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4. Integrative Molecular Structure Elucidation and Construction of an Extended Metabolic Pathway Associated with an Ancient Innate Immune Response in COVID-19 Patients

Author

Sala, Samuele, primary, Nitschke, Philipp, additional, Masuda, Reika, additional, Gray, Nicola, additional, Lawler, Nathan G., additional, Wood, James M., additional, Buckler, Joshua N., additional, Berezhnoy, Georgy, additional, Bolaños, Jose, additional, Boughton, Berin A., additional, Lonati, Caterina, additional, Rössler, Titus, additional, Singh, Yogesh, additional, Wilson, Ian D., additional, Lodge, Samantha, additional, Morillon, Aude-Claire, additional, Loo, Ruey Leng, additional, Hall, Drew, additional, Whiley, Luke, additional, Evans, Gary B., additional, Grove, Tyler L., additional, Almo, Steven C., additional, Harris, Lawrence D., additional, Holmes, Elaine, additional, Merle, Uta, additional, Trautwein, Christoph, additional, Nicholson, Jeremy K., additional, and Wist, Julien, additional

Published
2024
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7. SARS-CoV-2 Infection Biomarkers Reveal an Extended RSAD2 Dependant Metabolic Pathway

Author

Sala, Samuele, primary, Nitschke, Philipp, additional, Masuda, Reika, additional, Gray, Nicola, additional, Lawler, Nathan, additional, Wood, James M., additional, Berezhnoy, Georgy, additional, Bolanos, Alejandro, additional, Boughton, Berin A., additional, Lonati, Caterina, additional, Roessler, Titus, additional, Singh, Yogesh, additional, Wilson, Ian D., additional, Lodge, Samantha, additional, Morillon, Aude-Claire, additional, Loo, Ruey Leng, additional, Hall, Drew, additional, Whiley, Luke, additional, Evans, Gary B., additional, Grove, Tyler L., additional, Almo, Steven C., additional, Harris, Lawrence D., additional, Holmes, Elaine, additional, Merle, Uta, additional, Trautwein, Christoph, additional, Nicholson, Jeremy K., additional, and Wist, Julien, additional

Published
2023
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8. Demographic, Health and Lifestyle Factors Associated with the Metabolome in Older Women

Author

Navarro, Sandi L., primary, Nagana Gowda, G. A., additional, Bettcher, Lisa F., additional, Pepin, Robert, additional, Nguyen, Natalie, additional, Ellenberger, Mathew, additional, Zheng, Cheng, additional, Tinker, Lesley F., additional, Prentice, Ross L., additional, Huang, Ying, additional, Yang, Tao, additional, Tabung, Fred K., additional, Chan, Queenie, additional, Loo, Ruey Leng, additional, Liu, Simin, additional, Wactawski-Wende, Jean, additional, Lampe, Johanna W., additional, Neuhouser, Marian L., additional, and Raftery, Daniel, additional

Published
2023
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9. SARS-CoV-2 Infection Biomarkers Reveal Adaptive Evolutionary Chemistry of Antiviral Nucleoside Metabolism

Author

Sala, Samuele, Nitschke, Philipp, Masuda, Reika, Gray, Nicola, Lawler, Nathan, Wood M., James, Berezhnoy, Georgy, Bolaños, Alejandro, Boughton A., Berin, Lonati, Caterina, Roessler, Titus, Singh, Yogesh, Wilson D., Ian, Lodge, Samantha, Morillon, Aude-Claire, Loo, Ruey Leng, Hall, Drew, Whiley, Luke, Evans B., Gary, Grove L., Tyler, Almo C., Steven, Harris D., Lawrence, Holmes, Elaine, Merle, Uta, Trautwein, Christoph, Nicholson K., Jeremy, and Wist, Julien

Subjects
deoxydidehydronucleosides, NMR spectroscopy, antivirals, SARS-CoV-2, biomarkers, COVID-19, polypharmacy, urine, nucleosides
Abstract

