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Aitken J, Ambrose K, Barrell S, Beale R, Bineva-Todd G, Biswas D, Byrne R, Caidan S, Cherepanov P, Churchward L, Clark G, Crawford M, Cubitt L, Dearing V, Earl C, Edwards A, Ekin C, Fidanis E, Gaiba A, Gamblin S, Gandhi S, Goldman J, Goldstone R, Grant PR, Greco M, Heaney J, Hindmarsh S, Houlihan CF, Howell M, Hubank M, Hughes D, Instrell R, Jackson D, Jamal-Hanjani M, Jiang M, Johnson M, Jones L, Kanu N, Kassiotis G, Kirk S, Kjaer S, Levett A, Levett L, Levi M, Lu WT, MacRae JI, Matthews J, McCoy LE, Moore C, Moore D, Nastouli E, Nicod J, Nightingale L, Olsen J, O'Reilly N, Pabari A, Papayannopoulos V, Patel N, Peat N, Pollitt M, Ratcliffe P, Reis e Sousa C, Rosa A, Rosenthal R, Roustan C, Rowan A, Shin GY, Snell DM, Song OR, Spyer MJ, Strange A, Swanton C, Turner JMA, Turner M, Wack A, Walker PA, Ward S, Wong WK, Wright J, Wu M. Author Correction: Scalable and robust SARS-CoV-2 testing in an academic center. Nat Biotechnol 2020; 38:1000. [PMID: 32681136 PMCID: PMC7366556 DOI: 10.1038/s41587-020-0623-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
An amendment to this paper has been published and can be accessed via a link at the top of the paper.
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Affiliation(s)
| | | | | | - Rupert Beale
- The Francis Crick Institute, London, UK
- University College London, London, UK
| | | | | | | | | | | | - Laura Churchward
- University College London Hospitals, NHS Foundation Trust, London, UK
| | | | | | | | | | | | | | - Chris Ekin
- Health Services Laboratories, London, UK
| | | | | | | | - Sonia Gandhi
- The Francis Crick Institute, London, UK.
- University College London, London, UK.
- University College London Hospitals, NHS Foundation Trust, London, UK.
| | | | | | | | | | - Judith Heaney
- University College London Hospitals, NHS Foundation Trust, London, UK
| | | | | | | | - Michael Hubank
- The Institute of Cancer Research, London, UK
- The Royal Marsden Hospital, Surrey, UK
| | | | | | | | - Mariam Jamal-Hanjani
- University College London, London, UK
- University College London Hospitals, NHS Foundation Trust, London, UK
| | | | | | | | | | | | | | | | | | | | - Marcel Levi
- University College London Hospitals, NHS Foundation Trust, London, UK
| | | | | | | | | | | | - David Moore
- University College London, London, UK
- University College London Hospitals, NHS Foundation Trust, London, UK
| | - Eleni Nastouli
- University College London Hospitals, NHS Foundation Trust, London, UK.
- University College London GOS Institute of Child Health, London, UK.
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | - Gee Yen Shin
- University College London Hospitals, NHS Foundation Trust, London, UK
- Health Services Laboratories, London, UK
| | | | | | | | | | - Charles Swanton
- The Francis Crick Institute, London, UK.
- University College London, London, UK.
- University College London Hospitals, NHS Foundation Trust, London, UK.
