2024
Deletion of miPEP in adipocytes protects against obesity and insulin resistance by boosting muscle metabolism. Diaz Vegas, A., Cooke, K., Cutler, H., Yau, B., Masson, S., Harney, D., Fuller, O., Potter, M., Madsen, S., Craw, N., Zhang, Y., Moreno, C., Kebede, M., Neely, G., Stoeckli, J., Burchfield, J., James, D. Molecular Metabolism, 86, 2024
The metabolic consequences of 'yo-yo' dieting are markedly influenced by genetic diversity. Thillainadesan, S., Lambert, A., Cooke, K., Stoeckli, J., Yau, B., Masson, S., Howell, A., Potter, M., Fuller, O., Jiang, B., Kebede, M., James, D., Madsen, S., Hocking, S., et al. International Journal of Obesity, 48(8), 1170-1179, 2024
Exploratory physiological experiments are not clinical trials. Erik A Richter, David E James, John P Kirwan, Juleen R Zierath, Cell Metabolism 36 (5), 882-883, 2024
Genetics and diet shape the relationship between islet function and whole-body metabolism. Yau B., Madsen S., Healy M.E., Cooke K.C., Fritzen A.M., Thorius I.H., Stöckli J., James D.E., Kebede M.A. Am J Physiol Endocrinol Metab, 2024 ahead of print. PMID: 38568150.
Personalized phosphoproteomics of skeletal muscle insulin resistance and exercise links MINDY1 to insulin action. Elise J Needham, Janne R Hingst, Johan D Onslev, Alexis Diaz-Vegas, Magnus R Leandersson, Kristen Cooke, Guang Yang, Jonas M Kristensen, Kohei Kido, Benjamin L Parker, Kurt Højlund, Erik A Richter, Christian Pehmøller, Sean J Humphrey, David E James, Jørgen FP Wojtaszewski. medRxiv, 2024.03. 11.24304084, 2024
Dual Tracer Test to Measure Tissue-Specific Insulin Action in Individual Mice Identifies In Vivo Insulin Resistance Without Fasting Hyperinsulinemia. Cutler, H., Madsen, S., Masson, S., Cooke, K., Potter, M., Burchfield, J., Stoeckli, J., Nelson, M., Cooney, G., James, D. Diabetes, db230035. 2024.
The genetic and dietary landscape of the muscle insulin signalling network. van Gerwen J., Masson S.W.C., Cutler H.B., Vegas A.D., Potter M., Stöckli J., Madsen S., Nelson M.E., Humphrey S.J., James D.E. . Elife. 12:RP89212, 2024
2023
Mitochondrial electron transport chain, ceramide, and coenzyme Q are linked in a pathway that drives insulin resistance in skeletal muscle. Diaz-Vegas A., Madsen S., Cooke K.C., Carroll L., Khor J.X.Y., Turner N., Lim X.Y., Astore M.A., Morris J.C., Don A.S., Garfield A., Zarini S., Zemski Berry K.A., Ryan A.P., Bergman B.C., Brozinick J.T., James D.E., Burchfield J.G. Elife. 12:RP87340, 2023
Systems genetics approaches for understanding complex traits with relevance for human disease. Allayee, H., Farber, C.R., Seldin, M.M., Williams, E.G., James, D.E., Lusis, A.J. Elife. 12:e91004, 2023
eNODAL: an experimentally guided nutriomics data clustering method to unravel complex drug-diet interactions. Xiangnan Xu, Alistair M Senior, David G Le Couteur, Victoria C Cogger, David Raubenheimer, David E James, Benjamin Parker, Stephen J Simpson, Samuel Muller, Jean Yee Hwa Yang. bioRxiv, 2023.10. 03.560662, 2023
Genetic architecture of heart mitochondrial proteome influencing cardiac hypertrophy. Chella Krishnan K, El Hachem EJ, Keller MP, Patel SG, Carroll L, Vegas AD, Gerdes Gyuricza I, Light C, Cao Y, Pan C, Kaczor-Urbanowicz KE, Shravah V, Anum D, Pellegrini M, Lee CF, Seldin MM, Rosenthal NA, Churchill GA, Attie AD, Parker B,b Lusis AJ. Elife. 12:e82619, 2023
Leveraging genetic diversity to identify small molecules that reverse mouse skeletal muscle insulin resistance. Masson SWC, Madsen S, Cooke KC, Potter M, Vegas AD, Carroll L, Thillainadesan S, Cutler HB, Walder KR, Cooney GJ, Morahan G, Stöckli J, James DE. Elife, 12:RP86961. 2023
Vascular cells improve functionality of human cardiac organoids. Voges HK, Foster SR, Reynolds L, Parker BL, Devilée L, Quaife-Ryan GA, Fortuna PRJ, Mathieson E, Fitzsimmons R, Lor M, Batho C, Reid J, Pocock M, Friedman CE, Mizikovsky D, Francois M, Palpant NJ, Needham EJ, Peralta M, Monte-Nieto GD, Jones LK, Smyth IM, Mehdiabadi NR, Bolk F, Janbandhu V, Yao E, Harvey RP, Chong JJH, Elliott DA, Stanley EG, Wiszniak S, Schwarz Q, James DE, Mills RJ, Porrello ER, Hudson JE. Cell Rep, 5:112322. 2023
Mitochondrial electron transport chain, ceramide and Coenzyme Q are linked in a pathway that drives insulin resistance in skeletal muscle. Diaz-Vegas A, Madsen S, Cooke KC, Carroll L, Khor JXY, Turner N, Lim XY, Astore MA, Morris J, Don A, Garfield A, Zarini S, Zemski Berry KA, Ryan A, Bergman BC, Brozinick JT, James DE, Burchfield JG. eLife12:RP87340. 2023
