1
|
Kowalka AM, Alexiadou K, Cuenco J, Clarke RE, Minnion J, Williams EL, Bech P, Purkayastha S, Ahmed AR, Takats Z, Whitwell HJ, Romero MG, Bloom SR, Camuzeaux S, Lewis MR, Khoo B, Tan TM. The postprandial secretion of peptide YY 1-36 and 3-36 in obesity is differentially increased after gastric bypass versus sleeve gastrectomy. Clin Endocrinol (Oxf) 2023; 99:272-284. [PMID: 36345253 PMCID: PMC10952770 DOI: 10.1111/cen.14846] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/16/2022] [Revised: 10/13/2022] [Accepted: 11/04/2022] [Indexed: 11/09/2022]
Abstract
OBJECTIVES Peptide tyrosine tyrosine (PYY) exists as two species, PYY1-36 and PYY3-36 , with distinct effects on insulin secretion and appetite regulation. The detailed effects of bariatric surgery on PYY1-36 and PYY3-36 secretion are not known as previous studies have used nonspecific immunoassays to measure total PYY. Our objective was to characterize the effect of sleeve gastrectomy (SG) and Roux-en-Y gastric bypass (RYGB) on fasting and postprandial PYY1-36 and PYY3-36 secretion using a newly developed liquid chromatography-tandem mass spectrometry (LC-MS/MS) assay. DESIGN AND SUBJECTS Observational study in 10 healthy nonobese volunteers and 30 participants with obesity who underwent RYGB (n = 24) or SG (n = 6) at the Imperial Weight Centre [NCT01945840]. Participants were studied using a standardized mixed meal test (MMT) before and 1 year after surgery. The outcome measures were PYY1-36 and PYY3-36 concentrations. RESULTS Presurgery, the fasting and postprandial levels of PYY1-36 and PYY3-36 were low, with minimal responses to the MMT, and these did not differ from healthy nonobese volunteers. The postprandial secretion of both PYY1-36 and PYY3-36 at 1 year was amplified after RYGB, but not SG, with the response being significantly higher in RYGB compared with SG. CONCLUSIONS There appears to be no difference in PYY secretion between nonobese and obese volunteers at baseline. At 1 year after surgery, RYGB, but not SG, is associated with increased postprandial secretion of PYY1-36 and PYY3-36 , which may account for long-term differences in efficacy and adverse effects between the two types of surgery.
Collapse
Affiliation(s)
- Anna M. Kowalka
- Section of Diabetes, Endocrinology and Metabolism, Department of Metabolism, Digestion and ReproductionImperial College LondonLondonUK
| | - Kleopatra Alexiadou
- Section of Diabetes, Endocrinology and Metabolism, Department of Metabolism, Digestion and ReproductionImperial College LondonLondonUK
| | - Joyceline Cuenco
- Section of Diabetes, Endocrinology and Metabolism, Department of Metabolism, Digestion and ReproductionImperial College LondonLondonUK
| | | | - James Minnion
- Section of Diabetes, Endocrinology and Metabolism, Department of Metabolism, Digestion and ReproductionImperial College LondonLondonUK
| | - Emma L. Williams
- Department of Clinical Biochemistry, North West London PathologyCharing Cross HospitalLondonUK
| | - Paul Bech
- Section of Diabetes, Endocrinology and Metabolism, Department of Metabolism, Digestion and ReproductionImperial College LondonLondonUK
| | - Sanjay Purkayastha
- Department of Surgery and CancerImperial College Healthcare NHS TrustLondonUK
| | - Ahmed R. Ahmed
- Department of Surgery and CancerImperial College Healthcare NHS TrustLondonUK
| | - Zoltan Takats
- Section of Bioanalytical Chemistry, Department of Metabolism, Digestion and ReproductionImperial College LondonLondonUK
- National Phenome CentreImperial College LondonLondonUK
| | - Harry J. Whitwell
- Section of Bioanalytical Chemistry, Department of Metabolism, Digestion and ReproductionImperial College LondonLondonUK
- National Phenome CentreImperial College LondonLondonUK
| | - Maria Gomez Romero
- Section of Bioanalytical Chemistry, Department of Metabolism, Digestion and ReproductionImperial College LondonLondonUK
- National Phenome CentreImperial College LondonLondonUK
| | - Stephen R. Bloom
- Section of Diabetes, Endocrinology and Metabolism, Department of Metabolism, Digestion and ReproductionImperial College LondonLondonUK
| | - Stephane Camuzeaux
- Section of Bioanalytical Chemistry, Department of Metabolism, Digestion and ReproductionImperial College LondonLondonUK
- National Phenome CentreImperial College LondonLondonUK
| | - Matthew R. Lewis
- Section of Bioanalytical Chemistry, Department of Metabolism, Digestion and ReproductionImperial College LondonLondonUK
- National Phenome CentreImperial College LondonLondonUK
| | - Bernard Khoo
- Endocrinology, Division of MedicineUniversity College LondonLondonUK
| | - Tricia M.‐M. Tan
- Section of Diabetes, Endocrinology and Metabolism, Department of Metabolism, Digestion and ReproductionImperial College LondonLondonUK
| |
Collapse
|
2
|
Kowalka AM, Alexiadou K, Cuenco J, Clarke RE, Camuzeaux S, Minnion J, Williams EL, Bech P, Purkayastha S, Ahmed AR, Takats Z, Khoo B, Whitwell HJ, Romero MG, Bloom SR, Lewis MR, Tan TM. Commentary on "The road to reliable peptide assays is paved with good guidelines". Clin Endocrinol (Oxf) 2023; 98:763-765. [PMID: 36915993 PMCID: PMC10952462 DOI: 10.1111/cen.14894] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/13/2023] [Accepted: 02/14/2023] [Indexed: 03/16/2023]
Affiliation(s)
- Anna M. Kowalka
- Section of Diabetes, Endocrinology and Metabolism, Department of Metabolism, Digestion and ReproductionImperial College LondonLondonUK
| | - Kleopatra Alexiadou
- Section of Diabetes, Endocrinology and Metabolism, Department of Metabolism, Digestion and ReproductionImperial College LondonLondonUK
| | - Joyceline Cuenco
- Section of Diabetes, Endocrinology and Metabolism, Department of Metabolism, Digestion and ReproductionImperial College LondonLondonUK
| | | | - Stephane Camuzeaux
- Section of Bioanalytical Chemistry, Department of Metabolism, Digestion and ReproductionImperial College LondonLondonUK
- National Phenome CentreImperial College LondonLondonUK
| | - James Minnion
- Section of Diabetes, Endocrinology and Metabolism, Department of Metabolism, Digestion and ReproductionImperial College LondonLondonUK
| | - Emma L. Williams
- Department of Clinical Biochemistry, North West London PathologyCharing Cross HospitalLondonUK
| | - Paul Bech
- Section of Diabetes, Endocrinology and Metabolism, Department of Metabolism, Digestion and ReproductionImperial College LondonLondonUK
| | - Sanjay Purkayastha
- Department of Surgery and CancerImperial College Healthcare NHS TrustLondonUK
| | - Ahmed R. Ahmed
- Department of Surgery and CancerImperial College Healthcare NHS TrustLondonUK
| | - Zoltan Takats
- Section of Bioanalytical Chemistry, Department of Metabolism, Digestion and ReproductionImperial College LondonLondonUK
- National Phenome CentreImperial College LondonLondonUK
| | - Bernard Khoo
- Endocrinology, Division of MedicineUniversity College LondonLondonUK
| | - Harry J. Whitwell
- Section of Bioanalytical Chemistry, Department of Metabolism, Digestion and ReproductionImperial College LondonLondonUK
- National Phenome CentreImperial College LondonLondonUK
| | - Maria G. Romero
- Section of Bioanalytical Chemistry, Department of Metabolism, Digestion and ReproductionImperial College LondonLondonUK
- National Phenome CentreImperial College LondonLondonUK
| | - Stephen R. Bloom
- Section of Diabetes, Endocrinology and Metabolism, Department of Metabolism, Digestion and ReproductionImperial College LondonLondonUK
| | - Matthew R. Lewis
- Section of Bioanalytical Chemistry, Department of Metabolism, Digestion and ReproductionImperial College LondonLondonUK
- National Phenome CentreImperial College LondonLondonUK
| | - Tricia M.‐M. Tan
- Section of Diabetes, Endocrinology and Metabolism, Department of Metabolism, Digestion and ReproductionImperial College LondonLondonUK
| |
Collapse
|
3
|
Li HK, Zhi X, Vieira A, Whitwell HJ, Schricker A, Jauneikaite E, Li H, Yosef A, Andrew I, Game L, Turner CE, Lamagni T, Coelho J, Sriskandan S. Characterization of emergent toxigenic M1 UK Streptococcus pyogenes and associated sublineages. Microb Genom 2023; 9:mgen000994. [PMID: 37093716 PMCID: PMC10210942 DOI: 10.1099/mgen.0.000994] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2023] [Accepted: 02/23/2023] [Indexed: 04/25/2023] Open
Abstract
Streptococcus pyogenes genotype emm1 is a successful, globally distributed epidemic clone that is regarded as inherently virulent. An emm1 sublineage, M1UK, that produces increased levels of SpeA toxin was associated with increased scarlet fever and invasive infections in England in 2015/2016. Defined by 27 SNPs in the core genome, M1UK is now dominant in England. To more fully characterize M1UK, we undertook comparative transcriptomic and proteomic analyses of M1UK and contemporary non-M1UK emm1 strains (M1global). Just seven genes were differentially expressed by M1UK compared with contemporary M1global strains. In addition to speA, five genes in the operon that includes glycerol dehydrogenase were upregulated in M1UK (gldA, mipB/talC, pflD, and phosphotransferase system IIC and IIB components), while aquaporin (glpF2) was downregulated. M1UK strains have a stop codon in gldA. Deletion of gldA in M1global abrogated glycerol dehydrogenase activity, and recapitulated upregulation of gene expression within the operon that includes gldA, consistent with a feedback effect. Phylogenetic analysis identified two intermediate emm1 sublineages in England comprising 13/27 (M113SNPs) and 23/27 SNPs (M123SNPs), respectively, that had failed to expand in the population. Proteomic analysis of invasive strains from the four phylogenetic emm1 groups highlighted sublineage-specific changes in carbohydrate metabolism, protein synthesis and protein processing; upregulation of SpeA was not observed in chemically defined medium. In rich broth, however, expression of SpeA was upregulated ~10-fold in both M123SNPs and M1UK sublineages, compared with M113SNPs and M1global. We conclude that stepwise accumulation of SNPs led to the emergence of M1UK. While increased expression of SpeA is a key indicator of M1UK and undoubtedly important, M1UK strains have outcompeted M123SNPs and other emm types that produce similar or more superantigen toxin. We speculate that an accumulation of adaptive SNPs has contributed to a wider fitness advantage in M1UK on an inherently successful emm1 streptococcal background.