We present compelling evidence for the existence of an evolutionary adaptive response to viral agents such as SARS-CoV-2, that results in the human in vivo biosynthesis of a family of compounds with potential antiviral activity. Using nuclear magnetic resonance (NMR) spectroscopy, we detected a characteristic spin-system motif indicative of the presence of an extended panel of urinary and serum metabolites during the acute viral phase. The structure of eight of nucleoside analogues was elucidated (six of which have not previously been reported in human urine), and subsequently confirmed by total-synthesis and matrix spiking. The molecular structures of the nucleoside analogues and their correlation with an array of serum cytokines, including IFN-α2, IFN-γ and IL-10, suggest an association with the viperin enzyme contributing to an endogenous innate immune defense mechanism against viral infection., Acknowledgements: Acknowledgements: We thank The Spinnaker Health Research Foundation, WA, The McCusker Foundation, WA, The Western Australian State Government and the Medical Research Future Fund (EPCD000037 and MRF2014349) for financial support. We thank the Department of Jobs, Tourism, Science and Innovation, Government of a Western Australian Premier's Fellowship for RLL and the ARC for Laureate Fellowship funding for EH. JW thanks Ministerio de Ciencia, Tecnología e Innovación (Minciencias), Ministerio de Educación Nacional, Ministerio de Industria, Comercio y Turismo e ICETEX (792–2017) 2a Convocatoria Ecosistema Científico - Colombia Científica para la Financiación de Proyectos de I + D + i), World Bank and Vicerrectoría de Investigaciones, Pontificia Universidad Javeriana, Bogotá, Colombia (contract no. FP44842 - 221-2018). We gratefully thank the Werner Siemens Imaging Center under direction of Prof. Bernd Pichler for supporting this project as well as Aditi Kulkarni and Daniele Bucci for excellent technical assistance. JMW, GBE and LDH thank the New Zealand Ministry of Business Innovation & Employment for support (Endeavour Fund program contract UOOX1904 (NZ)).

Published
2023
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10. A Matrix-Assisted Laser Desorption/Ionization Magnetic Resonance Mass Spectrometry (Maldi-Mrms) Approach and Pipeline for Characterization of Inulin in Plant Products

Author

Chin, Sung-Tong, primary, Boughton, Berin, additional, Gay, Melvin, additional, Russell, Alyce, additional, Wang, Yimin, additional, Nambiar, Vimalnath, additional, McHenry, Mark P., additional, Holmes, Elaine, additional, Nicholson, Jeremy K., additional, and Loo, Ruey Leng, additional

Published
2023
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12. Blood pressure interactions with the DASH dietary pattern, sodium, and potassium: The International Study of Macro-/Micronutrients and Blood Pressure (INTERMAP)

Author

Chan, Queenie, primary, Wren, Gina M, additional, Lau, Chung-Ho E, additional, Ebbels, Timothy MD, additional, Gibson, Rachel, additional, Loo, Ruey Leng, additional, Aljuraiban, Ghadeer S, additional, Posma, Joram M, additional, Dyer, Alan R, additional, Steffen, Lyn M, additional, Rodriguez, Beatriz L, additional, Appel, Lawrence J, additional, Daviglus, Martha L, additional, Elliott, Paul, additional, Stamler, Jeremiah, additional, Holmes, Elaine, additional, and Van Horn, Linda, additional

Published
2022
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14. Exploration of Human Serum Lipoprotein Supramolecular Phospholipids Using Statistical Heterospectroscopy in n-Dimensions (SHY-n): Identification of Potential Cardiovascular Risk Biomarkers Related to SARS-CoV-2 Infection

Author

Masuda, Reika, primary, Lodge, Samantha, additional, Whiley, Luke, additional, Gray, Nicola, additional, Lawler, Nathan, additional, Nitschke, Philipp, additional, Bong, Sze-How, additional, Kimhofer, Torben, additional, Loo, Ruey Leng, additional, Boughton, Berin, additional, Zeng, Annie X., additional, Hall, Drew, additional, Schaefer, Hartmut, additional, Spraul, Manfred, additional, Dwivedi, Girish, additional, Yeap, Bu B., additional, Diercks, Tammo, additional, Bernardo-Seisdedos, Ganeko, additional, Mato, José M., additional, Lindon, John C., additional, Holmes, Elaine, additional, Millet, Oscar, additional, Wist, Julien, additional, and Nicholson, Jeremy K., additional