Human PIK3R1 mutations disrupt lymphocyte differentiation to cause activated PI3Kδ syndrome 2. Nguyen T, Lau A, Bier J, Cooke KC, Lenthall H, Ruiz-Diaz S, Avery DT, Brigden H, Zahra D, Sewell WA, Droney L, Okada S, Asano T, Abolhassani H, Chavoshzadeh Z, Abraham RS, Rajapakse N, Klee EW, Church JA, Williams A, Wong M, Burkhart C, Uzel G, Croucher DR, James DE, Ma CS, Brink R, Tangye SG, Deenick EK. J Exp Med, e20221020. 2023
Phosphoproteomics reveals rewiring of the insulin signaling network and multi-nodal defects in insulin resistance. Fazakerley DJ, van Gerwen J, Cooke KC, Duan X, Needham EJ, Díaz-Vegas A, Madsen S, Norris DM, Shun-Shion AS, Krycer JR, Burchfield JG, Yang P, Wade MR, Brozinick JT, James DE, Humphrey SJ. Nat Commun, 14(1):923. 2023
Deep Proteome Profiling of White Adipose Tissue Reveals Marked Conservation and Distinct Features Between Different Anatomical Depots. Madsen S, Nelson ME, Deshpande V, Humphrey SJ, Cooke KC, Howell A, Diaz-Vegas A, Burchfield JG, Stöckli J, James DE. Mol Cell Proteomics 22, 100508. 2023
2022
Systems-level analysis of insulin action in mouse strains provides insight into tissue- and pathway-specific interactions that drive insulin resistance. Nelson, M.E., Madsen, S., Cooke, K.C., Fritzen, A.M., Thorius, I.H., Masson, S.W.C., Carroll, L., Weiss, F.C., Seldin, M.M., Potter, M., Hocking, S.L., Fazakerley, D.F., Brandon, A.E., Thillainadesan, S., Senior, A.M., Cooney, G.J., Stockli, J., James, D.E. Cell Metabolism 34, 227-239, 2022
The role of mitochondrial reactive oxygen species in insulin resistance. Ayer A, Fazakerley DJ, James DE, Stocker R. Free Radic Biol Med 179, 339-362, 2022
Structural insights into Ras regulation by SIN1. Zheng Y, Ding L, Meng X, Potter M, Kearney AL, Zhang J, Sun J, James DE, Yang G, Zhou C. Proc Natl Acad Sci U S A 119, 2022
Personalized phosphoproteomics identifies functional signaling. Needham EJ, Hingst JR, Parker BL, Morrison KR, Yang G, Onslev J, Kristensen JM, Højlund K, Ling NXY, Oakhill JS, Richter EA, Kiens B, Petersen J, Pehmøller C, James DE, Wojtaszewski JFP, Humphrey SJ. Nat Biotechnol 40, 576-584, 2022
SILAC kinase screen identifies potential MASTL substrates. Marzec, K.A., Rogers, S., McCloy, R., Parker, B.L., James, D.E., Watkins, D.N., Burgess, A. Sci Rep. 12, 10568, 2022
Trafficking regulator of GLUT4-1 (TRARG1) is a GSK3 substrate. Duan, X., Norris, D.M., Humphrey, S.J., Yang, P., Cooke, K.C., Bultitude, W.P., Parker, B.L., Conway, O.J., Burchfield, J.G., Krycer, J.R., Brodsky, F.M., James, D.E., Fazakerley, D.J. Biochem J. 479, 1237-1256, 2022
A high-content endogenous GLUT4 trafficking assay reveals new aspects of adipocyte biology. Diaz-Vegas A, Norris D.M., Jall-Rogg S., Cooke K.C., Conway O.J., Shun-Shion A.S., Duan X., Potter M., van Gerwen J., Baird H.J., Humphrey S.J., James D.E., Fazakerley D.J., Burchfield J.G. Life Sci Alliance, 2022
Proteome-wide systems genetics identifies UFMylation as a regulator of skeletal muscle function. Molendijk J., Blazev R., Mills R.J., Ng Y.K., Watt K.I., Chau D., Gregorevic P., Crouch, P.J., Hilton, J.B.W., Lisowski, L., Zhang, P., Reue, K., Lusis, A.J., Hudson, J.E., James, D.E., Seldin, M.M., Parker, B.L. Elife 11, e82951, 2022
Reviews
The impact of weight cycling on health outcomes in animal models: A systematic review and meta-analysis. Thillainadesan S., Madsen S., James D.E., Hocking S.L.. Obesity Reviews 23, 2022
The role of mitochondrial reactive oxygen species in insulin resistance. Ayer, A., Fazakerley, D.J., James, D.E., Stocker, R. . Free Radic Biol Med. 179, 339-362, 2022
202-LB: Insulin Regulation of Lipolysis in Adipocytes. Jacqueline Stoeckli, Armella Zadoorian, Guang Yang, David E James. Diabetes 71 (Supplement_1), 2022
2021
Plasma bile acids more closely align with insulin resistance, visceral and hepatic adiposity than total adiposity. Bishay R.H., Tonks K.T., George J, Samocha-Bonet D, Meyerowitz-Katz G, Chisholm D.J., James D.E., Greenfield J.R. J Clin Endocrinol Metab 106, e1131-e1139, 2021
Defining the protein and lipid constituents of tubular recycling endosomes. Farmer T, Xie S, Naslavsky N, Stöckli J, James D.E, Caplan S. J Biol Chem 296, 100190, 2021