Collapse
Affiliation(s)
- Ho Kwong Li
- Department of Infectious Disease, Imperial College London, London, UK
- MRC Centre for Molecular Bacteriology & Infection (CMBI), Imperial College London, London, UK
| | - Xiangyun Zhi
- Department of Infectious Disease, Imperial College London, London, UK
- MRC Centre for Molecular Bacteriology & Infection (CMBI), Imperial College London, London, UK
| | - Ana Vieira
- Department of Infectious Disease, Imperial College London, London, UK
- MRC Centre for Molecular Bacteriology & Infection (CMBI), Imperial College London, London, UK
| | - Harry J. Whitwell
- National Phenome Centre and Imperial Clinical Phenotyping Centre, Department of Metabolism, Digestion and Reproduction, Imperial College London, London, UK
- Department of Metabolism, Digestion and Reproduction, Imperial College London, London, UK
| | - Amelia Schricker
- UK Dementia Research Institute, Department of Brain Sciences, Imperial College London, London, UK
| | - Elita Jauneikaite
- NIHR Health Protection Unit in Healthcare-associated Infection and Antimicrobial Resistance, Imperial College London, London, UK
- School of Public Health, Imperial College London, London, UK
| | - Hanqi Li
- Department of Infectious Disease, Imperial College London, London, UK
| | - Ahmed Yosef
- Department of Infectious Disease, Imperial College London, London, UK
| | - Ivan Andrew
- Genomics Facility, UKRI-MRC London Institute for Medical Sciences (LMS), Imperial College London, London, UK
| | - Laurence Game
- Genomics Facility, UKRI-MRC London Institute for Medical Sciences (LMS), Imperial College London, London, UK
| | - Claire E. Turner
- The Florey Institute, School of Biosciences, University of Sheffield, South Yorkshire, UK
| | - Theresa Lamagni
- NIHR Health Protection Unit in Healthcare-associated Infection and Antimicrobial Resistance, Imperial College London, London, UK
- Centre for Infections, UK Health Security Agency, London, UK
| | - Juliana Coelho
- NIHR Health Protection Unit in Healthcare-associated Infection and Antimicrobial Resistance, Imperial College London, London, UK
- Centre for Infections, UK Health Security Agency, London, UK
| | - Shiranee Sriskandan
- Department of Infectious Disease, Imperial College London, London, UK
- MRC Centre for Molecular Bacteriology & Infection (CMBI), Imperial College London, London, UK
- NIHR Health Protection Unit in Healthcare-associated Infection and Antimicrobial Resistance, Imperial College London, London, UK
| |
Collapse
|
4
|
Nené NR, Ney A, Nazarenko T, Blyuss O, Johnston HE, Whitwell HJ, Sedlak E, Gentry-Maharaj A, Apostolidou S, Costello E, Greenhalf W, Jacobs I, Menon U, Hsuan J, Pereira SP, Zaikin A, Timms JF. Serum biomarker-based early detection of pancreatic ductal adenocarcinomas with ensemble learning. Commun Med (Lond) 2023; 3:10. [PMID: 36670203 PMCID: PMC9860022 DOI: 10.1038/s43856-023-00237-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2021] [Accepted: 01/04/2023] [Indexed: 01/21/2023] Open
Abstract
BACKGROUND Earlier detection of pancreatic ductal adenocarcinoma (PDAC) is key to improving patient outcomes, as it is mostly detected at advanced stages which are associated with poor survival. Developing non-invasive blood tests for early detection would be an important breakthrough. METHODS The primary objective of the work presented here is to use a dataset that is prospectively collected, to quantify a set of cancer-associated proteins and construct multi-marker models with the capacity to predict PDAC years before diagnosis. The data used is part of a nested case-control study within the UK Collaborative Trial of Ovarian Cancer Screening and is comprised of 218 samples, collected from a total of 143 post-menopausal women who were diagnosed with pancreatic cancer within 70 months after sample collection, and 249 matched non-cancer controls. We develop a stacked ensemble modelling technique to achieve robustness in predictions and, therefore, improve performance in newly collected datasets. RESULTS Here we show that with ensemble learning we can predict PDAC status with an AUC of 0.91 (95% CI 0.75-1.0), sensitivity of 92% (95% CI 0.54-1.0) at 90% specificity, up to 1 year prior to diagnosis, and at an AUC of 0.85 (95% CI 0.74-0.93) up to 2 years prior to diagnosis (sensitivity of 61%, 95% CI 0.17-0.83, at 90% specificity). CONCLUSIONS The ensemble modelling strategy explored here outperforms considerably biomarker combinations cited in the literature. Further developments in the selection of classifiers balancing performance and heterogeneity should further enhance the predictive capacity of the method.
Collapse
Affiliation(s)
- Nuno R Nené
- Department of Women's Cancer, EGA Institute for Women's Health, University College London, 84-86 Chenies Mews, London, WC1E 6HU, UK.
- Institute for Women's Health, University College London, Cruciform Building 1.1, Gower Street, London, WC1E 6BT, UK.