Published
2022
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17. Integrative Modeling of Plasma Metabolic and Lipoprotein Biomarkers of SARS-CoV-2 Infection in Spanish and Australian COVID-19 Patient Cohorts

Author

Masuda, Reika, primary, Lodge, Samantha, additional, Nitschke, Philipp, additional, Spraul, Manfred, additional, Schaefer, Hartmut, additional, Bong, Sze-How, additional, Kimhofer, Torben, additional, Hall, Drew, additional, Loo, Ruey Leng, additional, Bizkarguenaga, Maider, additional, Bruzzone, Chiara, additional, Gil-Redondo, Rubén, additional, Embade, Nieves, additional, Mato, José M., additional, Holmes, Elaine, additional, Wist, Julien, additional, Millet, Oscar, additional, and Nicholson, Jeremy K., additional

Published
2021
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18. Incomplete Systemic Recovery and Metabolic Phenoreversion in Post-Acute-Phase Nonhospitalized COVID-19 Patients: Implications for Assessment of Post-Acute COVID-19 Syndrome

Author

Holmes, Elaine, primary, Wist, Julien, additional, Masuda, Reika, additional, Lodge, Samantha, additional, Nitschke, Philipp, additional, Kimhofer, Torben, additional, Loo, Ruey Leng, additional, Begum, Sofina, additional, Boughton, Berin, additional, Yang, Rongchang, additional, Morillon, Aude-Claire, additional, Chin, Sung-Tong, additional, Hall, Drew, additional, Ryan, Monique, additional, Bong, Sze-How, additional, Gay, Melvin, additional, Edgar, Dale W., additional, Lindon, John C., additional, Richards, Toby, additional, Yeap, Bu B., additional, Pettersson, Sven, additional, Spraul, Manfred, additional, Schaefer, Hartmut, additional, Lawler, Nathan G., additional, Gray, Nicola, additional, Whiley, Luke, additional, and Nicholson, Jeremy K., additional

Published
2021
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19. Correction to “Integrative Modeling of Quantitative Plasma Lipoprotein, Metabolic, and Amino Acid Data Reveals a Multiorgan Pathological Signature of SARS-CoV-2 Infection”

Author

Kimhofer, Torben, primary, Lodge, Samantha, additional, Whiley, Luke, additional, Gray, Nicola, additional, Loo, Ruey Leng, additional, Lawler, Nathan G., additional, Nitschke, Philipp, additional, Bong, Sze-How, additional, Morrison, David L., additional, Begum, Sofina, additional, Richards, Toby, additional, Yeap, Bu B., additional, Smith, Chris, additional, Smith, Kenneth G. C., additional, Holmes, Elaine, additional, and Nicholson, Jeremy K., additional

Published
2021
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20. Metabolic profiling and population screening of analgesic usage in nuclear magnetic resonance spectroscopy-based large-scale epidemiologic studies

Author

Loo, Ruey Leng, Coen, Muireann, Ebbels, Timothy, Cloarec, Olivier, Maibaum, Elaine, Bictash, Magda, Yap, Ivan, Elliott, Paul, Stamler, Jeremiah, Nicholson, Jeremy K., and Holmes, Elaine

Subjects
Nuclear magnetic resonance spectroscopy -- Methods, Acetaminophen -- Identification and classification, Acetaminophen -- Measurement, Ibuprofen -- Identification and classification, Ibuprofen -- Measurement, Epidemiologic methods -- Research, Chemistry
Abstract

The application of a [sup.1]H nuclear magnetic resonance (NMR) spectroscopy-based screening method for determining the use of two widely available analgesics (acetaminophen and ibuprofen) in epidemiologic studies has been investigated. We used samples and data from the cross-sectional INTERMAP Study involving participants from Japan (n = 1145), China (n = 839), U.K. (n = 501), and the U.S. (n = 2195). An orthogohal projection to latent structures discriminant analysis (OPLS-DA) algorithm with an incorporated Monte Carlo resampling function was applied to the NMR data set to determine which spectra contained analgesic metabolites. OPLS-DA preprocessing parameters (normalization, bin width, scaling, and input parameters) were assessed systematically to identify an optimal acetaminophen prediction model. Subsets of INTERMAP spectra were examined to verify and validate the presence/absence of acetaminophen/ibuprofen based on known chemical shift and coupling patterns. The optimized and validated acetaminophen model convexly predicted 98.2%, and the ibuprofen model correctly predicted 99.0% of the urine specimens containing these drug metabolites. The acetaminophen and ibuprofen models were subsequently used to predict the presence/absence of these drug metabolites for the remaining INTERMAP specimens. The acetaminophen model identified 415 out of 8436 spectra as containing acetaminophen metabolite signals while the ibuprofen model identified 245 out of 8604 spectra as containing ibuprofen metabolite signals from the global data set after excluding samples used to construct the prediction models. The NMR-based metabolic screening strategy provides a new objective approach for evaluation of self-reported medication data and is extendable to other aspects of population xenometabolome profiling.