Proteomics analysis of adipose depots after intermittent fasting reveals visceral fat preservation mechanisms. Harney, D.J., Cielesh, M., Chu, R., Cooke, K.C., James, D.E., Stockli, J., and Larance, M. Cell Rep 34, 108804, 2021
Akt phosphorylates insulin receptor substrate to limit PI3K-mediated PIP3 synthesis. Kearney, A.L., Norris, D.M., Ghomlaghi, M., Kin Lok Wong, M., Humphrey, S.J., Carroll, L., Yang, G., Cooke, K.C., Yang, P., Geddes, T.A., Shin, S., Fazakerley, D. J., Nguyen, L. K., James, D. E., Burchfield, J. G.. Elife 10, 2021
PhosR enables processing and functional analysis of phosphoproteomic data. Kim, H.J., Kim, T., Hoffman, N.J., Xiao, D., James, D.E., Humphrey, S.J., and Yang, P. Cell Rep 34, 108771, 2021
A hierarchical approach to removal of unwanted variation for large-scale metabolomics data. Kim, T., Tang, O., Vernon, S.T., Kott, K.A., Koay, Y.C., Park, J., James, D.E., Grieve, S.M., Speed, T.P., Yang, P., Figtree, G. A., O'Sullivan, J. F., Yang, J. Y. H. Nat Commun 12, 4992, 2021
BET inhibition blocks inflammation-induced cardiac dysfunction and SARS-CoV-2 infection. Mills, R.J., Humphrey, S.J., Fortuna, P.R.J., Lor, M., Foster, S.R., Quaife-Ryan, G.A., Johnston, R.L., Dumenil, T., Bishop, C., Rudraraju, R., Rawle, D. J., Le, T., Zhao, W., Lee, L., Mackenzie-Kludas, C., Mehdiabadi, N. R., Halliday, C., Gilham, D., Fu, L., Nicholls, S. J., Johansson, J., Sweeney, M., Wong, N. C. W., Kulikowski, E., Sokolowski, K. A., Tse, B. W. C., Devilee, L., Voges, H. K., Reynolds, L. T., Krumeich, S., Mathieson, E., Abu-Bonsrah, D., Karavendzas, K., Griffen, B., Titmarsh, D., Elliott, D. A., McMahon, J., Suhrbier, A., Subbarao, K., Porrello, E. R., Smyth, M. J., Engwerda, C. R., MacDonald, K. P. A., Bald, T., James, D.E., Hudson, J. E. Cell 184, 2167-2182 e2122, 2021
Global phosphoproteomics reveals DYRK1A regulates CDK1 activity in glioblastoma cells. Recasens, A., Humphrey, S.J., Ellis, M., Hoque, M., Abbassi, R.H., Chen, B., Longworth, M., Needham, E.J., James, D.E., Johns, T.G., Day, B. W., Kassiou, M., Yang, P., Munoz, L. Cell Death Discov 7, 81, 2021
Dissecting the biology of mTORC1 beyond rapamycin. Yang, G., Francis, D., Krycer, J.R., Larance, M., Zhang, Z., Novotny, C.J., Diaz-Vegas, A., Shokat, K.M., and James, D.E. Sci Signal 14, eabe0161, 2021
Genetic screening reveals phospholipid metabolism as a key regulator of the biosynthesis of the redox-active lipid coenzyme Q. Ayer, A., Fazakerley, D.J., Suarna, C., Maghzal, G.J., Sheipouri, D., Lee, K.J., Bradley, M.C., Fernandez-Del-Rio, L., Tumanov, S., Kong, S.M., van der Veen, J. N., Yang, A., Ho, J. W. K., Clarke, S. G., James, D. E., Dawes, I. W., Vance, D. E., Clarke, C. F., Jacobs, R. L., Stocker, R. Redox Biol 46, 102127. 2021
Dynamic modelling of the PI3K/MTOR signalling network uncovers biphasic dependence of mTORC1 activity on the mTORC2 subunit SIN1. Ghomlaghi, M., Yang, G., Shin, S., James, D.E., and Nguyen, L.K. PLoS Comput Biol 17, e1008513. 2021
Genome wide analysis in Drosophila reveals diet by gene interactions and uncovers diet-responsive genes. Francis, D., Ghazanfar, S., Havula, E., Krycer,J.R, Senior, A., Minard, A.Y., Geddes, T., Weiss, F., Stöckli, J., Yang, J.Y. & James, D.E. G3 Genes, jkab171, 2021
Personalised phosphoproteomics identifies functional signalling. Needham, E.J., Hingst, J.R., Parker, B.L., Kaitlin R. Morrison, K.R., Yang, G., Onslev, J., Kristensen, J.M., Højlund, K., Ling, N.X.Y., Oakhill, J.S., Richter, E.A., Kiens, B., Petersen, J., Pehmøller, C., James, D.E., Wojtaszewski, J.F.P, Humphrey1, S.J. Nature Biotechnology. 40, 576-584. 2021
Nutritional reprogramming of mouse liver proteome is dampened by metformin, resveratrol, and rapamycin. David G Le Couteur, Samantha M Solon-Biet, Benjamin L Parker, Tamara Pulpitel, Amanda E Brandon, Nicholas J Hunt, Jibran A Wali, Rahul Gokarn, Alistair M Senior, Gregory J Cooney, David Raubenheimer, Victoria C Cogger, David E James, Stephen J Simpson. Cell Metabolism 33 (12), 2367-2379. e4, 2021
Proteomic pathways to metabolic disease and type 2 diabetes in the pancreatic islet. Belinda Yau, Sheyda Naghiloo, Alexis Diaz-Vegas, Austin V Carr, Julian Van Gerwen, Elise J Needham, Dillon Jevon, Sing-Young Chen, Kyle L Hoehn, Amanda E Brandon, Laurence Macia, Gregory J Cooney, Michael R Shortreed, Lloyd M Smith, Mark P Keller, Peter Thorn, Mark Larance, David E James, Sean J Humphrey, Melkam A Kebede, IScience 24 (10), vol 24. 103099, 2021