| | - Alexander Ney
- Institute for Liver and Digestive Health, University College London, Upper 3rd Floor, Royal Free Campus, Rowland Hill Street, London, NW3 2PF, UK
| | - Tatiana Nazarenko
- Department of Women's Cancer, EGA Institute for Women's Health, University College London, 84-86 Chenies Mews, London, WC1E 6HU, UK
- Department of Mathematics, University College London, London, WC1H 0AY, UK
| | - Oleg Blyuss
- Department of Women's Cancer, EGA Institute for Women's Health, University College London, 84-86 Chenies Mews, London, WC1E 6HU, UK
- Wolfson Institute of Population Health, Queen Mary University of London, Charterhouse Square, EC1M 6BQ, London, UK
| | - Harvey E Johnston
- Department of Women's Cancer, EGA Institute for Women's Health, University College London, 84-86 Chenies Mews, London, WC1E 6HU, UK
- Babraham Institute, Babraham Research Campus, Cambridge, CB22 3AT, UK
| | - Harry J Whitwell
- Department of Women's Cancer, EGA Institute for Women's Health, University College London, 84-86 Chenies Mews, London, WC1E 6HU, UK
- National Phenome Centre and Imperial Clinical Phenotyping Centre, Department of Metabolism, Digestion and Reproduction, IRDB Building, Imperial College London, Hammersmith Campus, London, W12 0NN, UK
- Section of Bioanalytical Chemistry, Division of Systems Medicine, Department of Metabolism, Digestion and Reproduction, Imperial College London, South Kensington Campus, London, SW7 2AZ, UK
| | - Eva Sedlak
- Department of Women's Cancer, EGA Institute for Women's Health, University College London, 84-86 Chenies Mews, London, WC1E 6HU, UK
| | - Aleksandra Gentry-Maharaj
- MRC Clinical Trials Unit at UCL, Institute of Clinical Trials and Methodology, UCL, 90 High Holborn, 2nd Floor, London, WC1V 6LJ, UK
| | - Sophia Apostolidou
- MRC Clinical Trials Unit at UCL, Institute of Clinical Trials and Methodology, UCL, 90 High Holborn, 2nd Floor, London, WC1V 6LJ, UK
| | - Eithne Costello
- Department of Molecular and Clinical Cancer Medicine, University of Liverpool, Liverpool, UK
| | - William Greenhalf
- Liverpool Experimental Cancer Medicine Centre, University of Liverpool, Liverpool, L69 3GL, UK
| | - Ian Jacobs
- Department of Women's Cancer, EGA Institute for Women's Health, University College London, 84-86 Chenies Mews, London, WC1E 6HU, UK
- University of New South Wales, Sydney, NSW, 2052, Australia
| | - Usha Menon
- MRC Clinical Trials Unit at UCL, Institute of Clinical Trials and Methodology, UCL, 90 High Holborn, 2nd Floor, London, WC1V 6LJ, UK
| | - Justin Hsuan
- Institute for Liver and Digestive Health, University College London, Upper 3rd Floor, Royal Free Campus, Rowland Hill Street, London, NW3 2PF, UK
| | - Stephen P Pereira
- Institute for Liver and Digestive Health, University College London, Upper 3rd Floor, Royal Free Campus, Rowland Hill Street, London, NW3 2PF, UK
| | - Alexey Zaikin
- Department of Women's Cancer, EGA Institute for Women's Health, University College London, 84-86 Chenies Mews, London, WC1E 6HU, UK
- Department of Mathematics, University College London, London, WC1H 0AY, UK
| | - John F Timms
- Department of Women's Cancer, EGA Institute for Women's Health, University College London, 84-86 Chenies Mews, London, WC1E 6HU, UK
| |
Collapse
|
5
|
Alzaydi MM, Abdul-Salam VB, Whitwell HJ, Russomanno G, Glynos A, Capece D, Szabadkai G, Wilkins MR, Wojciak-Stothard B. Intracellular Chloride Channels Regulate Endothelial Metabolic Reprogramming in Pulmonary Arterial Hypertension. Am J Respir Cell Mol Biol 2023; 68:103-115. [PMID: 36264759 PMCID: PMC9817916 DOI: 10.1165/rcmb.2022-0111oc] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
Mitochondrial fission and a metabolic switch from oxidative phosphorylation to glycolysis are key features of vascular pathology in pulmonary arterial hypertension (PAH) and are associated with exuberant endothelial proliferation and apoptosis. The underlying mechanisms are poorly understood. We describe the contribution of two intracellular chloride channel proteins, CLIC1 and CLIC4, both highly expressed in PAH and cancer, to mitochondrial dysfunction and energy metabolism in PAH endothelium. Pathological overexpression of CLIC proteins induces mitochondrial fragmentation, inhibits mitochondrial cristae formation, and induces metabolic shift toward glycolysis in human pulmonary artery endothelial cells, consistent with changes observed in patient-derived cells. Interactions of CLIC proteins with structural components of the inner mitochondrial membrane offer mechanistic insights. Endothelial CLIC4 excision and mitofusin 2 supplementation have protective effects in human PAH cells and preclinical PAH. This study is the first to demonstrate the key role of endothelial intracellular chloride channels in the regulation of mitochondrial structure, biogenesis, and metabolic reprogramming in expression of the PAH phenotype.
Collapse
Affiliation(s)
- Mai M. Alzaydi
- National Heart and Lung Institute,,National Center for Biotechnology, King Abdulaziz City for Science and Technology (KACST), Riyadh, Saudi Arabia
| | - Vahitha B. Abdul-Salam
- National Heart and Lung Institute,,Centre for Cardiovascular Medicine and Device Innovation, William Harvey Research Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London, United Kingdom
| | - Harry J. Whitwell
- National Phenome Centre and Imperial Clinical Phenotyping Centre, and,Section of Bioanalytical Chemistry, Division of Systems Medicine, Department of Metabolism, Digestion, and Reproduction, and
| | - Giusy Russomanno
- National Heart and Lung Institute,,Medical Research Council (MRC) Centre for Drug Safety Science, Department of Pharmacology and Therapeutics, Institute of Systems, Molecular, and Integrative Biology, University of Liverpool, Liverpool, United Kingdom
| | - Angelos Glynos
- Mitochondrial Biology Unit, Medical Research Council, University of Cambridge, Cambridge, United Kingdom; and
| | - Daria Capece
- Centre for Cell Signalling and Inflammation, Department of Immunology and Inflammation, Imperial College London, London, United Kingdom
| | - Gyorgy Szabadkai
- Cell and Developmental Biology, University College London, London, United Kingdom
| | | | | |
Collapse
|
6
|
Demichev V, Tober-Lau P, Nazarenko T, Lemke O, Kaur Aulakh S, Whitwell HJ, Röhl A, Freiwald A, Mittermaier M, Szyrwiel L, Ludwig D, Correia-Melo C, Lippert LJ, Helbig ET, Stubbemann P, Olk N, Thibeault C, Grüning NM, Blyuss O, Vernardis S, White M, Messner CB, Joannidis M, Sonnweber T, Klein SJ, Pizzini A, Wohlfarter Y, Sahanic S, Hilbe R, Schaefer B, Wagner S, Machleidt F, Garcia C, Ruwwe-Glösenkamp C, Lingscheid T, Bosquillon de Jarcy L, Stegemann MS, Pfeiffer M, Jürgens L, Denker S, Zickler D, Spies C, Edel A, Müller NB, Enghard P, Zelezniak A, Bellmann-Weiler R, Weiss G, Campbell A, Hayward C, Porteous DJ, Marioni RE, Uhrig A, Zoller H, Löffler-Ragg J, Keller MA, Tancevski I, Timms JF, Zaikin A, Hippenstiel S, Ramharter M, Müller-Redetzky H, Witzenrath M, Suttorp N, Lilley K, Mülleder M, Sander LE, Kurth F, Ralser M. A proteomic survival predictor for COVID-19 patients in intensive care. PLOS Digit Health 2022; 1:e0000007. [PMID: 36812516 PMCID: PMC9931303 DOI: 10.1371/journal.pdig.0000007] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/11/2021] [Accepted: 11/18/2021] [Indexed: 02/07/2023]
Abstract
Global healthcare systems are challenged by the COVID-19 pandemic. There is a need to optimize allocation of treatment and resources in intensive care, as clinically established risk assessments such as SOFA and APACHE II scores show only limited performance for predicting the survival of severely ill COVID-19 patients. Additional tools are also needed to monitor treatment, including experimental therapies in clinical trials. Comprehensively capturing human physiology, we speculated that proteomics in combination with new data-driven analysis strategies could produce a new generation of prognostic discriminators. We studied two independent cohorts of patients with severe COVID-19 who required intensive care and invasive mechanical ventilation. SOFA score, Charlson comorbidity index, and APACHE II score showed limited performance in predicting the COVID-19 outcome. Instead, the quantification of 321 plasma protein groups at 349 timepoints in 50 critically ill patients receiving invasive mechanical ventilation revealed 14 proteins that showed trajectories different between survivors and non-survivors. A predictor trained on proteomic measurements obtained at the first time point at maximum treatment level (i.e. WHO grade 7), which was weeks before the outcome, achieved accurate classification of survivors (AUROC 0.81). We tested the established predictor on an independent validation cohort (AUROC 1.0). The majority of proteins with high relevance in the prediction model belong to the coagulation system and complement cascade. Our study demonstrates that plasma proteomics can give rise to prognostic predictors substantially outperforming current prognostic markers in intensive care.