Published
2009

21. Diffusion and Relaxation Edited Proton NMR Spectroscopy of Plasma Reveals a High-Fidelity Supramolecular Biomarker Signature of SARS-CoV-2 Infection

Author

Lodge, Samantha, primary, Nitschke, Philipp, additional, Kimhofer, Torben, additional, Wist, Julien, additional, Bong, Sze-How, additional, Loo, Ruey Leng, additional, Masuda, Reika, additional, Begum, Sofina, additional, Richards, Toby, additional, Lindon, John C., additional, Bermel, Wolfgang, additional, Reinsperger, Tony, additional, Schaefer, Hartmut, additional, Spraul, Manfred, additional, Holmes, Elaine, additional, and Nicholson, Jeremy K., additional

Published
2021
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22. Low Volume in Vitro Diagnostic Proton NMR Spectroscopy of Human Blood Plasma for Lipoprotein and Metabolite Analysis: Application to SARS-CoV-2 Biomarkers

Author

Lodge, Samantha, primary, Nitschke, Philipp, additional, Loo, Ruey Leng, additional, Kimhofer, Torben, additional, Bong, Sze-How, additional, Richards, Toby, additional, Begum, Sofina, additional, Spraul, Manfred, additional, Schaefer, Hartmut, additional, Lindon, John C., additional, Holmes, Elaine, additional, and Nicholson, Jeremy K., additional

Published
2021
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23. NMR Spectroscopic Windows on the Systemic Effects of SARS-CoV-2 Infection on Plasma Lipoproteins and Metabolites in Relation to Circulating Cytokines

Author

Lodge, Samantha, primary, Nitschke, Philipp, additional, Kimhofer, Torben, additional, Coudert, Jerome D., additional, Begum, Sofina, additional, Bong, Sze-How, additional, Richards, Toby, additional, Edgar, Dale, additional, Raby, Edward, additional, Spraul, Manfred, additional, Schaefer, Hartmut, additional, Lindon, John C., additional, Loo, Ruey Leng, additional, Holmes, Elaine, additional, and Nicholson, Jeremy K., additional

Published
2021
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24. Human metabolic phenotype diversity and its association with diet and blood pressure

Author

Holmes, Elaine, Loo, Ruey Leng, Stamler, Jeremiah, Bictash, Magda, Yap, Ivan K.S., Chan, Queenie, Ebbels, Tim, De Iorio, Maria, Brown, Ian J., Veselkov, Kirill A., Daviglus, Martha L., Kesteloot, Hugo, Ueshima, Hirotsugu, Zhao, Liancheng, Nicholson, Jeremy K., and Elliott, Paul

Subjects
Blood pressure -- Physiological aspects -- Research, Diet -- Physiological aspects -- Research, Environmental issues, Science and technology, Zoology and wildlife conservation, Physiological aspects, Research
Abstract

Metabolic phenotypes are the products of interactions among a variety of factors--dietary, other lifestyle/environmental, gut microbial and genetic (1-3). We use a large-scale exploratory analytical approach to investigate metabolic phenotype [...]

Published
2008

25. Detection of urinary drug metabolite (xenometabolome) signatures in molecular epidemiology studies via statistical total correlation (NMR) spectroscopy

Author

Holmes, Elaine, Loo, Ruey Leng, Cloarec, Olivier, Coen, Muireann, Tang, Huiru, Maibaum, Elaine, Bruce, Stephen, Chan, Queenie, Elliott, Paul, Stamler, Jeremiah, Wilson, Ian D., Lindon, John C., and Nicholson, Jeremy K.