Bilirubin deficiency renders mice susceptible to hepatic steatosis in the absence of insulin resistance. Weiyu Chen, Sergey Tumanov, Daniel J Fazakerley, James Cantley, David E James, Louise L Dunn, Taqi Shaik, Cacang Suarna, Roland Stocker. Redox Biology 47, 102152, 2021
Signaling Heterogeneity is Defined by Pathway Architecture and Intercellular Variability in Protein Expression. Norris, D., Yang, P., Shin, S., Kearney, A., Kim, H., Geddes, T., Senior, A., Fazakerley, D., Nguyen, L., James, D., Burchfield, J. iScience, 24(2), 102118, 2021
Reviews
The aetiology and molecular landscape of insulin resistance. James, D.E., Stockli, J., and Birnbaum, M.J. Nat Rev Mol Cell Biol, 2021
A co-receptor that represses beta-cell insulin action. Burchfield, J.G., and James, D.E. Nat Metab 3, 126-127, 2021
Mike Mueckler (1953-2021) - the father of the mammalian SLC2 glucose transporter family. James, D.E., and Thorens, B. Am J Physiol Endocrinol Metab. 2021
2020
Kinetic Trans-omic Analysis Reveals Key Regulatory Mechanisms for Insulin-Regulated Glucose Metabolism in Adipocytes . Ohno S, Quek L.E., Krycer J.R., Yugi K., Hirayama A., Ikeda S., Shoji F., Suzuki K., Soga T., James D.E., Kuroda S. iScience,23(9):101479. 2020
Insulin signaling requires glucose to promote lipid anabolism in adipocytes. Krycer J.R., Quek L.E., Francis D., Zadoorian A., Weiss F.C., Cooke K.C., Nelson M.E., Diaz-Vegas A., Humphrey S.J., Scalzo R., Hirayama A., Ikeda S., Shoji F., Suzuki K., Huynh K., Giles C., Varney B., Nagarajan S.R., Hoy A.J., Soga T., Meikle P.J., Cooney G.J., Fazakerley D.J., James D.E. . J Biol Chem. 295(38):13250-13266. 2020
Dynamic (13)C Flux Analysis Captures the Reorganization of Adipocyte Glucose Metabolism in Response to Insulin. Quek, L.E., Krycer, J.R., Ohno, S., Yugi, K., Fazakerley, D.J., Scalzo, R., Elkington, S.D., Dai, Z., Hirayama, A., Ikeda, S., Shoji, F., Suzuki, K., Locasale, J.W., Soga, T., James, D.E. & Kuroda, S.. iScience 23, 100855, 2020.
Lactate production is a prioritized feature of adipocyte metabolism. Krycer, J.R., Quek, L.E., Francis, D., Fazakerley, D.J., Elkington, S.D., Diaz-Vegas, A., Cooke, K.C., Weiss, F.C., Duan, X., Kurdyukov, S., Zhou, P.X., Tambar, U.K., Hirayama, A., Ikeda, S., Kamei, Y., Soga, T., Cooney, G.J. & James, D.E. J. Biol. Chem. 295, 83-98, 2020.
Mitochondrial oxidants, but not respiration, are sensitive to glucose in adipocytes. Krycer, J.R., Elkington, S.D., Diaz-Vegas, A., Cooke, K.C., Burchfield, J.G., Fisher-Wellman, K.H., Cooney, G.J., Fazakerley, D.J. & James, D.E. J. Biol. Chem. 295, 99-110, 2020.
Growth Factor-Dependent and -Independent Activation of mTORC2. Trends Endocrinol. Knudsen, J.R., Fritzen, A.M., James, D.E., Jensen, T.E., Kleinert, M. & Richter, E.A. Metab. 31, 13-24, 2020.
Quantification of exercise-regulated ubiquitin signaling in human skeletal muscle identifies protein modification cross talk via NEDDylation. Parker, B.L., Kiens, B., Wojtaszewski, J.F.P., Richter, E.A. & James, D.E. FASEB J. 34, 5906-5916, 2020.
Phosphoproteomics reveals conserved exercise-stimulated signaling and AMPK regulation of store-operated calcium entry. Nelson, M.E., Parker, B.L., Burchfield, J.G., Hoffman, N.J., Needham, E.J., Cooke, K.C., Naim, T., Sylow, L., Ling, N.X., Francis, D., Norris, D.M., Chaudhuri, R., Oakhill, J.S., Richter, E.A., Lynch, G.S., Stockli, J. & James, D.E. EMBO J. 39, e104246, 2020.
PGC1alpha Controls Sucrose Taste Sensitization in Drosophila. Wang, Q.P., Lin, Y.Q., Lai, M.L., Su, Z., Oyston, L.J., Clark, T., Park, S.J., Khuong, T.M., Lau, M.T., Shenton, V., Shi, Y.C., James, D.E., Ja, W.W., Herzog, H., Simpson, S.J. & Neely, G.G. Cell Rep 31, 107480, 2020.
Core functional nodes and sex-specific pathways in human ischaemic and dilated cardiomyopathy. Li, M., Parker, B.L., Pearson, E., Hunter, B., Cao, J., Koay, Y.C., Guneratne, O., James, D.E., Yang, J., Lal, S. & O'Sullivan, J.F. Nat Commun 11, 2843, 2020.
2019
Phosphoproteomics of Acute Cell Stressors Targeting Exercise Signaling Networks Reveal Drug Interactions Regulating Protein Secretion. Needham, E.J., Humphrey, S.J., Cooke, K.C., Fazakerley, D.J., Duan, X., Parker, B.L. & James, D.E. Cell Rep 29, 1524-1538 e1526, 2019.
