Dr Lodge completed her PhD in protein biochemistry in 2013 at the University of Kent using NMR spectroscopy and a variety of other analytical techniques. After finishing her PhD she spent six months in the protein laboratory at the University of Kent to develop new NMR techniques to measure the reduction potentials of proteins, before changing her research interests to metabolomics and joining the National Phenome Centre at Imperial College London, as an NMR technician. In 2016 Sam became the NMR coordinator at the Clinical Phenome Centre based at Imperial College London. In April 2019 she moved to the Australian National Phenome Centre to lead the NMR team.
Currently, the centre has six operational 600 MHz IVDr NMR instruments fitted with SampleJets to allow the high throughput of human biofluid samples. The operational capacity of these instruments is 400-500 samples per day dependant on the biofluid being analysed. There is a sixth 600 MHz NMR fitted with a sample changer and a 600 MHz HR-MAS NMR for the measurements of tissue samples, which is fitted with a MAS sample changer. In addition to these there is a 400 MHz food screener allowing the authentication of honey, wine and juice in automation plus the analysis of whole fruits and vegetable, oils, spirits and spices. In addition to the NMR instruments we have a range of preparation instruments, including SamplePro robotics and BT pH Bruker preparation units. In early 2021 installation of a further 600 MHz NMR spectrometer and the 800 MHz spectrometer will be completed and consolidation of all the instruments on to the one site at the Harry Perkins Research Institute will be finished and will result in the largest collection of NMR instruments within Australia.
The main work of the laboratory is the high throughput profiling of human biofluid samples. This includes both urine and blood plasma and serum. Large scale metabolic phenotyping of healthy populations is conducted to compare metabolic variation and changes in metabolite concentrations. In addition blood and urine samples can be collected from different patients with different disease states (for example diabetes and cardiovascular disease) and be analysed to determine the metabolic markers in comparison to healthy controls.
The main area of interest within the centre this year has been to determine the metabolic profile of SARS-CoV-2 positive patients and to identify the metabolic markers of disease using NMR. NMR can be used to show the untargeted metabolic changes of the blood or urine profile, but equally changes in lipoproteins and small molecules can be monitored. A multi-organ pathological signature was identified in SARS-CoV-2 patients within the laboratory, combining both NMR and mass spectrometry analysis. In addition to this, experiment optimisation is being completed to assist in the determination of severity of the disease, as well as how the metabolic changes differ from other diseases (such as influenza).
Samples are now currently arriving from the follow up patients of SARs-CoV-2 from around the world. Work is ongoing to answer key questions regarding the disease. Are the patients truly recovered? Metabolically, have they returned to a healthy state? How long does the full recovery take? Do the patients that had severe SAR-CoV-2 infection take longer to recover than the those that were asymptomatic or had very mild symptoms?
Optimisation of sample preparation is ongoing, this year a paper was published from the centre to advise the optimal handling of samples pre analysis. In addition to this, work is being undertaken to allow the miniaturisation of sample volume and validation of the methods. This will allow a smaller blood volume to be collected and analysed, a key advantage when analysing samples from babies and children.
In addition to the high throughput profiling and modelling of human biofluid samples by NMR. Food samples and dietary intervention studies are conducted within the centre. A project currently running through the centre is the SMART-2 project. It aims to understand why individuals respond differently to the same foods. Blood, urine and faecal samples will be analysed to determine the factors which impact an individual’s response. From this, we hope to create an algorithm to predict how people will respond to any food, and then accurately plan their diet accordingly to provide them with the best health outcomes.
Teaching and students
Currently, I supervise one PhD student at Murdoch University, who is using NMR to determine the composition and therefore quality of herbal weight loss supplements. In addition the in vitro toxicity will be determined by NMR using in cell NMR experiments of various cell lines.
I will be teaching both the theory and practical sessions of NMR and sample preparation and analysis on the new short courses and Master of Research in Systems Medicine program at Murdoch University starting in early 2021.
T.Kimhofer, S.Lodge, L.Whiley, N.Gray, R.L.Loo, N.G.Lawler, P.Nitschke, SH.Bong, D.L.Morrison, S.Begum, T.Richards, B.B.Yeap, C.Smith, K.G.C.Smith, E.Holmes, J.K.Nicholson (2020) Integrative Modeling of Quantitative Plasma Lipoprotein, Metabolic, and Amino Acid Data Reveals a Multiorgan Pathological Signature of SARS-CoV-2 Infection. Journal of Proteome Research 19 (11) 4442-4454.
R.L.Loo, S.Lodge, T.Kimhofer, SH.Bong, S.Begum, L.Whiley, N. Gray, J.C.Lindon, P.Nitschke, N.G.Lawler, H.Schafer, M.Spraul, T.Richards, J.K.Nicholson, E.Holmes (2020) Quantitative In-Vitro Diagnostic NMR Spectroscopy for Lipoprotein and Metabolite Measurements in Plasma and Serum: Recommendations for Analytical Artefact Minimization with Special Reference to COVID-19/SARS-CoV-2 Samples. Journal of Proteome Research 19 (11) 4428-4441.
B.Jimenez, E.Holmes, C.Heude, R.Tolson, N.Harvey, S.Lodge, A.Cherwynd, C.Cannet, F.Fang, J.Pearce, M.Lewis, M.Viant, J.Lindon, M.Spraul, H.Schafer, J.K.Nicholson (2018) Quantitative Lipoprotein Subclass and Low Molecular Weight Metabolite Analysis in Human Serum and Plasma by 1H NMR Spectroscopy in a Multilaboratory Trial. Analytical Chemistry, Vol:90, ISSN:0003-2700, Pages:11962-11971.
S.L. Taylor, H.Crawley-Snowdon, J.L. Wagstaff, M.L. Rowe, M.Shepherd, R.A. Williamson, M.J. Howard. (2013) Measuring protein reduction potentials using 15N HSQC NMR spectroscopy. Chem. Commun. 49 (18) 1847-1849.