Subjects
Nuclear magnetic resonance spectroscopy -- Usage, Drugs -- Analysis, Metabolites -- Analysis, Chemistry
Abstract

Western populations use prescription and nonprescription drugs extensively, but large-scale population usage is rarely assessed objectively in epidemiological studies. Here we apply statistical methods to characterize structural pathway connectivities of metabolites of commonly used drugs detected routinely in [sup.1]H NMR spectra of urine in a human population study. XH NMR spectra were measured for two groups of urine samples obtained from U.S. participants in a known population study. The novel application of a statistical total correlation spectroscopy (STOCSY) approach enabled rapid identification of the major and certain minor drug metabolites in common use in the population, in particular, from acetaminophen and ibuprofen metabolites. This work shows that statistical connectivities between drug metabolites can be established in routine 'high-throughput' NMR screening of human samples from participants who have randomly self-administered drugs. This approach should be of value in considering interpopulation patterns of drug metabolism in epidemiological and pharmacogenetic studies.

Published
2007

27. Quantitative In-Vitro Diagnostic NMR Spectroscopy for Lipoprotein and Metabolite Measurements in Plasma and Serum: Recommendations for Analytical Artifact Minimization with Special Reference to COVID-19/SARS-CoV-2 Samples

Author

Loo, Ruey Leng, primary, Lodge, Samantha, additional, Kimhofer, Torben, additional, Bong, Sze-How, additional, Begum, Sofina, additional, Whiley, Luke, additional, Gray, Nicola, additional, Lindon, John C., additional, Nitschke, Philipp, additional, Lawler, Nathan G., additional, Schäfer, Hartmut, additional, Spraul, Manfred, additional, Richards, Toby, additional, Nicholson, Jeremy K., additional, and Holmes, Elaine, additional

Published
2020
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28. Integrative Modeling of Quantitative Plasma Lipoprotein, Metabolic, and Amino Acid Data Reveals a Multiorgan Pathological Signature of SARS-CoV-2 Infection

Author

Kimhofer, Torben, primary, Lodge, Samantha, additional, Whiley, Luke, additional, Gray, Nicola, additional, Loo, Ruey Leng, additional, Lawler, Nathan G., additional, Nitschke, Philipp, additional, Bong, Sze-How, additional, Morrison, David L., additional, Begum, Sofina, additional, Richards, Toby, additional, Yeap, Bu B., additional, Smith, Chris, additional, Smith, Kenneth G. C., additional, Holmes, Elaine, additional, and Nicholson, Jeremy K., additional

Published
2020
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31. The association of fish consumption and its urinary metabolites with cardiovascular risk factors: the International Study of Macro-/Micronutrients and Blood Pressure (INTERMAP)

Author

Gibson, Rachel, primary, Lau, Chung-Ho E, additional, Loo, Ruey Leng, additional, Ebbels, Timothy MD, additional, Chekmeneva, Elena, additional, Dyer, Alan R, additional, Miura, Katsuyuki, additional, Ueshima, Hirotsugu, additional, Zhao, Liancheng, additional, Daviglus, Martha L, additional, Stamler, Jeremiah, additional, Van Horn, Linda, additional, Elliott, Paul, additional, Holmes, Elaine, additional, and Chan, Queenie, additional

Published
2020
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32. Medicine-related services in community pharmacy: public preferences for pharmacy attributes and promotional methods and comparison with pharmacists' perceptions

Author

Krska, Janet, Corlett, S.A., Gammie, Shivaun M, Loo, Ruey Leng, and Rodgers, Ruth

Subjects
health care facilities, manpower, and services, health services administration, education, health care economics and organizations, RS
Abstract