Insulin Tolerance Test under Anaesthesia to Measure Tissue-specific Insulin-stimulated Glucose Disposal. Fazakerley, D., Fritzen, A., Nelson, M., Thorius, I., Cooke, K., Humphrey, S., Cooney, G., James, DE. Bio-protocol. 2019 9(2), 1-13
ABHD15 regulates adipose tissue lipolysis and hepatic lipid accumulation. Stöckli J, Zadoorian A, Cooke KC, Deshpande V, Yau B, Herrmann G, Kebede MA, Humphrey SJ, James DE. Mol Metab. 2019 Jul;25:83-94. doi: 10.1016/j.molmet.2019.05.002.
Multi-omic Profiling Reveals Dynamics of the Phased Progression of Pluripotency. Yang P, Humphrey SJ, Cinghu S, Pathania R, Oldfield AJ, Kumar D, Perera D, Yang JYH, James DE, Mann M, Jothi R. Cell Syst. 2019 May 22;8(5):427-445.e10. doi: 10.1016/j.cels.2019.03.012.
Reduced insulin action in muscle of high fat diet rats over the diurnal cycle is not associated with defective insulin signaling. Small L, Brandon AE, Parker BL, Deshpande V, Samsudeen AF, Kowalski GM, Reznick J, Wilks DL, Preston E, Bruce CR, James DE, Turner N, Cooney GJ. Mol Metab. 2019 Jul;25:107-118. doi: 10.1016/j.molmet.2019.04.006
Targeting host metabolism by inhibition of acetyl-Coenzyme A carboxylase reduces flavivirus infection in mouse models. Jiménez de Oya N, Esler WP, Huard K, El-Kattan AF, Karamanlidis G, Blázquez AB, Ramos-Ibeas P, Escribano-Romero E, Louloudes-Lázaro A, Casas J, Sobrino F, Hoehn K, James DE, Gutiérrez-Adán A, Saiz JC, Martín-Acebes MA. Emerg Microbes Infect. 2019;8(1):624-636. doi: 10.1080/22221751.2019.1604084.
Drug Screening in Human PSC-Cardiac Organoids Identifies Pro-proliferative Compounds Acting via the Mevalonate Pathway. Mills RJ, Parker BL, Quaife-Ryan GA, Voges HK, Needham EJ, Bornot A, Ding M, Andersson H, Polla M, Elliott DA, Drowley L, Clausen M, Plowright AT, Barrett IP, Wang QD, James DE, Porrello ER, Hudson JE. Cell Stem Cell. 2019 Jun 6;24(6):895-907.e6. doi: 10.1016/j.stem.2019.03.009.
Proteomic Analysis of Human Plasma during Intermittent Fasting. Harney DJ, Hutchison AT, Hatchwell L, Humphrey SJ, James DE, Hocking S, Heilbronn LK, Larance M. J Proteome Res. 2019 May 3;18(5):2228-2240. doi: 10.1021/acs.jproteome.9b00090.
An integrative systems genetic analysis of mammalian lipid metabolism. Parker BL, Calkin AC, Seldin MM, Keating MF, Tarling EJ, Yang P, Moody SC, Liu Y, Zerenturk EJ, Needham EJ, Miller ML, Clifford BL, Morand P, Watt MJ, Meex RCR, Peng KY, Lee R, Jayawardana K, Pan C, Mellett NA, Weir JM, Lazarus R, Lusis AJ, Meikle PJ, James DE, de Aguiar Vallim TQ, Drew BG. Nature. 2019 Mar;567(7747):187-193. doi: 10.1038/s41586-019-0984-y.
Illuminating the dark phosphoproteome. Needham EJ, Parker BL, Burykin T, James DE, Humphrey SJ. Sci Signal. 2019 Jan 22;12(565). pii: eaau8645. doi: 10.1126/scisignal.aau8645.
RagC phosphorylation autoregulates mTOR complex 1. Yang G, Humphrey SJ, Murashige DS, Francis D, Wang QP, Cooke KC, Neely G, James DE. EMBO J. 2019 Feb 1;38(3). pii: e99548. doi: 10.15252/embj.201899548.
Development of a human skeletal micro muscle platform with pacing capabilities. Mills RJ, Parker BL, Monnot P, Needham EJ, Vivien CJ, Ferguson C, Parton RG, James DE, Porrello ER, Hudson JE. Biomaterials. 2019 Apr;198:217-227. doi.org: 10.1016/j.biomaterials.2018.11.030
Disruption of beta cell acetyl-CoA carboxylase-1 in mice impairs insulin secretion and beta cell mass. Cantley J, Davenport A, Vetterli L, Nemes NJ, Whitworth PT, Boslem E, Thai LM, Mellett N, Meikle PJ, Hoehn KL, James DE, Biden TJ. Diabetologia. 2019 Jan;62(1):99-111. doi: 10.1007/s00125-018-4743-7.