| | | | | | | | | | - Sophia Ward
- The Francis Crick Institute, London, UK
- University College London, London, UK
| | - Wai Keong Wong
- University College London Hospitals, NHS Foundation Trust, London, UK
| | | | - Mary Wu
- The Francis Crick Institute, London, UK
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Aitken J, Ambrose K, Barrell S, Beale R, Bineva-Todd G, Biswas D, Byrne R, Caidan S, Cherepanov P, Churchward L, Clark G, Crawford M, Cubitt L, Dearing V, Earl C, Edwards A, Ekin C, Fidanis E, Gaiba A, Gamblin S, Gandhi S, Goldman J, Goldstone R, Grant PR, Greco M, Heaney J, Hindmarsh S, Houlihan CF, Howell M, Hubank M, Hughes D, Instrell R, Jackson D, Jamal-Hanjani M, Jiang M, Johnson M, Jones L, Kanu N, Kassiotis G, Kirk S, Kjaer S, Levett A, Levett L, Levi M, Lu WT, MacRae JI, Matthews J, McCoy LE, Moore C, Moore D, Nastouli E, Nicod J, Nightingale L, Olsen J, O'Reilly N, Pabari A, Papayannopoulos V, Patel N, Peat N, Pollitt M, Ratcliffe P, Reis e Sousa C, Rosa A, Rosenthal R, Roustan C, Rowan A, Shin GY, Snell DM, Song OR, Spyer MJ, Strange A, Swanton C, Turner JMA, Turner M, Wack A, Walker PA, Ward S, Wong WK, Wright J, Wu M. Scalable and robust SARS-CoV-2 testing in an academic center. Nat Biotechnol 2020; 38:927-931. [PMID: 32555528 DOI: 10.1038/s41587-020-0588-y] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Affiliation(s)
| | | | | | - Rupert Beale
- The Francis Crick Institute, London, UK
- University College London, London, UK
| | | | | | | | | | | | - Laura Churchward
- University College London Hospitals, NHS Foundation Trust, London, UK
| | | | | | | | | | | | | | - Chris Ekin
- Health Services Laboratories, London, UK
| | | | | | | | - Sonia Gandhi
- The Francis Crick Institute, London, UK.
- University College London, London, UK.
- University College London Hospitals, NHS Foundation Trust, London, UK.
| | | | | | | | | | - Judith Heaney
- University College London Hospitals, NHS Foundation Trust, London, UK
| | | | | | | | - Michael Hubank
- The Institute of Cancer Research, London, UK
- The Royal Marsden Hospital, Surrey, UK
| | | | | | | | - Mariam Jamal-Hanjani
- University College London, London, UK
- University College London Hospitals, NHS Foundation Trust, London, UK
| | | | | | | | | | | | | | | | | | | | - Marcel Levi
- University College London Hospitals, NHS Foundation Trust, London, UK
| | | | | | | | | | | | - David Moore
- University College London, London, UK
- University College London Hospitals, NHS Foundation Trust, London, UK
| | - Eleni Nastouli
- University College London Hospitals, NHS Foundation Trust, London, UK.
- University College London GOS Institute of Child Health, London, UK.
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | - Gee Yen Shin
- University College London Hospitals, NHS Foundation Trust, London, UK
- Health Services Laboratories, London, UK
| | | | | | | | | | - Charles Swanton
- The Francis Crick Institute, London, UK.
- University College London, London, UK.
- University College London Hospitals, NHS Foundation Trust, London, UK.
| | | | | | | | | | - Sophia Ward
- The Francis Crick Institute, London, UK
- University College London, London, UK
| | - Wai Keong Wong
- University College London Hospitals, NHS Foundation Trust, London, UK
| | | | - Mary Wu
- The Francis Crick Institute, London, UK
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Gu W, Nowak WN, Xie Y, Le Bras A, Hu Y, Deng J, Issa Bhaloo S, Lu Y, Yuan H, Fidanis E, Saxena A, Kanno T, Mason AJ, Dulak J, Cai J, Xu Q. Single-Cell RNA-Sequencing and Metabolomics Analyses Reveal the Contribution of Perivascular Adipose Tissue Stem Cells to Vascular Remodeling. Arterioscler Thromb Vasc Biol 2019; 39:2049-2066. [PMID: 31340667 PMCID: PMC6766361 DOI: 10.1161/atvbaha.119.312732] [Citation(s) in RCA: 61] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
OBJECTIVE Perivascular adipose tissue (PVAT) plays a vital role in maintaining vascular homeostasis. However, most studies ascribed the function of PVAT in vascular remodeling to adipokines secreted by the perivascular adipocytes. Whether mesenchymal stem cells exist in PVAT and play a role in vascular regeneration remain unknown. Approach and Results: Single-cell RNA-sequencing allowed direct visualization of the heterogeneous PVAT-derived mesenchymal stem cells (PV-ADSCs) at a high resolution and revealed 2 distinct subpopulations, among which one featured signaling pathways crucial for smooth muscle differentiation. Pseudotime analysis of cultured PV-ADSCs unraveled their smooth muscle differentiation trajectory. Transplantation of cultured PV-ADSCs in mouse vein graft model suggested the contribution of PV-ADSCs to vascular remodeling through smooth muscle differentiation. Mechanistically, treatment with TGF-β1 (transforming growth factor β1) and transfection of microRNA (miR)-378a-3p mimics induced a similar metabolic reprogramming of PV-ADSCs, including upregulated mitochondrial potential and altered lipid levels, such as increased cholesterol and promoted smooth muscle differentiation. CONCLUSIONS Single-cell RNA-sequencing allows direct visualization of PV-ADSC heterogeneity at a single-cell level and uncovers 2 subpopulations with distinct signature genes and signaling pathways. The function of PVAT in vascular regeneration is partly attributed to PV-ADSCs and their differentiation towards smooth muscle lineage. Mechanistic study presents miR-378a-3p which is a potent regulator of metabolic reprogramming as a potential therapeutic target for vascular regeneration.