Background: Public awareness of pharmacy services designed to support use of medicines is low, yet little is known about how the public view promotion of these services or their preferences for the attributes of pharmacies from which they would like to receive them.\ud Objective: To compare the public’s preferred attributes of pharmacies and methods for promoting medicine-related services with community pharmacists’ perceptions of their customers’ views.\ud Method: Parallel surveys of the general public, using a street survey, and community pharmacists, via a postal survey in South East England. \ud Results: Response rates were: public 47.2% (1000/2012) and pharmacists 40.8% (341/836) respectively. Pharmacists’ perceptions of customer preferences for using the same pharmacy, independent ownership and personal knowledge of the pharmacist were higher than actual public preferences. More pharmacists also thought approachability and previous good service would be important than the public. The public’s desires for long opening hours and for a pharmacy with a good relationship with their doctor’s surgery was higher than pharmacists believed. The majority of the public prefer not to interrupt a pharmacist busy in the dispensary, which was not perceived by pharmacists as a factor. Pharmacists’ perceptions aligned more with the preferences of regular medicines users and frequent pharmacy users. Both groups viewed direct recommendation as the most effective approach for promoting pharmacy services, particularly by doctors and pharmacy staff. Pharmacists’ expectations of the effectiveness of posters and mass media methods were much higher than those of the public. \ud Conclusions: Pharmacists and pharmacy owners must ensure good relationships with local medical practices to enable them to maximise opportunities for using the promotional methods judged most effective in encouraging use of medicine-related services. Staff must be approachable and enable access to pharmacists ensuring perceptions of pharmacist busyness are not a deterrent.

Published
2016

37. Statistical HOmogeneous Cluster SpectroscopY (SHOCSY): an optimized statistical approach for clustering of ¹H NMR spectral data to reduce interference and enhance robust biomarkers selection

Author

Zou, Xin, Holmes, Elaine, Nicholson, Jeremy K., and Loo, Ruey Leng

Subjects
QA76
Abstract

We propose a novel statistical approach to improve the reliability of (1)H NMR spectral analysis in complex metabolic studies. The Statistical HOmogeneous Cluster SpectroscopY (SHOCSY) algorithm aims to reduce the variation within biological classes by selecting subsets of homogeneous (1)H NMR spectra that contain specific spectroscopic metabolic signatures related to each biological class in a study. In SHOCSY, we used a clustering method to categorize the whole data set into a number of clusters of samples with each cluster showing a similar spectral feature and hence biochemical composition, and we then used an enrichment test to identify the associations between the clusters and the biological classes in the data set. We evaluated the performance of the SHOCSY algorithm using a simulated (1)H NMR data set to emulate renal tubule toxicity and further exemplified this method with a (1)H NMR spectroscopic study of hydrazine-induced liver toxicity study in rats. The SHOCSY algorithm improved the predictive ability of the orthogonal partial least-squares discriminatory analysis (OPLS-DA) model through the use of "truly" representative samples in each biological class (i.e., homogeneous subsets). This method ensures that the analyses are no longer confounded by idiosyncratic responders and thus improves the reliability of biomarker extraction. SHOCSY is a useful tool for removing irrelevant variation that interfere with the interpretation and predictive ability of models and has widespread applicability to other spectroscopic data, as well as other "omics" type of data.

Published
2014

41. Metabolic phenotyping in epidemiology and metabolome-wide association studies

Author

Bictash, Magda, Ebbels, Timothy, Chan, Queenie, Loo, Ruey Leng, Yap, Ivan, Brown, Ian J, De Iorio, Maria, Daviglus, Martha, Holmes, Elaine, Stamler, Jeremiah, Nicholson, Jeremy K., and Elliott, Paul

Subjects
Molecular Epidemiology, Phenotype, Metabolome, Humans, Metabolomics, Reproducibility of Results, Risk Assessment, Article, Biomarkers
Abstract

Metabolic phenotyping of humans allows information to be captured on the interactions between dietary, xenobiotic, other lifestyle and environmental exposures, and genetic variation, which together influence the balance between health and disease risks at both individual and population levels.We describe here the main procedures in large-scale metabolic phenotyping and their application to metabolome-wide association (MWA) studies.By use of high-throughput technologies and advanced spectroscopic methods, application of metabolic profiling to large-scale epidemiologic sample collections, including metabolome-wide association (MWA) studies for biomarker discovery and identification.Metabolic profiling at epidemiologic scale requires optimization of experimental protocol to maximize reproducibility, sensitivity, and quantitative reliability, and to reduce analytical drift. Customized multivariate statistical modeling approaches are needed for effective data visualization and biomarker discovery with control for false-positive associations since 100s or 1,000s of complex metabolic spectra are being processed.Metabolic profiling is an exciting addition to the armamentarium of the epidemiologist for the discovery of new disease-risk biomarkers and diagnostics, and to provide novel insights into etiology, biological mechanisms, and pathways.