Protein Kinase C Epsilon Deletion in Adipose Tissue, but Not in Liver, Improves Glucose Tolerance. Brandon AE, Liao BM, Diakanastasis B, Parker BL, Raddatz K, McManus SA, O'Reilly L, Kimber E, van der Kraan AG, Hancock D, Henstridge DC, Meikle PJ, Cooney GJ, James DE, Reibe S, Febbraio MA, Biden TJ, Schmitz-Peiffer C. Cell Metabolism 2019 Jan8;29(1):183-191.e7, 2019
Novel Regulation of Cholesterol Metabolism Using a Systems Biology Approach. Benjamin L Parker, Thomas Q VALLIM, Marcus M Seldin, Michael F Keating, Elizabeth J Tarling, Eser J Zerenturk, Sarah C Moody, Yingying Liu, Calvin Pan, Peter J Meikle, Aldons J Lusis, David E James, Brian G Drew, Anna C Calki. Arteriosclerosis, Thrombosis, and Vascular Biology 39 (Suppl_1), A343-A343, 2019
Global redox proteome and phosphoproteome analysis reveals redox switch in Akt. Su, Z., Burchfield, J., Yang, P., Humphrey, S., Yang, G., Francis, D., Yasmin, S., Shin, S., Norris, D., Kearney, A., Astore, M., Scavuzzo, J., Wang, Q., Parker, B., Neely, G., Vafaee, F., Chiu, J., Yeo, R., Hogg, P., Fazakerley, D., Kuyucak, S., James, D., et al. Nature Communications, 10(1), 1-18, 2019
Serine 474 phosphorylation is essential for maximal Akt2 kinase activity in adipocytes. Kearney, A., Cooke, K., Norris, D., Zadoorian, A., Krycer, J., Fazakerley, D., Burchfield, J., James, D. Journal of Biological Chemistry, 294(45), 16729-16739, 2019
Small-protein enrichment assay enables the rapid, unbiased analysis of over 100 low abundance factors from human plasma. Harney, D., Hutchison, A., Su, Z., Hatchwell, L., Heilbronn, L., Hocking, S., James, D., Larance, M. (2019). Molecular and Cellular Proteomics, 18(9), 1899-1915, 2019
A modified gas-trapping method for high-throughput metabolic experiments in Drosophila melanogaster. Francis, D., Krycer, J., Cooney, G., James, D. (2019). BioTechniques, 67(3), 123-125, 2019
An integrative systems genetic analysis of mammalian lipid metabolism. Parker, B., Calkin, A., Seldin, M., Keating, M., Tarling, E., Yang, P., Moody, S., Liu, Y., Zerenturk, E., Needham, E., James, D., et al. Nature, 567(7747), 187-193, 2019
Muscle and adipose tissue insulin resistance: malady without mechanism? Fazakerley, D., Krycer, J., Kearney, A., Hocking, S., James, D. Journal of Lipid Research, 60(10), 1720-1732, 2019
Phosphoproteomics reveals conserved exercise-stimulated signaling and AMPK regulation of store-operated calcium entry. Nelson, M., Parker, B., Burchfield, J., Hoffman, N., Needham, E., Cooke, K., Naim, T., Sylow, L., Ling, N., Francis, D., Norris, D., Chaudhuri, R., Stoeckli, J., James, D., et al (2019). EMBO Journal, 38(24), 1-20, 2019
Rate-oriented trans-omics: integration of multiple omic data on the basis of reaction kinetics. Yugi, K., Ohno, S., Krycer, J., James, D., Kuroda, S. (2019). Current Opinion in Systems Biology, 15, 109-120, 2019
2018
Exercise-induced molecular mechanisms promoting glycogen supercompensation in human skeletal muscle. Hingst JR, Bruhn L, Hansen MB, Rosschou MF, Birk JB, Fentz J, Foretz M, Viollet B, Sakamoto K, Færgeman NJ, Havelund JF, Parker BL, James DE, Kiens B, Richter EA, Jensen J, Wojtaszewski JFP. Mol Metab. 2018 Oct;16:24-34. doi: 10.1016/j.molmet.2018.07.001.
High-throughput and high-sensitivity phosphoproteomics with the EasyPhos platform. Humphrey SJ, Karayel O, James DE, Mann M. Nat Protoc. 2018 Sep;13(9):1897-1916. doi: 10.1038/s41596-018-0014-9.
Acute activation of pyruvate dehydrogenase increases glucose oxidation in muscle without changing glucose uptake. Small L, Brandon AE, Quek LE, Krycer JR, James DE, Turner N, Cooney GJ. Am J Physiol Endocrinol Metab. 2018 Aug 1;315(2):E258-E266. doi: 10.1152/ajpendo.00386.2017
MASTL overexpression promotes chromosome instability and metastasis in breast cancer. Rogers S, McCloy RA, Parker BL, Gallego-Ortega D, Law AMK, Chin VT, Conway JRW, Fey D, Millar EKA, O'Toole S, Deng N, Swarbrick A, Chastain PD, Cesare A, Timpson P, Caldon CE, Croucher DR1, James DE, Watkins DN, Burgess A. Oncogene. 2018 Aug;37(33):4518-4533. doi: 10.1038/s41388-018-0295-z
Muscle and adipose tissue insulin resistance: malady without mechanism? Fazakerley DJ, Krycer JR, Kearney AL, Hocking SL, James DE. J Lipid Res. 2018 Jul 27. pii: jlr.R087510. doi: 10.1194/jlr.R087510.
Membrane Topology of Trafficking Regulator of GLUT4 1 (TRARG1). Duan X, Krycer JR, Cooke KC, Yang G, James DE, Fazakerley DJ. Biochemistry. 2018 Jul 3;57(26):3606-3615. doi: 10.1021/acs.biochem.8b00361
Quantitative proteomic characterization of cellular pathways associated with altered insulin sensitivity in skeletal muscle following high-fat diet feeding and exercise training. Kleinert M, Parker BL, Jensen TE, Raun SH, Pham P, Han X, James DE, Richter EA, Sylow L. Sci Rep. 2018 Jul 16;8(1):10723. doi: 10.1038/s41598-018-28540-5.
Tankyrase modulates insulin sensitivity in skeletal muscle cells by regulating the stability of GLUT4 vesicle proteins. Su Z, Deshpande V, James DE, Stöckli J. J Biol Chem. 2018 Jun 1;293(22):8578-8587. doi: 10.1074/jbc.RA117.001058.