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Affiliation(s)
- Wenduo Gu
- From the School of Cardiovascular Medicine and Sciences, King's College London, BHF Centre, United Kingdom (W.G., W.N.N., Y.X., A.L.B., Y.H., J. Deng, S.I.B., Q.X.)
| | - Witold N Nowak
- From the School of Cardiovascular Medicine and Sciences, King's College London, BHF Centre, United Kingdom (W.G., W.N.N., Y.X., A.L.B., Y.H., J. Deng, S.I.B., Q.X.)
| | - Yao Xie
- From the School of Cardiovascular Medicine and Sciences, King's College London, BHF Centre, United Kingdom (W.G., W.N.N., Y.X., A.L.B., Y.H., J. Deng, S.I.B., Q.X.)
| | - Alexandra Le Bras
- From the School of Cardiovascular Medicine and Sciences, King's College London, BHF Centre, United Kingdom (W.G., W.N.N., Y.X., A.L.B., Y.H., J. Deng, S.I.B., Q.X.)
| | - Yanhua Hu
- From the School of Cardiovascular Medicine and Sciences, King's College London, BHF Centre, United Kingdom (W.G., W.N.N., Y.X., A.L.B., Y.H., J. Deng, S.I.B., Q.X.)
| | - Jiacheng Deng
- From the School of Cardiovascular Medicine and Sciences, King's College London, BHF Centre, United Kingdom (W.G., W.N.N., Y.X., A.L.B., Y.H., J. Deng, S.I.B., Q.X.)
| | - Shirin Issa Bhaloo
- From the School of Cardiovascular Medicine and Sciences, King's College London, BHF Centre, United Kingdom (W.G., W.N.N., Y.X., A.L.B., Y.H., J. Deng, S.I.B., Q.X.)
| | - Yao Lu
- Center of Clinical Pharmacology, Department of Cardiology, Third Xiangya Hospital, Central South University, Changsha, China (Y.L., H.Y., J.C.)
| | - Hong Yuan
- Center of Clinical Pharmacology, Department of Cardiology, Third Xiangya Hospital, Central South University, Changsha, China (Y.L., H.Y., J.C.)
| | - Efthymios Fidanis
- Genomics Research Platform, Biomedical Research Centre at Guy's Hospital, London, United Kingdom (E.F., A.S.)
| | - Alka Saxena
- Genomics Research Platform, Biomedical Research Centre at Guy's Hospital, London, United Kingdom (E.F., A.S.)
| | - Tokuwa Kanno
- Institute of Pharmaceutical Science, School of Cancer & Pharmaceutical Science, King's College London, Franklin-Wilkins Building, London, United Kingdom (T.K., A.J.M.)
| | - A James Mason
- Institute of Pharmaceutical Science, School of Cancer & Pharmaceutical Science, King's College London, Franklin-Wilkins Building, London, United Kingdom (T.K., A.J.M.)
| | - Jozef Dulak
- Department of Medical Biotechnology, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Kraków, Poland (J. Dulak)
| | - Jingjing Cai
- Center of Clinical Pharmacology, Department of Cardiology, Third Xiangya Hospital, Central South University, Changsha, China (Y.L., H.Y., J.C.)
| | - Qingbo Xu
- From the School of Cardiovascular Medicine and Sciences, King's College London, BHF Centre, United Kingdom (W.G., W.N.N., Y.X., A.L.B., Y.H., J. Deng, S.I.B., Q.X.)