Collapse
Affiliation(s)
- Vadim Demichev
- Charité–Universitätsmedizin Berlin, Department of Biochemistry, Berlin, Germany
- The Francis Crick Institute, Molecular Biology of Metabolism Laboratory, London, United Kingdom
- The University of Cambridge, Department of Biochemistry and Cambridge Centre for Proteomics, Cambridge, United Kingdom
| | - Pinkus Tober-Lau
- Charité–Universitätsmedizin Berlin, Department of Infectious Diseases and Respiratory Medicine, Berlin, Germany
| | - Tatiana Nazarenko
- University College London, Department of Mathematics, London, United Kingdom
- University College London, Department of Women’s Cancer, EGA Institute for Women’s Health, London, United Kingdom
| | - Oliver Lemke
- Charité–Universitätsmedizin Berlin, Department of Biochemistry, Berlin, Germany
| | - Simran Kaur Aulakh
- The Francis Crick Institute, Molecular Biology of Metabolism Laboratory, London, United Kingdom
| | - Harry J. Whitwell
- National Phenome Centre and Imperial Clinical Phenotyping Centre, Department of Metabolism, Digestion and Reproduction, Imperial College London, London, United Kingdom
- Lobachevsky University, Laboratory of Systems Medicine of Healthy Ageing, Nizhny Novgorod, Russia
- Imperial College London, Section of Bioanalytical Chemistry, Division of Systems Medicine, Department of Metabolism, Digestion and Reproduction, London, United Kingdom
| | - Annika Röhl
- Charité–Universitätsmedizin Berlin, Department of Biochemistry, Berlin, Germany
| | - Anja Freiwald
- Charité–Universitätsmedizin Berlin, Department of Biochemistry, Berlin, Germany
| | - Mirja Mittermaier
- Charité–Universitätsmedizin Berlin, Department of Infectious Diseases and Respiratory Medicine, Berlin, Germany
- Berlin Institute of Health, Berlin, Germany
| | - Lukasz Szyrwiel
- The Francis Crick Institute, Molecular Biology of Metabolism Laboratory, London, United Kingdom
| | - Daniela Ludwig
- Charité–Universitätsmedizin Berlin, Department of Biochemistry, Berlin, Germany
| | - Clara Correia-Melo
- The Francis Crick Institute, Molecular Biology of Metabolism Laboratory, London, United Kingdom
| | - Lena J. Lippert
- Charité–Universitätsmedizin Berlin, Department of Infectious Diseases and Respiratory Medicine, Berlin, Germany
| | - Elisa T. Helbig
- Charité–Universitätsmedizin Berlin, Department of Infectious Diseases and Respiratory Medicine, Berlin, Germany
| | - Paula Stubbemann
- Charité–Universitätsmedizin Berlin, Department of Infectious Diseases and Respiratory Medicine, Berlin, Germany
| | - Nadine Olk
- Charité–Universitätsmedizin Berlin, Department of Infectious Diseases and Respiratory Medicine, Berlin, Germany
| | - Charlotte Thibeault
- Charité–Universitätsmedizin Berlin, Department of Infectious Diseases and Respiratory Medicine, Berlin, Germany
| | - Nana-Maria Grüning
- Charité–Universitätsmedizin Berlin, Department of Biochemistry, Berlin, Germany
| | - Oleg Blyuss
- Lobachevsky University, Department of Applied Mathematics, Nizhny Novgorod, Russia
- University of Hertfordshire, School of Physics, Astronomy and Mathematics, Hatfield, United Kingdom
- Sechenov First Moscow State Medical University, Department of Paediatrics and Paediatric Infectious Diseases, Moscow, Russia
| | - Spyros Vernardis
- The Francis Crick Institute, Molecular Biology of Metabolism Laboratory, London, United Kingdom
| | - Matthew White
- The Francis Crick Institute, Molecular Biology of Metabolism Laboratory, London, United Kingdom
| | - Christoph B. Messner
- Charité–Universitätsmedizin Berlin, Department of Biochemistry, Berlin, Germany
- The Francis Crick Institute, Molecular Biology of Metabolism Laboratory, London, United Kingdom
| | - Michael Joannidis
- Medical University Innsbruck, Division of Intensive Care and Emergency Medicine, Department of Internal Medicine, Innsbruck, Austria
| | - Thomas Sonnweber
- Medical University of Innsbruck, Department of Internal Medicine II, Innsbruck, Austria
| | - Sebastian J. Klein
- Medical University Innsbruck, Division of Intensive Care and Emergency Medicine, Department of Internal Medicine, Innsbruck, Austria
| | - Alex Pizzini
- Medical University of Innsbruck, Department of Internal Medicine II, Innsbruck, Austria
| | - Yvonne Wohlfarter
- Medical University of Innsbruck, Institute of Human Genetics, Innsbruck, Austria
| | - Sabina Sahanic
- Medical University of Innsbruck, Department of Internal Medicine II, Innsbruck, Austria
| | - Richard Hilbe
- Medical University of Innsbruck, Department of Internal Medicine II, Innsbruck, Austria
| | - Benedikt Schaefer
- Medical University of Innsbruck, Christian Doppler Laboratory for Iron and Phosphate Biology, Department of Internal Medicine I, Innsbruck, Austria
| | - Sonja Wagner
- Medical University of Innsbruck, Christian Doppler Laboratory for Iron and Phosphate Biology, Department of Internal Medicine I, Innsbruck, Austria
| | - Felix Machleidt
- Charité–Universitätsmedizin Berlin, Department of Infectious Diseases and Respiratory Medicine, Berlin, Germany
| | - Carmen Garcia
- Charité–Universitätsmedizin Berlin, Department of Infectious Diseases and Respiratory Medicine, Berlin, Germany
| | - Christoph Ruwwe-Glösenkamp
- Charité–Universitätsmedizin Berlin, Department of Infectious Diseases and Respiratory Medicine, Berlin, Germany
| | - Tilman Lingscheid
- Charité–Universitätsmedizin Berlin, Department of Infectious Diseases and Respiratory Medicine, Berlin, Germany
| | - Laure Bosquillon de Jarcy
- Charité–Universitätsmedizin Berlin, Department of Infectious Diseases and Respiratory Medicine, Berlin, Germany
| | - Miriam S. Stegemann
- Charité–Universitätsmedizin Berlin, Department of Infectious Diseases and Respiratory Medicine, Berlin, Germany
| | - Moritz Pfeiffer
- Charité–Universitätsmedizin Berlin, Department of Infectious Diseases and Respiratory Medicine, Berlin, Germany
| | - Linda Jürgens
- Charité–Universitätsmedizin Berlin, Department of Infectious Diseases and Respiratory Medicine, Berlin, Germany
| | - Sophy Denker
- Charité–Universitätsmedizin Berlin, Medical Department of Hematology, Oncology & Tumor Immunology, Virchow Campus & Molekulares Krebsforschungszentrum, Berlin, Germany
| | - Daniel Zickler
- Charité–Universitätsmedizin Berlin, Department of Nephrology and Internal Intensive Care Medicine, Berlin, Germany
| | - Claudia Spies
- Charité–Universitätsmedizin Berlin, Department of Anesthesiology and Intensive Care, Berlin, Germany
| | - Andreas Edel
- Charité–Universitätsmedizin Berlin, Department of Anesthesiology and Intensive Care, Berlin, Germany
| | - Nils B. Müller
- Charité–Universitätsmedizin Berlin, Department of Nephrology and Internal Intensive Care Medicine, Berlin, Germany
| | - Philipp Enghard
- Charité–Universitätsmedizin Berlin, Department of Nephrology and Internal Intensive Care Medicine, Berlin, Germany
| | - Aleksej Zelezniak
- The Francis Crick Institute, Molecular Biology of Metabolism Laboratory, London, United Kingdom
- Chalmers University of Technology, Department of Biology and Biological Engineering, Gothenburg, Sweden
| | - Rosa Bellmann-Weiler
- Medical University of Innsbruck, Department of Internal Medicine II, Innsbruck, Austria
| | - Günter Weiss
- Medical University of Innsbruck, Department of Internal Medicine II, Innsbruck, Austria
| | - Archie Campbell
- University of Edinburgh, Centre for Genomic and Experimental Medicine, Institute of Genetics and Cancer, United Kingdom
- University of Edinburgh, Usher Institute, Edinburgh, United Kingdom
| | - Caroline Hayward
- University of Edinburgh, MRC Human Genetics Unit, Institute of Genetics and Cancer, Edinburgh, United Kingdom
| | - David J. Porteous
- University of Edinburgh, Centre for Genomic and Experimental Medicine, Institute of Genetics and Cancer, United Kingdom
- University of Edinburgh, Usher Institute, Edinburgh, United Kingdom
| | - Riccardo E. Marioni
- University of Edinburgh, Centre for Genomic and Experimental Medicine, Institute of Genetics and Cancer, United Kingdom
| | - Alexander Uhrig
- Charité–Universitätsmedizin Berlin, Department of Infectious Diseases and Respiratory Medicine, Berlin, Germany
| | - Heinz Zoller
- Medical University of Innsbruck, Christian Doppler Laboratory for Iron and Phosphate Biology, Department of Internal Medicine I, Innsbruck, Austria
| | - Judith Löffler-Ragg
- Medical University of Innsbruck, Department of Internal Medicine II, Innsbruck, Austria
| | - Markus A. Keller
- Medical University of Innsbruck, Institute of Human Genetics, Innsbruck, Austria
| | - Ivan Tancevski
- Medical University of Innsbruck, Department of Internal Medicine II, Innsbruck, Austria
| | - John F. Timms
- University College London, Department of Women’s Cancer, EGA Institute for Women’s Health, London, United Kingdom
| | - Alexey Zaikin
- University College London, Department of Mathematics, London, United Kingdom
- University College London, Department of Women’s Cancer, EGA Institute for Women’s Health, London, United Kingdom
- Lobachevsky University, Laboratory of Systems Medicine of Healthy Ageing, Nizhny Novgorod, Russia
- Centre for Analysis of Complex Systems, Sechenov First Moscow State Medical University, Moscow, Russia
| | - Stefan Hippenstiel
- Charité–Universitätsmedizin Berlin, Department of Infectious Diseases and Respiratory Medicine, Berlin, Germany
- German Centre for Lung Research, Germany
| | - Michael Ramharter
- Bernhard Nocht Institute for Tropical Medicine, Department of Tropical Medicine, and University Medical Center Hamburg-Eppendorf, Department of Medicine, Hamburg, Germany
| | - Holger Müller-Redetzky
- Charité–Universitätsmedizin Berlin, Department of Infectious Diseases and Respiratory Medicine, Berlin, Germany
| | - Martin Witzenrath
- Charité–Universitätsmedizin Berlin, Department of Infectious Diseases and Respiratory Medicine, Berlin, Germany
- German Centre for Lung Research, Germany
| | - Norbert Suttorp
- Charité–Universitätsmedizin Berlin, Department of Infectious Diseases and Respiratory Medicine, Berlin, Germany
- German Centre for Lung Research, Germany
| | - Kathryn Lilley
- The University of Cambridge, Department of Biochemistry and Cambridge Centre for Proteomics, Cambridge, United Kingdom
| | - Michael Mülleder
- Charité–Universitätsmedizin Berlin, Core Facility—High-Throughput Mass Spectrometry, Berlin, Germany
| | - Leif Erik Sander
- Charité–Universitätsmedizin Berlin, Department of Infectious Diseases and Respiratory Medicine, Berlin, Germany
- German Centre for Lung Research, Germany
| | | | - Florian Kurth
- Charité–Universitätsmedizin Berlin, Department of Infectious Diseases and Respiratory Medicine, Berlin, Germany
- Bernhard Nocht Institute for Tropical Medicine, Department of Tropical Medicine, and University Medical Center Hamburg-Eppendorf, Department of Medicine, Hamburg, Germany
- * E-mail:
| | - Markus Ralser
- Charité–Universitätsmedizin Berlin, Department of Biochemistry, Berlin, Germany
- The Francis Crick Institute, Molecular Biology of Metabolism Laboratory, London, United Kingdom
| |
Collapse
|
7
|
Nazarenko T, Whitwell HJ, Blyuss O, Zaikin A. Parenclitic and Synolytic Networks Revisited. Front Genet 2021; 12:733783. [PMID: 34745212 PMCID: PMC8564045 DOI: 10.3389/fgene.2021.733783] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Accepted: 09/28/2021] [Indexed: 11/14/2022] Open
Abstract
Parenclitic networks provide a powerful and relatively new way to coerce multidimensional data into a graph form, enabling the application of graph theory to evaluate features. Different algorithms have been published for constructing parenclitic networks, leading to the question-which algorithm should be chosen? Initially, it was suggested to calculate the weight of an edge between two nodes of the network as a deviation from a linear regression, calculated for a dependence of one of these features on the other. This method works well, but not when features do not have a linear relationship. To overcome this, it was suggested to calculate edge weights as the distance from the area of most probable values by using a kernel density estimation. In these two approaches only one class (typically controls or healthy population) is used to construct a model. To take account of a second class, we have introduced synolytic networks, using a boundary between two classes on the feature-feature plane to estimate the weight of the edge between these features. Common to all these approaches is that topological indices can be used to evaluate the structure represented by the graphs. To compare these network approaches alongside more traditional machine-learning algorithms, we performed a substantial analysis using both synthetic data with a priori known structure and publicly available datasets used for the benchmarking of ML-algorithms. Such a comparison has shown that the main advantage of parenclitic and synolytic networks is their resistance to over-fitting (occurring when the number of features is greater than the number of subjects) compared to other ML approaches. Secondly, the capability to visualise data in a structured form, even when this structure is not a priori available allows for visual inspection and the application of well-established graph theory to their interpretation/application, eliminating the "black-box" nature of other ML approaches.