Mitochondrial oxidative stress causes insulin resistance without disrupting oxidative phosphorylation. Fazakerley DJ, Minard AY, Krycer JR, Thomas KC, Stöckli J, Harney DJ, Burchfield JG, Maghzal GJ, Caldwell ST, Hartley RC, Stocker R, Murphy MP, James DE. J Biol Chem. 2018 May 11;293(19):7315-7328. doi: 10.1074/jbc.RA117.001254
Mitochondrial CoQ deficiency is a common driver of mitochondrial oxidants and insulin resistance. Fazakerley DJ, Chaudhuri R, Yang P, Maghzal GJ, Thomas KC, Krycer JR, Humphrey SJ, Parker BL, Fisher-Wellman KH, Meoli CC, Hoffman NJ, Diskin C, Burchfield JG, Cowley MJ, Kaplan W, Modrusan Z, Kolumam G, Yang JY, Chen DL, Samocha-Bonet D, Greenfield JR, Hoehn KL, Stocker R, James DE. Elife. 2018 Feb 6;7. pii: e32111. doi: 10.7554/eLife.32111
The transcriptional response to oxidative stress is part of, but not sufficient for, insulin resistance in adipocytes. Chaudhuri, R., Krycer, J.R., Fazakerley, DJ., Fisher-Wellman, KH, Su, Z, Hoehn, KL, Yang, JYH, Kuncic, Z, Vafaee, F, James, DE. Sci Rep 8. 2018 Jan28;(8):1774. doi:10.1038/s41598-018-20104-x
Extracellular Vesicles Provide a Means for Tissue Crosstalk during Exercise. Whitham M, Parker BL, Friedrichsen M, Hingst JR, Hjorth M, Hughes WE, Egan CL, Cron L, Watt KI, Kuchel RP, Jayasooriah N, Estevez E, Petzold T, Suter CM, Gregorevic P, Kiens B, Richter EA, James DE, Wojtaszewski JFP, Febbraio MA. Cell Metab. 2018 Jan 9;27(1):237-251.e4. doi: 10.1016/j.cmet.2017.12.001.
A gas trapping method for high-throughput metabolic experiments. Krycer JR, Diskin C, Nelson ME, Zeng XY, Fazakerley DJ, James DE. Biotechniques. 2018 Jan 1;64(1):27-29. doi: 10.2144/000114629
2017
High dietary fat and sucrose results in an extensive and time-dependent deterioration in health of multiple physiological systems in mice. Burchfield JG, Kebede MA, Meoli CC, Stöckli J, Whitworth PT, Wright AL, Hoffman NJ, Minard AY, Ma X, Krycer JR, Nelson ME, Tan SX, Yau B, Thomas K, Wee NKY, Khor EC, Enriquez RF, Vissel B, Biden TJ, Baldock PA, Hoehn KL, Cantley J, Cooney GJ, James DE, Fazakerley DJ. J Biol Chem. 2018 Apr 13;293(15):5731-5745. doi: 10.1074/jbc.RA117.000808.
The Geometric Framework for Nutrition as a tool in precision medicine. Simpson, SJ, Le Couteur, DG, James, DE, George, J, Gunton, JE, Solon-Biet, SM & Raubenheimer, D. Nutr Healthy Aging. 2017 Dec7;4(3): 217–226. doi: 10.3233/NHA-170027
Dynamic Metabolomics Reveals that Insulin Primes the Adipocyte for Glucose Metabolism. Krycer JR, Yugi K, Hirayama A, Fazakerley DJ, Quek LE, Scalzo R, Ohno S, Hodson MP, Ikeda S, Shoji F, Suzuki K, Domanova W, Parker BL, Nelson ME, Humphrey SJ, Turner N, Hoehn KL, Cooney GJ, Soga T, Kuroda S, James DE. Cell Rep. 2017 Dec 19;21(12):3536-3547. doi: 10.1016/j.celrep.2017.11.085.
Glucose Transport: Methods for Interrogating GLUT4 Trafficking in Adipocytes. Norris DM, Geddes TA, James DE, Fazakerley DJ, Burchfield JG. Methods Mol Biol. 2018;1713:193-215. doi: 10.1007/978-1-4939-7507-5_15.
Metabolomic analysis of insulin resistance across different mouse strains and diets. Stöckli J, Fisher-Wellman KH, Chaudhuri R, Zeng XY, Fazakerley DJ, Meoli CC, Thomas KC, Hoffman NJ, Mangiafico SP, Xirouchaki CE, Yang CH, Ilkayeva O, Wong K, Cooney GJ, Andrikopoulos S, Muoio DM, James DE. J Biol Chem. 2017 Nov 24;292(47):19135-19145. doi: 10.1074/jbc.M117.818351. Epub 2017 Oct 5.
Multiplexed Temporal Quantification of the Exercise-regulated Plasma Peptidome. Parker BL, Burchfield JG, Clayton D, Geddes TA, Payne RJ, Kiens B, Wojtaszewski JFP, Richter EA, James DE. Mol Cell Proteomics. 2017 Dec;16(12):2055-2068. doi: 10.1074/mcp.RA117.000020. Epub 2017 Oct 5.
Functional screening in human cardiac organoids reveals a metabolic mechanism for cardiomyocyte cell cycle arrest. Mills RJ, Titmarsh DM, Koenig X, Parker BL, Ryall JG, Quaife-Ryan GA, Voges HK, Hodson MP, Ferguson C, Drowley L, Plowright AT, Needham EJ, Wang QD, Gregorevic P, Xin M, Thomas WG, Parton RG, Nielsen LK, Launikonis BS, James DE, Elliott DA, Porrello ER, Hudson JE. Proc Natl Acad Sci U S A. 2017 Oct 3;114(40):E8372-E8381. doi: 10.1073/pnas.1707316114. Epub 2017 Sep 15.
An improved Akt reporter reveals intra- and inter-cellular heterogeneity and oscillations in signal transduction. Norris DM, Yang P, Krycer JR, Fazakerley DJ, James DE, Burchfield JG. J Cell Sci. 2017 Aug 15;130(16):2757-2766. doi: 10.1242/jcs.205369. Epub 2017 Jun 29.