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Banerji CRS, Panamarova M, Pruller J, Figeac N, Hebaishi H, Fidanis E, Saxena A, Contet J, Sacconi S, Severini S, Zammit PS. Dynamic transcriptomic analysis reveals suppression of PGC1α/ERRα drives perturbed myogenesis in facioscapulohumeral muscular dystrophy. Hum Mol Genet 2019; 28:1244-1259. [PMID: 30462217 PMCID: PMC6452176 DOI: 10.1093/hmg/ddy405] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2018] [Revised: 11/12/2018] [Accepted: 11/14/2018] [Indexed: 01/06/2023] Open
Abstract
Facioscapulohumeral muscular dystrophy (FSHD) is a prevalent, incurable myopathy, linked to epigenetic derepression of D4Z4 repeats on chromosome 4q, leading to ectopic DUX4 expression. FSHD patient myoblasts have defective myogenic differentiation, forming smaller myotubes with reduced myosin content. However, molecular mechanisms driving such disrupted myogenesis in FSHD are poorly understood. We performed high-throughput morphological analysis describing FSHD and control myogenesis, revealing altered myogenic differentiation results in hypotrophic myotubes. Employing polynomial models and an empirical Bayes approach, we established eight critical time points during which human healthy and FSHD myogenesis differ. RNA-sequencing at these eight nodal time points in triplicate, provided temporal depth for a multivariate regression analysis, allowing assessment of interaction between progression of differentiation and FSHD disease status. Importantly, the unique size and structure of our data permitted identification of many novel FSHD pathomechanisms undetectable by previous approaches. For further analysis here, we selected pathways that control mitochondria: of interest considering known alterations in mitochondrial structure and function in FSHD muscle, and sensitivity of FSHD cells to oxidative stress. Notably, we identified suppression of mitochondrial biogenesis, in particular via peroxisome proliferator-activated receptor gamma coactivator 1-α (PGC1α), the cofactor and activator of oestrogen-related receptor α (ERRα). PGC1α knock-down caused hypotrophic myotubes to form from control myoblasts. Known ERRα agonists and safe food supplements biochanin A, daidzein or genistein, each rescued the hypotrophic FSHD myotube phenotype. Together our work describes transcriptomic changes in high resolution that occur during myogenesis in FSHD ex vivo, identifying suppression of the PGC1α-ERRα axis leading to perturbed myogenic differentiation, which can effectively be rescued by readily available food supplements.
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Affiliation(s)
- Christopher R S Banerji
- Randall Centre for Cell and Molecular Biophysics, New Hunt's House, Guy's Campus, King's College London, London, UK
- Department of Computer Science, University College London, London, UK
- Centre of Mathematics and Physics in the Life Sciences and Experimental Biology, University College London, London, UK
| | - Maryna Panamarova
- Randall Centre for Cell and Molecular Biophysics, New Hunt's House, Guy's Campus, King's College London, London, UK
| | - Johanna Pruller
- Randall Centre for Cell and Molecular Biophysics, New Hunt's House, Guy's Campus, King's College London, London, UK
| | - Nicolas Figeac
- Randall Centre for Cell and Molecular Biophysics, New Hunt's House, Guy's Campus, King's College London, London, UK
| | - Husam Hebaishi
- Randall Centre for Cell and Molecular Biophysics, New Hunt's House, Guy's Campus, King's College London, London, UK
| | - Efthymios Fidanis
- Genomics Research Platform, Biomedical Research Centre at Guy’s and St Thomas’ Trust and Kings College London, Guy’s Hospital, London, UK
| | - Alka Saxena
- Genomics Research Platform, Biomedical Research Centre at Guy’s and St Thomas’ Trust and Kings College London, Guy’s Hospital, London, UK
| | - Julian Contet
- Institute for Research on Cancer and Aging of Nice, Faculty of Medicine, Université Côte d'Azur, Nice, Cedex, France
| | - Sabrina Sacconi
- Institute for Research on Cancer and Aging of Nice, Faculty of Medicine, Université Côte d'Azur, Nice, Cedex, France
- Peripheral Nervous System, Muscle and ALS Department, Université Côte d'Azur, Nice, France
| | - Simone Severini
- Department of Computer Science, University College London, London, UK
| | - Peter S Zammit
- Randall Centre for Cell and Molecular Biophysics, New Hunt's House, Guy's Campus, King's College London, London, UK