Collapse
Affiliation(s)
- Tatiana Nazarenko
- Department of Mathematics and Institute for Women’s Health, University College London, London, United Kingdom
| | - Harry J. Whitwell
- National Phenome Centre and Imperial Clinical Phenotyping Centre, Department of Metabolism, Digestion and Reproduction, Imperial College London, Hammersmith Campus, London, United Kingdom
- Section of Bioanalytical Chemistry, Division of Systems Medicine, Department of Metabolism, Digestion, Imperial College London, South Kensington Campus, London, United Kingdom
- Lobachevsky State University of Nizhny Novgorod, Nizhny Novgorod, Russia
- World-Class Research Center “Digital Biodesign and Personalized Healthcare”, Sechenov First Moscow State Medical University, Moscow, Russia
| | - Oleg Blyuss
- Department of Mathematics and Institute for Women’s Health, University College London, London, United Kingdom
- Lobachevsky State University of Nizhny Novgorod, Nizhny Novgorod, Russia
- School of Physics, Astronomy and Mathematics, University of Hertfordshire, Harfield, United Kingdom
- Department of Pediatrics and Pediatric Infectious Diseases, Institute of Child’s Health, Sechenov First Moscow State Medical University (Sechenov University), Moscow, Russia
| | - Alexey Zaikin
- Department of Mathematics and Institute for Women’s Health, University College London, London, United Kingdom
- Lobachevsky State University of Nizhny Novgorod, Nizhny Novgorod, Russia
- World-Class Research Center “Digital Biodesign and Personalized Healthcare”, Sechenov First Moscow State Medical University, Moscow, Russia
| |
Collapse
|
8
|
Shinde P, Whitwell HJ, Verma RK, Ivanchenko M, Zaikin A, Jalan S. Impact of modular mitochondrial epistatic interactions on the evolution of human subpopulations. Mitochondrion 2021; 58:111-122. [PMID: 33618020 DOI: 10.1016/j.mito.2021.02.004] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2019] [Revised: 09/22/2020] [Accepted: 02/03/2021] [Indexed: 12/23/2022]
Abstract
Investigation of human mitochondrial (mt) genome variation has been shown to provide insights to the human history and natural selection. By analyzing 24,167 human mt-genome samples, collected for five continents, we have developed a co-mutation network model to investigate characteristic human evolutionary patterns. The analysis highlighted richer co-mutating regions of the mt-genome, suggesting the presence of epistasis. Specifically, a large portion of COX genes was found to co-mutate in Asian and American populations, whereas, in African, European, and Oceanic populations, there was greater co-mutation bias in hypervariable regions. Interestingly, this study demonstrated hierarchical modularity as a crucial agent for these co-mutation networks. More profoundly, our ancestry-based co-mutation module analyses showed that mutations cluster preferentially in known mitochondrial haplogroups. Contemporary human mt-genome nucleotides most closely resembled the ancestral state, and very few of them were found to be ancestral-variants. Overall, these results demonstrated that subpopulation-based biases may favor mitochondrial gene specific epistasis.
Collapse
Affiliation(s)
- Pramod Shinde
- Department of Biosciences and Biomedical Engineering, Indian Institute of Technology Indore, Khandwa Road, Simrol, Indore 453552, India.
| | - Harry J Whitwell
- National Phenome Centre and Imperial Clinical Phenotyping Centre, Department of Metabolism, Digestion and Reproduction, Imperial College London, London, UK; Division of Systems Medicine, Department of Metabolism, Digestion and Reproduction, Imperial College London, London, UK; Centre for Analysis of Complex Systems, Sechenov First Moscow State Medical University, Moscow, Russia
| | - Rahul Kumar Verma
- Department of Biosciences and Biomedical Engineering, Indian Institute of Technology Indore, Khandwa Road, Simrol, Indore 453552, India
| | - Mikhail Ivanchenko
- Department of Applied Mathematics and Centre of Bioinformatics, Lobachevsky State University of Nizhny Novgorod, Nizhny Novgorod, Russia
| | - Alexey Zaikin
- Centre for Analysis of Complex Systems, Sechenov First Moscow State Medical University, Moscow, Russia; Department of Applied Mathematics and Centre of Bioinformatics, Lobachevsky State University of Nizhny Novgorod, Nizhny Novgorod, Russia; Department of Mathematics and Institute for Women's Health, University College London, London WC1E 6BT, UK
| | - Sarika Jalan
- Department of Biosciences and Biomedical Engineering, Indian Institute of Technology Indore, Khandwa Road, Simrol, Indore 453552, India; Complex Systems Lab, Department of Physics, Indian Institute of Technology Indore, Khandwa Road, Simrol, Indore 453552, India; Center for Theoretical Physics of Complex Systems, Institute for Basic Science(IBS), Daejeon 34126, Korea.
| |
Collapse
|
9
|
Di Blasi R, Blyuss O, Timms JF, Conole D, Ceroni F, Whitwell HJ. Non-Histone Protein Methylation: Biological Significance and Bioengineering Potential. ACS Chem Biol 2021; 16:238-250. [PMID: 33411495 DOI: 10.1021/acschembio.0c00771] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Protein methylation is a key post-translational modification whose effects on gene expression have been intensively studied over the last two decades. Recently, renewed interest in non-histone protein methylation has gained momentum for its role in regulating important cellular processes and the activity of many proteins, including transcription factors, enzymes, and structural complexes. The extensive and dynamic role that protein methylation plays within the cell also highlights its potential for bioengineering applications. Indeed, while synthetic histone protein methylation has been extensively used to engineer gene expression, engineering of non-histone protein methylation has not been fully explored yet. Here, we report the latest findings, highlighting how non-histone protein methylation is fundamental for certain cellular functions and is implicated in disease, and review recent efforts in the engineering of protein methylation.