Published
2010

46. Differential Effects of Two Fermentable Carbohydrates on Central Appetite Regulation and Body Composition

Author

Arora, Tulika, primary, Loo, Ruey Leng, additional, Anastasovska, Jelena, additional, Gibson, Glenn R., additional, Tuohy, Kieran M., additional, Sharma, Raj Kumar, additional, Swann, Jonathan R., additional, Deaville, Eddie R., additional, Sleeth, Michele L., additional, Thomas, E. Louise, additional, Holmes, Elaine, additional, Bell, Jimmy D., additional, and Frost, Gary, additional

Published
2012
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47. Metabolome-Wide Association Study Identifies Multiple Biomarkers that Discriminate North and South Chinese Populations at Differing Risks of Cardiovascular Disease: INTERMAP Study

Author

Yap, Ivan K. S., primary, Brown, Ian J., additional, Chan, Queenie, additional, Wijeyesekera, Anisha, additional, Garcia-Perez, Isabel, additional, Bictash, Magda, additional, Loo, Ruey Leng, additional, Chadeau-Hyam, Marc, additional, Ebbels, Timothy, additional, Iorio, Maria De, additional, Maibaum, Elaine, additional, Zhao, Liancheng, additional, Kesteloot, Hugo, additional, Daviglus, Martha L., additional, Stamler, Jeremiah, additional, Nicholson, Jeremy K., additional, Elliott, Paul, additional, and Holmes, Elaine, additional

Published
2010
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48. Detection of Urinary Drug Metabolite (Xenometabolome) Signatures in Molecular Epidemiology Studies via Statistical Total Correlation (NMR) Spectroscopy

Author

Holmes, Elaine, primary, Loo, Ruey Leng, additional, Cloarec, Olivier, additional, Coen, Muireann, additional, Tang, Huiri, additional, Maibaum, Elaine, additional, Bruce, Stephen, additional, Chan, Queenie, additional, Elliott, Paul, additional, Stamler, Jeremiah, additional, Wilson, Ian D., additional, Lindon, John C., additional, and Nicholson, Jeremy K., additional

Published
2008
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49. Individual variability of effort-based training prescriptions in competitive cyclists

Author

O'Grady, Ciarán, Hopker, James, Passfield, Louis, and Loo, Ruey-Leng

Subjects
Sports sciences
Abstract

The aim of this thesis was to investigate the use of effort-based intensity prescriptions as a method to reduce individual variability and the occurrence of training non-response. Specifically, this thesis explores the physiological, psychological, and metabolomic responses to the interaction of training duration and effort-based intensity on a single-bout basis, whole session basis, and during chronic training intervention. The first experimental study (Chapter 4) investigated individual variability during self- paced exercise bouts at a rating of perceived exertion (RPE) of either 9, 13, or 17, conducted for either 1, 4, or 8 min. The study found that effort-based intensity prescriptions at higher RPEs and shorter durations result in lower levels of individual variability. The second study (Chapter 5) investigated individual variability during maximal isoeffort training sessions in either short interval (30 sec), long interval (5 min), or continuous exercise matched for total training duration. Long intervals displayed lowest variability in both how the session was performed as well as physiological response compared to short intervals and continuous sessions. The third study (Chapter 6) comprised a 6-week training intervention using maximal isoeffort intensity prescriptions using short (30 sec) or long interval (5 min) session formats, as well as a control group. Whilst short intervals resulted in higher levels of individual variability, a greater training response was found following this session format compared to both the long interval and control groups. The fourth study (Chapter 7) investigated the metabolomic differences between session formats, and between variable and consistent responding participants from Chapter 5. Distinct metabolomic differences were found between all session formats, and key metabolites were found relating to energy turnover, purine metabolism, and amino acid metabolism based on whether individuals were consistent or variable in session performance. The fifth study (Chapter 8) investigated the chronic changes in the urinary metabolome following the training interventions as described in Chapter 6. Several metabolomic markers differentiated between training responders and non-responders, in addition to metabolites associated with increased MMP or V̇O2max across all training groups. The main finding of this thesis was that the use of higher intensity effort-based targets and shorter interval durations has potential in reducing the occurrence of non-response to training.