Bicarbonate alters cellular responses in respiration assays. Krycer JR, Fisher-Wellman KH, Fazakerley DJ, Muoio DM, James DE. Biochem Biophys Res Commun. 2017 Aug 5;489(4):399-403. doi: 10.1016/j.bbrc.2017.05.151. Epub 2017 May 27.
Mammalian target of rapamycin complex 2 regulates muscle glucose uptake during exercise in mice. Kleinert M, Parker BL, Fritzen AM, Knudsen JR, Jensen TE, Kjøbsted R, Sylow L, Ruegg M, James DE, Richter EA. J Physiol. 2017 Jul 15;595(14):4845-4855. doi: 10.1113/JP274203. Epub 2017 Jun 11.
Inhibition of hepatic lipogenesis enhances liver tumorigenesis by increasing antioxidant defence and promoting cell survival. Nelson ME, Lahiri S, Chow JD, Byrne FL, Hargett SR, Breen DS, Olzomer EM, Wu LE, Cooney GJ, Turner N, James DE, Slack-Davis JK, Lackner C, Caldwell SH, Hoehn KL. Nat Commun. 2017 Mar 14;8:14689. doi: 10.1038/ncomms14689.
The amino acid transporter, SLC1A3, is plasma membrane-localised in adipocytes and its activity is insensitive to insulin. Krycer JR, Fazakerley DJ, Cater RJ, C Thomas K, Naghiloo S, Burchfield JG, Humphrey SJ, Vandenberg RJ, Ryan RM, James DE. FEBS Lett. 2017 Jan;591(2):322-330. doi: 10.1002/1873-3468.12549. Epub 2017 Jan 13.
2016
A novel Rab10-EHBP1-EHD2 complex essential for the autophagic engulfment of lipid droplets. Li Z, Schulze RJ, Weller SG, Krueger EW, Schott MB, Zhang X, Casey CA, Liu J, Stöckli J, James DE, McNiven MA. Sci Adv. 2016 Dec 16;2(12):e1601470. doi: 10.1126/sciadv.1601470. eCollection 2016 Dec.
Hyperactivation of the Insulin Signaling Pathway Improves Intracellular Proteostasis by Coordinately Up-regulating the Proteostatic Machinery in Adipocytes. Minard AY, Wong MK, Chaudhuri R, Tan SX, Humphrey SJ, Parker BL, Yang JY, Laybutt DR, Cooney GJ, Coster AC, Stöckli J, James DE. J Biol Chem. 2016 Dec 2;291(49):25629-25640. Epub 2016 Oct 13.
Defining the Nutritional and Metabolic Context of FGF21 Using the Geometric Framework. Solon-Biet SM, Cogger VC, Pulpitel T, Heblinski M, Wahl D, McMahon AC, Warren A, Durrant-Whyte J, Walters KA, Krycer JR, Ponton F, Gokarn R, Wali JA, Ruohonen K, Conigrave AD, James DE, Raubenheimer D, Morrison CD, Le Couteur DG, Simpson SJ. Cell Metab. 2016 Oct 11;24(4):555-565. doi: 10.1016/j.cmet.2016.09.001. Epub 2016 Sep 29.
mTORC1 Is a Major Regulatory Node in the FGF21 Signaling Network in Adipocytes. Minard AY, Tan SX, Yang P, Fazakerley DJ, Domanova W, Parker BL, Humphrey SJ, Jothi R, Stöckli J, James DE. Cell Rep. 2016 Sep 27;17(1):29-36. doi: 10.1016/j.celrep.2016.08.086.
14-3-3ζ regulates the mitochondrial respiratory reserve linked to platelet phosphatidylserine exposure and procoagulant function. Schoenwaelder SM, Darbousset R, Cranmer SL, Ramshaw HS, Orive SL, Sturgeon S, Yuan Y, Yao Y, Krycer JR, Woodcock J, Maclean J, Pitson S, Zheng Z, Henstridge DC, van der Wal D, Gardiner EE, Berndt MC, Andrews RK, James DE, Lopez AF, Jackson SP. Nat Commun. 2016 Sep 27;7:12862. doi: 10.1038/ncomms12862. Erratum in: Nat Commun. 2017 Aug 30;8:16125.
mTORC2 and AMPK differentially regulate muscle triglyceride content via Perilipin 3. Kleinert M, Parker BL, Chaudhuri R, Fazakerley DJ, Serup A, Thomas KC, Krycer JR, Sylow L, Fritzen AM, Hoffman NJ, Jeppesen J, Schjerling P, Ruegg MA, Kiens B, James DE, Richter EA. Mol Metab. 2016 Jun 22;5(8):646-55. doi: 10.1016/j.molmet.2016.06.007. eCollection 2016 Aug.
Integrated expression analysis of muscle hypertrophy identifies Asb2 as a negative regulator of muscle mass. Davey JR, Watt KI, Parker BL, Chaudhuri R, Ryall JG, Cunningham L, Qian H, Sartorelli V, Sandri M, Chamberlain J, James DE, Gregorevic P. JCI Insight. 2016 Apr 21;1(5). pii: e85477.
KinasePA: Phosphoproteomics data annotation using hypothesis driven kinase perturbation analysis. Yang P, Patrick E, Humphrey SJ, Ghazanfar S, James DE, Jothi R, Yang JY. Proteomics. 2016 Jul;16(13):1868-71. doi: 10.1002/pmic.201600068. Epub 2016 May 27.
Skeletal muscle and plasma lipidomic signatures of insulin resistance and overweight/obesity in humans. Tonks KT, Coster AC, Christopher MJ, Chaudhuri R, Xu A, Gagnon-Bartsch J, Chisholm DJ, James DE, Meikle PJ, Greenfield JR, Samocha-Bonet D. Obesity (Silver Spring). 2016 Apr;24(4):908-16. doi: 10.1002/oby.21448. Epub 2016 Feb 24.