Collapse
Affiliation(s)
- Roberto Di Blasi
- Department of Chemical Engineering, Faculty of Engineering, Imperial College London, London, U.K
- Imperial College Centre for Synthetic Biology, Imperial College London, London, U.K
| | - Oleg Blyuss
- School of Physics, Astronomy and Mathematics, University of Hertfordshire, Hatfield, U.K
- Department of Paediatrics and Paediatric Infectious Diseases, Sechenov First Moscow State Medical University, Moscow, Russia
- Department of Applied Mathematics, Lobachevsky State University of Nizhny Novgorod, Nizhny Novgorod, Russia
| | - John F Timms
- Department of Women's Cancer, EGA Institute for Women's Health, University College London, London, U.K
| | - Daniel Conole
- Department of Chemistry, Molecular Sciences Research Hub, Imperial College London, London, U.K
| | - Francesca Ceroni
- Department of Chemical Engineering, Faculty of Engineering, Imperial College London, London, U.K
- Imperial College Centre for Synthetic Biology, Imperial College London, London, U.K
| | - Harry J Whitwell
- Department of Applied Mathematics, Lobachevsky State University of Nizhny Novgorod, Nizhny Novgorod, Russia
- National Phenome Centre and Imperial Clinical Phenotyping Centre, Department of Metabolism, Digestion and Reproduction, IRDB Building, Imperial College London, Hammersmith Campus, London, W12 0NN, U.K
- Division of Systems Medicine, Department of Metabolism, Digestion and Reproduction, Sir Alexander Fleming Building, Imperial College London, Hammersmith Campus, London, SW7 2AZ, U.K
| |
Collapse
|
10
|
Watson A, Sørensen GL, Holmskov U, Whitwell HJ, Madsen J, Clark H. Generation of novel trimeric fragments of human SP-A and SP-D after recombinant soluble expression in E. coli. Immunobiology 2020; 225:151953. [PMID: 32747028 PMCID: PMC7422833 DOI: 10.1016/j.imbio.2020.151953] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2020] [Accepted: 04/28/2020] [Indexed: 01/19/2023]
Abstract
Surfactant treatment for neonatal respiratory distress syndrome has dramatically improved survival of preterm infants. However, this has resulted in a markedly increased incidence of sequelae such as neonatal chronic inflammatory lung disease. The current surfactant preparations in clinical use lack the natural lung defence proteins surfactant proteins (SP)-A and D. These are known to have anti-inflammatory and anti-infective properties essential for maintaining healthy non-inflamed lungs. Supplementation of currently available animal derived surfactant therapeutics with these anti-inflammatory proteins in the first few days of life could prevent the development of inflammatory lung disease in premature babies. However, current systems for production of recombinant versions of SP-A and SP-D require a complex solubilisation and refolding protocol limiting expression at scale for drug development. Using a novel solubility tag, we describe the expression and purification of recombinant fragments of human (rfh) SP-A and SP-D using Escherichia coli without the need for refolding. We obtained a mean (± SD) of 23.3 (± 5.4) mg and 86 mg (± 3.5) per litre yield of rfhSP-A and rfhSP-D, respectively. rfhSP-D was trimeric and 68% bound to a ManNAc-affinity column, giving a final yield of 57.5 mg/litre of highly pure protein, substantially higher than the 3.3 mg/litre obtained through the standard refolding protocol. Further optimisation of this novel lab based method could potentially make rfhSP-A and rfhSP-D production more commercially feasible to enable development of novel therapeutics for the treatment of lung infection and inflammation.
Collapse
MESH Headings
- Cloning, Molecular
- Escherichia coli/genetics
- Escherichia coli/metabolism
- Gene Expression
- Humans
- Models, Molecular
- Protein Conformation
- Protein Multimerization
- Receptors, Cell Surface/chemistry
- Receptors, Cell Surface/genetics
- Receptors, Cell Surface/isolation & purification
- Receptors, Cell Surface/metabolism
- Receptors, Immunologic/chemistry
- Receptors, Immunologic/genetics
- Receptors, Immunologic/isolation & purification
- Receptors, Immunologic/metabolism
- Recombinant Proteins
- Structure-Activity Relationship
Collapse
Affiliation(s)
- Alastair Watson
- Department of Child Health, Division of Clinical and Experimental Sciences, Faculty of Medicine, University of Southampton, Southampton General Hospital, Southampton, United Kingdom.
| | - Grith L Sørensen
- Institute of Molecular Medicine, Department of Cardiovascular and Renal Research, Faculty of Health Sciences, University of Southern Denmark, Odense, Denmark
| | - Uffe Holmskov
- Department of Cancer and Inflammation, University of Southern Denmark, Odense, Denmark
| | - Harry J Whitwell
- Department of Chemical Engineering, Faculty of Engineering, Imperial College London, London, UK; Department of Metabolomics, Digestion and Reproduction, Faculty of Medicine, Imperial College London, London, UK
| | - Jens Madsen
- Department of Child Health, Division of Clinical and Experimental Sciences, Faculty of Medicine, University of Southampton, Southampton General Hospital, Southampton, United Kingdom
| | - Howard Clark
- Department of Child Health, Division of Clinical and Experimental Sciences, Faculty of Medicine, University of Southampton, Southampton General Hospital, Southampton, United Kingdom
| |
Collapse
|
11
|
Whitwell HJ, Bacalini MG, Blyuss O, Chen S, Garagnani P, Gordleeva SY, Jalan S, Ivanchenko M, Kanakov O, Kustikova V, Mariño IP, Meyerov I, Ullner E, Franceschi C, Zaikin A. The Human Body as a Super Network: Digital Methods to Analyze the Propagation of Aging. Front Aging Neurosci 2020; 12:136. [PMID: 32523526 PMCID: PMC7261843 DOI: 10.3389/fnagi.2020.00136] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [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] [Received: 02/09/2020] [Accepted: 04/22/2020] [Indexed: 12/13/2022] Open
Abstract
Biological aging is a complex process involving multiple biological processes. These can be understood theoretically though considering them as individual networks-e.g., epigenetic networks, cell-cell networks (such as astroglial networks), and population genetics. Mathematical modeling allows the combination of such networks so that they may be studied in unison, to better understand how the so-called "seven pillars of aging" combine and to generate hypothesis for treating aging as a condition at relatively early biological ages. In this review, we consider how recent progression in mathematical modeling can be utilized to investigate aging, particularly in, but not exclusive to, the context of degenerative neuronal disease. We also consider how the latest techniques for generating biomarker models for disease prediction, such as longitudinal analysis and parenclitic analysis can be applied to as both biomarker platforms for aging, as well as to better understand the inescapable condition. This review is written by a highly diverse and multi-disciplinary team of scientists from across the globe and calls for greater collaboration between diverse fields of research.
Collapse
Affiliation(s)
- Harry J Whitwell
- Department of Chemical Engineering, Imperial College London, London, United Kingdom
| | | | - Oleg Blyuss
- School of Physics, Astronomy and Mathematics, University of Hertfordshire, Harfield, United Kingdom.,Department of Paediatrics and Paediatric Infectious Diseases, Sechenov First Moscow State Medical University (Sechenov University), Moscow, Russia
| | - Shangbin Chen
- Britton Chance Centre for Biomedical Photonics, Wuhan National Laboratory for Optoelectronics-Huazhong University of Science and Technology, Wuhan, China
| | - Paolo Garagnani
- Department of Experimental, Diagnostic and Specialty Medicine (DIMES), University of Bologna, Bologna, Italy
| | - Susan Yu Gordleeva
- Laboratory of Systems Medicine of Healthy Aging, Lobachevsky State University of Nizhny Novgorod, Nizhny Novgorod, Russia
| | - Sarika Jalan
- Complex Systems Laboratory, Discipline of Physics, Indian Institute of Technology Indore, Indore, India.,Centre for Bio-Science and Bio-Medical Engineering, Indian Institute of Technology Indore, Indore, India
| | - Mikhail Ivanchenko
- Institute of Information Technologies, Mathematics and Mechanics, Lobachevsky State University of Nizhny Novgorod, Nizhny Novgorod, Russia
| | - Oleg Kanakov
- Laboratory of Systems Medicine of Healthy Aging, Lobachevsky State University of Nizhny Novgorod, Nizhny Novgorod, Russia
| | - Valentina Kustikova
- Institute of Information Technologies, Mathematics and Mechanics, Lobachevsky State University of Nizhny Novgorod, Nizhny Novgorod, Russia
| | - Ines P Mariño
- Department of Biology and Geology, Physics and Inorganic Chemistry, Universidad Rey Juan Carlos, Madrid, Spain
| | - Iosif Meyerov
- Institute of Information Technologies, Mathematics and Mechanics, Lobachevsky State University of Nizhny Novgorod, Nizhny Novgorod, Russia
| | - Ekkehard Ullner
- Department of Physics (SUPA), Institute for Complex Systems and Mathematical Biology, University of Aberdeen, Aberdeen, United Kingdom
| | - Claudio Franceschi
- Laboratory of Systems Medicine of Healthy Aging, Lobachevsky State University of Nizhny Novgorod, Nizhny Novgorod, Russia.,Institute of Information Technologies, Mathematics and Mechanics, Lobachevsky State University of Nizhny Novgorod, Nizhny Novgorod, Russia
| | - Alexey Zaikin
- Department of Paediatrics and Paediatric Infectious Diseases, Sechenov First Moscow State Medical University (Sechenov University), Moscow, Russia.,Institute of Information Technologies, Mathematics and Mechanics, Lobachevsky State University of Nizhny Novgorod, Nizhny Novgorod, Russia.,Department of Mathematics, Institute for Women's Health, University College London, London, United Kingdom
| |
Collapse
|
12
|
Whitwell HJ, Worthington J, Blyuss O, Gentry-Maharaj A, Ryan A, Gunu R, Kalsi J, Menon U, Jacobs I, Zaikin A, Timms JF. Improved early detection of ovarian cancer using longitudinal multimarker models. Br J Cancer 2020; 122:847-856. [PMID: 31937926 PMCID: PMC7078315 DOI: 10.1038/s41416-019-0718-9] [Citation(s) in RCA: 48] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2019] [Revised: 12/06/2019] [Accepted: 12/16/2019] [Indexed: 12/20/2022] Open
Abstract
BACKGROUND Ovarian cancer has a poor survival rate due to late diagnosis and improved methods are needed for its early detection. Our primary objective was to identify and incorporate additional biomarkers into longitudinal models to improve on the performance of CA125 as a first-line screening test for ovarian cancer. METHODS This case-control study nested within UKCTOCS used 490 serial serum samples from 49 women later diagnosed with ovarian cancer and 31 control women who were cancer-free. Proteomics-based biomarker discovery was carried out using pooled samples and selected candidates, including those from the literature, assayed in all serial samples. Multimarker longitudinal models were derived and tested against CA125 for early detection of ovarian cancer. RESULTS The best performing models, incorporating CA125, HE4, CHI3L1, PEBP4 and/or AGR2, provided 85.7% sensitivity at 95.4% specificity up to 1 year before diagnosis, significantly improving on CA125 alone. For Type II cases (mostly high-grade serous), models achieved 95.5% sensitivity at 95.4% specificity. Predictive values were elevated earlier than CA125, showing the potential of models to improve lead time. CONCLUSIONS We have identified candidate biomarkers and tested longitudinal multimarker models that significantly improve on CA125 for early detection of ovarian cancer. These models now warrant independent validation.