Published
2021
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50. Integrative Modeling of Quantitative Plasma Lipoprotein, Metabolic, and Amino Acid Data Reveals a Multiorgan Pathological Signature of SARS-CoV-2 Infection

Author

Sofina Begum, Samantha Lodge, Chris Smith, Nicola Gray, Kenneth G. C. Smith, Toby Richards, Jeremy K. Nicholson, Ruey Leng Loo, Luke Whiley, Elaine Holmes, Philipp Nitschke, Bu B. Yeap, David Morrison, Nathan G. Lawler, Torben Kimhofer, Sze-How Bong, Kimhofer, Torben [0000-0001-7158-9930], Whiley, Luke [0000-0002-9088-4799], Gray, Nicola [0000-0002-0094-5245], Loo, Ruey Leng [0000-0001-5307-5709], Lawler, Nathan G [0000-0001-9649-425X], Holmes, Elaine [0000-0002-0556-8389], and Apollo - University of Cambridge Repository

Subjects
Blood Glucose, Male, 0301 basic medicine, Very low-density lipoprotein, Magnetic Resonance Spectroscopy, medicine.disease_cause, Biochemistry, mosaic disease, chemistry.chemical_compound, Medicine, mass spectrometry, Coronavirus, biology, multiorgan damage, Middle Aged, systems model, Metabolome, Female, Apolipoprotein A1, Coronavirus Infections, 03 Chemical Sciences, Biochemistry & Molecular Biology, medicine.medical_specialty, metabolic phenotyping, Multiple Organ Failure, Pneumonia, Viral, Models, Biological, Article, Betacoronavirus, 03 medical and health sciences, NMR spectroscopy, Diabetes mellitus, Internal medicine, Humans, Pandemics, Aged, amino acids, 030102 biochemistry & molecular biology, SARS-CoV-2, business.industry, COVID-19, biomarkers, General Chemistry, 06 Biological Sciences, medicine.disease, lipoproteins, Glutamine, 030104 developmental biology, Endocrinology, chemistry, biology.protein, business, Kynurenine, Dyslipidemia, Lipoprotein
Abstract

The metabolic effects of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection on human blood plasma were characterized using multi-platform metabolic phenotyping with Nuclear Magnetic Resonance (NMR) spectroscopy and liquid chromatography-mass spectrometry (LC-MS). Quantitative measurements of lipoprotein sub-fractions, alpha-1-acid glycoprotein, glucose and biogenic amines were made on samples from symptomatic coronavirus disease 19 (COVID-19) patients who had tested positive for the SARS-CoV-2 virus (n = 17) and from age and gender-matched controls (n = 25). Data were analyzed using an orthogonal-projections to latent structures (O-PLS) method and used to construct an exceptionally strong (AUROC=1) hybrid NMR-MS model that enabled detailed metabolic discrimination between the groups and their biochemical relationships. Key discriminant metabolites included markers of inflammation including elevated alpha-1 acid glycoprotein and an increased kynurenine/tryptophan ratio. There was also an abnormal lipoprotein, glucose and amino acid signature consistent with diabetes and coronary artery disease (low total and HDL Apolipoprotein A1, low HDL triglycerides, high LDL and VLDL triglycerides). Plus, multiple highly significant amino acid markers of liver dysfunction (including the elevated glutamine/glutamate and Fischer’s ratios) that present themselves as part of a distinct SARS-CoV-2 infection pattern. A multivariate training-test set model was validated using independent samples from additional SARS-CoV-2 positive patients and controls. The predictive model showed a sensitivity of 100% for SARS-CoV-2 positivity. The breadth of the disturbed pathways indicates a systemic signature of SARS-CoV-2 positivity that includes elements of liver dysfunction, dyslipidaemia, diabetes, and coronary heart disease risk that are consistent with recent reports that COVID-19 is a systemic disease affecting multiple organs and systems. Metabolights study reference: MTBLS2014.

Published
2020

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