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Yeo L, Woodwyk A, Sood S, Lorenc A, Eichmann M, Pujol-Autonell I, Melchiotti R, Skowera A, Fidanis E, Dolton GM, Tungatt K, Sewell AK, Heck S, Saxena A, Beam CA, Peakman M. Autoreactive T effector memory differentiation mirrors β cell function in type 1 diabetes. J Clin Invest 2018; 128:3460-3474. [PMID: 29851415 DOI: 10.1172/jci120555] [Citation(s) in RCA: 41] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2018] [Accepted: 05/23/2018] [Indexed: 12/26/2022] Open
Abstract
In type 1 diabetes, cytotoxic CD8+ T cells with specificity for β cell autoantigens are found in the pancreatic islets, where they are implicated in the destruction of insulin-secreting β cells. In contrast, the disease relevance of β cell-reactive CD8+ T cells that are detectable in the circulation, and their relationship to β cell function, are not known. Here, we tracked multiple, circulating β cell-reactive CD8+ T cell subsets and measured β cell function longitudinally for 2 years, starting immediately after diagnosis of type 1 diabetes. We found that change in β cell-specific effector memory CD8+ T cells expressing CD57 was positively correlated with C-peptide change in subjects below 12 years of age. Autoreactive CD57+ effector memory CD8+ T cells bore the signature of enhanced effector function (higher expression of granzyme B, killer-specific protein of 37 kDa, and CD16, and reduced expression of CD28) compared with their CD57- counterparts, and network association modeling indicated that the dynamics of β cell-reactive CD57+ effector memory CD8+ T cell subsets were strongly linked. Thus, coordinated changes in circulating β cell-specific CD8+ T cells within the CD57+ effector memory subset calibrate to functional insulin reserve in type 1 diabetes, providing a tool for immune monitoring and a mechanism-based target for immunotherapy.
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Affiliation(s)
- Lorraine Yeo
- Department of Immunobiology, Faculty of Life Sciences and Medicine, King's College London, London, United Kingdom.,National Institute of Health Research Biomedical Research Centre at Guy's and St Thomas' Hospital and King's College London, London, United Kingdom
| | - Alyssa Woodwyk
- Division of Epidemiology and Biostatistics, Department of Biomedical Sciences, Western Michigan University Homer Stryker M.D. School of Medicine, Kalamazoo, Michigan, USA
| | - Sanjana Sood
- National Institute of Health Research Biomedical Research Centre at Guy's and St Thomas' Hospital and King's College London, London, United Kingdom
| | - Anna Lorenc
- Department of Immunobiology, Faculty of Life Sciences and Medicine, King's College London, London, United Kingdom
| | - Martin Eichmann
- Department of Immunobiology, Faculty of Life Sciences and Medicine, King's College London, London, United Kingdom
| | - Irma Pujol-Autonell
- Department of Immunobiology, Faculty of Life Sciences and Medicine, King's College London, London, United Kingdom
| | - Rosella Melchiotti
- National Institute of Health Research Biomedical Research Centre at Guy's and St Thomas' Hospital and King's College London, London, United Kingdom
| | - Ania Skowera
- Department of Immunobiology, Faculty of Life Sciences and Medicine, King's College London, London, United Kingdom
| | - Efthymios Fidanis
- National Institute of Health Research Biomedical Research Centre at Guy's and St Thomas' Hospital and King's College London, London, United Kingdom
| | - Garry M Dolton
- Division of Infection and Immunity and Systems Immunity Research Institute, Cardiff University School of Medicine, Cardiff, United Kingdom
| | - Katie Tungatt
- Division of Infection and Immunity and Systems Immunity Research Institute, Cardiff University School of Medicine, Cardiff, United Kingdom
| | - Andrew K Sewell
- Division of Infection and Immunity and Systems Immunity Research Institute, Cardiff University School of Medicine, Cardiff, United Kingdom
| | - Susanne Heck
- National Institute of Health Research Biomedical Research Centre at Guy's and St Thomas' Hospital and King's College London, London, United Kingdom
| | - Alka Saxena
- National Institute of Health Research Biomedical Research Centre at Guy's and St Thomas' Hospital and King's College London, London, United Kingdom
| | - Craig A Beam
- Division of Epidemiology and Biostatistics, Department of Biomedical Sciences, Western Michigan University Homer Stryker M.D. School of Medicine, Kalamazoo, Michigan, USA
| | - Mark Peakman
- Department of Immunobiology, Faculty of Life Sciences and Medicine, King's College London, London, United Kingdom.,National Institute of Health Research Biomedical Research Centre at Guy's and St Thomas' Hospital and King's College London, London, United Kingdom.,King's Health Partners Institute of Diabetes, Endocrinology and Obesity, London, United Kingdom
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