Collapse
Affiliation(s)
- Harry J Whitwell
- Department of Women's Cancer, Institute for Women's Health, University College London, Gower Street, London, WC1E 6BT, UK
| | - Jenny Worthington
- Department of Women's Cancer, Institute for Women's Health, University College London, Gower Street, London, WC1E 6BT, UK
| | - Oleg Blyuss
- Department of Women's Cancer, Institute for Women's Health, University College London, Gower Street, London, WC1E 6BT, UK
- Department of Paediatrics, Sechenov University, Moscow, 119146, Russia
- School of Physics, Astronomy and Mathematics, University of Hertfordshire, College Lane, Hatfield, UK
| | | | - Andy Ryan
- MRC Clinical Trials Unit at UCL, 90 High Holborn, London, WC1V 6LJ, UK
| | - Richard Gunu
- Department of Women's Cancer, Institute for Women's Health, University College London, Gower Street, London, WC1E 6BT, UK
| | - Jatinderpal Kalsi
- Department of Women's Cancer, Institute for Women's Health, University College London, Gower Street, London, WC1E 6BT, UK
- MRC Clinical Trials Unit at UCL, 90 High Holborn, London, WC1V 6LJ, UK
| | - Usha Menon
- MRC Clinical Trials Unit at UCL, 90 High Holborn, London, WC1V 6LJ, UK
| | - Ian Jacobs
- Department of Women's Cancer, Institute for Women's Health, University College London, Gower Street, London, WC1E 6BT, UK
- President and Vice-Chancellor's Office, University of New South Wales, Sydney, NSW, 2052, Australia
| | - Alexey Zaikin
- Department of Women's Cancer, Institute for Women's Health, University College London, Gower Street, London, WC1E 6BT, UK
- Department of Paediatrics, Sechenov University, Moscow, 119146, Russia
- Department of Mathematics, University College London, London, W1T 7DN, UK
- Department of Applied Mathematics, Lobachevsky State University of Nizhniy Novgorod, Nizhniy Novgorod, 603022, Russia
| | - John F Timms
- Department of Women's Cancer, Institute for Women's Health, University College London, Gower Street, London, WC1E 6BT, UK.
| |
Collapse
|
13
|
Whitwell HJ, DiMaggio P. HiLight-PTM: an online application to aid matching peptide pairs with isotopically labelled PTMs. Bioinformatics 2020; 36:938-939. [PMID: 31424526 PMCID: PMC9883675 DOI: 10.1093/bioinformatics/btz654] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2019] [Revised: 08/06/2019] [Accepted: 08/17/2019] [Indexed: 02/02/2023] Open
Abstract
MOTIVATION Database searching of isotopically labelled PTMs can be problematic and we frequently find that only one, or neither in a heavy/light pair are assigned. In such cases, having a pair of MS/MS spectra that differ due to an isotopic label can assist in identifying the relevant m/z values that support the correct peptide annotation or can be used for de novo sequencing. RESULTS We have developed an online application that identifies matching peaks and peaks differing by the appropriate mass shift (difference between heavy and light PTM) between two MS/MS spectra. Furthermore, the application predicts, from the exact-match peaks, the mass of their complementary ions and highlights these as high confidence matches between the two spectra. The result is a tool to visually compare two spectra, and downloadable peaks lists that can be used to support de novo sequencing. AVAILABILITY AND IMPLEMENTATION HiLight-PTM is released using shinyapps.io by RStudio, and can be accessed from any internet browser at https://harrywhitwell.shinyapps.io/hilight-ptm/. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
Collapse
Affiliation(s)
- Harry J Whitwell
- Department of Chemical Engineering, Imperial College London, London, SW7 2AZ, UK
| | - Peter DiMaggio
- Department of Chemical Engineering, Imperial College London, London, SW7 2AZ, UK
| |
Collapse
|
14
|
Abstract
Prediction and diagnosis of complex disease may not always be possible with a small number of biomarkers. Modern 'omics' technologies make it possible to cheaply and quantitatively assay hundreds of molecules generating large amounts of data from individual samples. In this study, we describe a parenclitic network-based approach to disease classification using a synthetic data set modelled on data from the United Kingdom Collaborative Trial of Ovarian Cancer Screening (UKCTOCS) and serological assay data from a nested set of samples from the same study. This approach allows us to integrate quantitative proteomic and categorical metadata into a single network, and then use network topologies to construct logistic regression models for disease classification. In this study of ovarian cancer, comprising of 30 controls and cases with samples taken <14 months to diagnosis (n = 30) and/or >34 months to diagnosis (n = 29), we were able to classify cases with a sensitivity of 80.3% within 14 months of diagnosis and 18.9% in samples exceeding 34 months to diagnosis at a specificity of 98%. Furthermore, we use the networks to make observations about proteins within the cohort and identify GZMH and FGFBP1 as changing in cases (in relation to controls) at time points most distal to diagnosis. We conclude that network-based approaches may offer a solution to the problem of complex disease classification that can be used in personalised medicine and to describe the underlying biology of cancer progression at a system level.
Collapse
Affiliation(s)
- Harry J. Whitwell
- Chemical Engineering, Imperial College London, London, United Kingdom
| | - Oleg Blyuss
- Wolfson Institute of Preventive Medicine, Queen Mary University of London, London, United Kingdom
| | - Usha Menon
- Institute for Women's Health, University College London, London, United Kingdom
| | - John F. Timms
- Institute for Women's Health, University College London, London, United Kingdom
| | - Alexey Zaikin
- Institute for Women's Health, University College London, London, United Kingdom
- Department of Mathematics, University College London, London, United Kingdom
| |
Collapse
|
15
|
Cuenco J, Wehnert N, Blyuss O, Kazarian A, Whitwell HJ, Menon U, Dawnay A, Manns MP, Pereira SP, Timms JF. Identification of a serum biomarker panel for the differential diagnosis of cholangiocarcinoma and primary sclerosing cholangitis. Oncotarget 2018; 9:17430-17442. [PMID: 29707118 PMCID: PMC5915126 DOI: 10.18632/oncotarget.24732] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [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] [Received: 01/04/2018] [Accepted: 03/06/2018] [Indexed: 01/02/2023] Open
Abstract
The non-invasive differentiation of malignant and benign biliary disease is a clinical challenge. Carbohydrate antigen 19-9 (CA19-9), leucine-rich α2-glycoprotein (LRG1), interleukin 6 (IL6), pyruvate kinase M2 (PKM2), cytokeratin 19 fragment (CYFRA21.1) and mucin 5AC (MUC5AC) have reported utility for differentiating cholangiocarcinoma (CCA) from benign biliary disease. Herein, serum levels of these markers were tested in 66 cases of CCA and 62 cases of primary sclerosing cholangitis (PSC) and compared with markers of liver function and inflammation. Markers panels were assessed for their ability to discriminate malignant and benign disease. Several of the markers were also assessed in pre-diagnosis biliary tract cancer (BTC) samples with performances evaluated at different times prior to diagnosis. We show that LRG1 and IL6 were unable to accurately distinguish CCA from PSC, whereas CA19-9, PKM2, CYFRA21.1 and MUC5AC were significantly elevated in malignancy. Area under the receiver operating characteristic curves for these individual markers ranged from 0.73–0.84, with the best single marker (PKM2) providing 61% sensitivity at 90% specificity. A panel combining PKM2, CYFRA21.1 and MUC5AC gave 76% sensitivity at 90% specificity, which increased to 82% sensitivity by adding gamma-glutamyltransferase (GGT). In the pre-diagnosis setting, LRG1, IL6 and PKM2 were poor predictors of BTC, whilst CA19-9 and C-reactive protein were elevated up to 2 years before diagnosis. In conclusion, LRG1, IL6 and PKM2 were not useful for early detection of BTC, whilst a model combining PKM2, CYFRA21.1, MUC5AC and GGT was beneficial in differentiating malignant from benign biliary disease, warranting validation in a prospective trial.
