Anne, Lyons, Paul A., Smith, Kenneth G. C., Thomson, Wendy, Kirk, Paul D. W., and Wallace, Chris

Abstract

Additional file 3: Fig. S1-S21. Distribution of SNPs across the basis components, reconstruction plot error, hierarchical clustering of basis diseases and their basis counterparts using different thresholds, delta plots for the 13 principal components in the IMD basis, test for consistency across trait groups, comparison of projections across different ancestries, distribution of entries in the rotation matrix for each component in the basis, and QQ plots of p-values for driver SNPs on trait-significant components.

Published
2020
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