Collapse
Affiliation(s)
- Joy Cuenco
- Institute for Women's Health, University College London, London, WC1E 6BT, UK
| | - Natascha Wehnert
- Hannover Medical School, Department of Gastroenterology, Hepatology and Endocrinology, Hannover, 30625, Germany
| | - Oleg Blyuss
- Institute for Women's Health, University College London, London, WC1E 6BT, UK
| | - Anna Kazarian
- Institute for Women's Health, University College London, London, WC1E 6BT, UK
| | - Harry J Whitwell
- Institute for Women's Health, University College London, London, WC1E 6BT, UK
| | - Usha Menon
- Institute for Women's Health, University College London, London, WC1E 6BT, UK
| | - Anne Dawnay
- Clinical Biochemistry, University College London Hospitals NHS Foundation Trust, London, W1T 4EU, UK
| | - Michael P Manns
- Hannover Medical School, Department of Gastroenterology, Hepatology and Endocrinology, Hannover, 30625, Germany
| | - Stephen P Pereira
- Institute for Liver and Digestive Health, University College London, Royal Free Hospital, London, NW3 2PG, UK
| | - John F Timms
- Institute for Women's Health, University College London, London, WC1E 6BT, UK
| |
Collapse
|
16
|
Wolhuter K, Whitwell HJ, Switzer CH, Burgoyne JR, Timms JF, Eaton P. Evidence against Stable Protein S-Nitrosylation as a Widespread Mechanism of Post-translational Regulation. Mol Cell 2018; 69:438-450.e5. [PMID: 29358077 PMCID: PMC5807093 DOI: 10.1016/j.molcel.2017.12.019] [Citation(s) in RCA: 74] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2017] [Revised: 11/01/2017] [Accepted: 12/20/2017] [Indexed: 11/27/2022]
Abstract
S-nitrosation, commonly referred to as S-nitrosylation, is widely regarded as a ubiquitous, stable post-translational modification that directly regulates many proteins. Such a widespread role would appear to be incompatible with the inherent lability of the S-nitroso bond, especially its propensity to rapidly react with thiols to generate disulfide bonds. As anticipated, we observed robust and widespread protein S-nitrosation after exposing cells to nitrosocysteine or lipopolysaccharide. Proteins detected using the ascorbate-dependent biotin switch method are typically interpreted to be directly regulated by S-nitrosation. However, these S-nitrosated proteins are shown to predominantly comprise transient intermediates leading to disulfide bond formation. These disulfides are likely to be the dominant end effectors resulting from elevations in nitrosating cellular nitric oxide species. We propose that S-nitrosation primarily serves as a transient intermediate leading to disulfide formation. Overall, we conclude that the current widely held perception that stable S-nitrosation directly regulates the function of many proteins is significantly incorrect. Protein S-nitrosation is commonly regarded as a stable, regulatory modification However, S-nitrosothiols are labile and rapidly react with thiols to form disulfides Here disulfides are shown to be the dominant end effectors of nitrosative signaling Protein S-nitrosation as a regulatory end effector may occur, but this may be rare
Collapse
Affiliation(s)
- Kathryn Wolhuter
- King's College London, School of Cardiovascular Medicine & Sciences, British Heart Foundation Centre of Research Excellence the Rayne Institute, St. Thomas' Hospital, London SE1 7EH, UK
| | - Harry J Whitwell
- Institute for Women's Health, University College London, Gower Street, London WC1E 6BT, UK
| | - Christopher H Switzer
- King's College London, School of Cardiovascular Medicine & Sciences, British Heart Foundation Centre of Research Excellence the Rayne Institute, St. Thomas' Hospital, London SE1 7EH, UK
| | - Joseph R Burgoyne
- King's College London, School of Cardiovascular Medicine & Sciences, British Heart Foundation Centre of Research Excellence the Rayne Institute, St. Thomas' Hospital, London SE1 7EH, UK
| | - John F Timms
- Institute for Women's Health, University College London, Gower Street, London WC1E 6BT, UK
| | - Philip Eaton
- King's College London, School of Cardiovascular Medicine & Sciences, British Heart Foundation Centre of Research Excellence the Rayne Institute, St. Thomas' Hospital, London SE1 7EH, UK.
| |
Collapse
|
17
|
Thawer S, Auret J, Schnoeller C, Chetty A, Smith K, Darby M, Roberts L, Mackay RM, Whitwell HJ, Timms JF, Madsen J, Selkirk ME, Brombacher F, Clark HW, Horsnell WGC. Surfactant Protein-D Is Essential for Immunity to Helminth Infection. PLoS Pathog 2016; 12:e1005461. [PMID: 26900854 PMCID: PMC4763345 DOI: 10.1371/journal.ppat.1005461] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [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: 08/28/2015] [Accepted: 01/28/2016] [Indexed: 11/26/2022] Open
Abstract
Pulmonary epithelial cell responses can enhance type 2 immunity and contribute to control of nematode infections. An important epithelial product is the collectin Surfactant Protein D (SP-D). We found that SP-D concentrations increased in the lung following Nippostrongylus brasiliensis infection; this increase was dependent on key components of the type 2 immune response. We carried out loss and gain of function studies of SP-D to establish if SP-D was required for optimal immunity to the parasite. N. brasiliensis infection of SP-D-/- mice resulted in profound impairment of host innate immunity and ability to resolve infection. Raising pulmonary SP-D levels prior to infection enhanced parasite expulsion and type 2 immune responses, including increased numbers of IL-13 producing type 2 innate lymphoid cells (ILC2), elevated expression of markers of alternative activation by alveolar macrophages (alvM) and increased production of the type 2 cytokines IL-4 and IL-13. Adoptive transfer of alvM from SP-D-treated parasite infected mice into naïve recipients enhanced immunity to N. brasiliensis. Protection was associated with selective binding by the SP-D carbohydrate recognition domain (CRD) to L4 parasites to enhance their killing by alvM. These findings are the first demonstration that the collectin SP-D is an essential component of host innate immunity to helminths. Infections by parasitic worms are very common, and controlling them is a major medical and veterinary challenge. Very few drugs exist to treat them, and the parasites can develop resistance to these. In order to find new ways to control worm infections, understanding how our immune system responds to them is essential. Many important parasitic worm infections move through the host lung. In this study we show that a major secreted protein in the lung, Surfactant Protein D (SP-D), is essential for immunity to a parasitic worm infection. We found that this protein binds to worm larvae in the lung to help the immune system kill them. Infecting mice that do not express SP-D with worms demonstrates SP-D is important in this immune response. These mice are unable to launch an effective anti-worm immune response and have many more worms in their intestine compared to mice that do express SP-D. We also show that if we increase SP-D levels in the lung the mouse has better immunity to worms. Together this shows for the first time that SP-D is very important for immunity to worm infections.
Collapse
Affiliation(s)
- Sumaiyya Thawer
- Institute of Infectious Disease and Molecular Medicine, International Centre for Genetic Engineering and Biotechnology and Division of Immunology, University of Cape Town, Cape Town, South Africa
| | - Jennifer Auret
- Institute of Infectious Disease and Molecular Medicine, International Centre for Genetic Engineering and Biotechnology and Division of Immunology, University of Cape Town, Cape Town, South Africa
| | - Corinna Schnoeller
- Department of Life Sciences, Imperial College London, London, United Kingdom
| | - Alisha Chetty
- Institute of Infectious Disease and Molecular Medicine, International Centre for Genetic Engineering and Biotechnology and Division of Immunology, University of Cape Town, Cape Town, South Africa
| | - Katherine Smith
- Institute of Infectious Disease and Molecular Medicine, International Centre for Genetic Engineering and Biotechnology and Division of Immunology, University of Cape Town, Cape Town, South Africa
- Institute of Infection and Immunity, University of Cardiff, Cardiff, United Kingdom
| | - Matthew Darby
- Institute of Infectious Disease and Molecular Medicine, International Centre for Genetic Engineering and Biotechnology and Division of Immunology, University of Cape Town, Cape Town, South Africa
| | - Luke Roberts
- Department of Life Sciences, Imperial College London, London, United Kingdom
| | - Rosie-Marie Mackay
- Clinical & Experimental Sciences Academic Unit, Southampton General Hospital, University of Southampton, Southampton, United Kingdom
| | - Harry J. Whitwell
- Cancer Proteomics, Institute for Women’s Health, University College London, London, United Kingdom
| | - John F. Timms
- Cancer Proteomics, Institute for Women’s Health, University College London, London, United Kingdom
| | - Jens Madsen
- Clinical & Experimental Sciences Academic Unit, Southampton General Hospital, University of Southampton, Southampton, United Kingdom
| | - Murray E. Selkirk
- Department of Life Sciences, Imperial College London, London, United Kingdom
| | - Frank Brombacher
- Institute of Infectious Disease and Molecular Medicine, International Centre for Genetic Engineering and Biotechnology and Division of Immunology, University of Cape Town, Cape Town, South Africa
| | - Howard William Clark
- Clinical & Experimental Sciences Academic Unit, Southampton General Hospital, University of Southampton, Southampton, United Kingdom
- * E-mail: (HWC); (WGCH)
| | - William G. C. Horsnell
- Institute of Infectious Disease and Molecular Medicine, International Centre for Genetic Engineering and Biotechnology and Division of Immunology, University of Cape Town, Cape Town, South Africa
- * E-mail: (HWC); (WGCH)
| |
Collapse
|