Comprehensive multiscale analysis of lactate metabolic dynamics in vitro and in vivo using highly responsive biosensors

Aoxue Wang, Yejun Zou, Shuning Liu, Xiuze Zhang, Ting Li, Lijuan Zhang, Ruwen Wang, Yale Xia, Xie Li, Zhuo Zhang, Tiemin Liu, Zhenyu Ju, Ru Wang, Joseph Loscalzo, Yi Yang, Yuzheng Zhao

Published: 2024-02-02 DOI: 10.1038/s41596-023-00948-y

fluorescence imaging

lactate metabolism

FiLa biosensors

multiscale analysis

bioenergetic flux

AI 解读

Deoxyfluorination of phenols for chemoselective18F-labeling of peptides

Stable isotope tracing to assess tumor metabolism in vivo

Measuring DNA modifications with the comet assay: a compendium of protocols

Detect-seq, a chemical labeling and biotin pull-down approach for the unbiased and genome-wide off-target evaluation of programmable cytosine base editors

A systems-level mass spectrometry-based technique for accurate and sensitive quantification of the RNA cap epitranscriptome

Spooling electrochemiluminescence spectroscopy: development, applications and beyond

Chronic, cortex-wide imaging of specific cell populations during behavior

Chromatin accessibility profiling by ATAC-seq

Global analysis of RNA-binding protein dynamics by comparative and enhanced RNA interactome capture

Pooled genetic perturbation screens with image-based phenotypes

查看全部

Sections

Figures

References

Introduction
Materials
Procedure
Troubleshooting
Timing
Anticipated results
Acknowledgements

Harjes, U. Metabolism: more lactate, please. Nat. Rev. Cancer 17, 707 (2017).
Vander Heiden, M. G., Cantley, L. C. & Thompson, C. B. Understanding the Warburg effect: the metabolic requirements of cell proliferation. Science 324, 1029–1033 (2009).
Rabinowitz, J. D. & Enerbäck, S. Lactate: the ugly duckling of energy metabolism. Nat. Metab. 2, 566–571 (2020).
Martinez-Reyes, I. & Chandel, N. S. Waste not, want not: lactate oxidation fuels the TCA cycle. Cell Metab. 26, 803–804 (2017).
Hui, S. et al. Glucose feeds the TCA cycle via circulating lactate. Nature 551, 115–118 (2017).
Zhang, W. et al. Lactate is a natural suppressor of RLR signaling by targeting MAVS. Cell 178, 176–189 (2019).
Daw, C. C. et al. Lactate elicits ER–mitochondrial Mg2+ dynamics to integrate cellular metabolism. Cell 183, 474–489 (2020).
Zhang, D. et al. Metabolic regulation of gene expression by histone lactylation. Nature 574, 575–580 (2019).
Brooks, G. A. The science and translation of lactate shuttle theory. Cell Metab. 27, 757–785 (2018).
Boussouar, F. & Benahmed, M. Lactate and energy metabolism in male germ cells. Trends Endocrinol. Metab. 15, 345–350 (2004).
Oginuma, M. et al. A gradient of glycolytic activity coordinates FGF and Wnt signaling during elongation of the body axis in amniote embryos. Dev. Cell 40, 342–353 (2017).
Du, J. et al. A small-molecule cocktail promotes mammalian cardiomyocyte proliferation and heart regeneration. Cell Stem Cell 29, 545–558 (2022).
Velentzas, P. D. et al. The proton-coupled monocarboxylate transporter hermes is necessary for autophagy during cell death. Dev. Cell 47, 281–293 (2018).
Jia, M. et al. ULK1-mediated metabolic reprogramming regulates Vps34 lipid kinase activity by its lactylation. Sci. Adv. 9, eadg4993 (2023).
Lee, D. C. et al. A lactate-induced response to hypoxia. Cell 161, 595–609 (2015).
Torrini, C. et al. Lactate is an epigenetic metabolite that drives survival in model systems of glioblastoma. Mol. Cell 82, 3061–3076 (2022).
Scheiman, J. et al. Meta-omics analysis of elite athletes identifies a performance-enhancing microbe that functions via lactate metabolism. Nat. Med. 25, 1104–1109 (2019).
Zeni, A. I., Hoffman, M. D. & Clifford, P. S. Energy expenditure with indoor exercise machines. J. Am. Med. Assoc. 275, 1424–1427 (1996).
Marin, E. et al. Human tolerogenic dendritic cells regulate immune responses through lactate synthesis. Cell Metab. 30, 1075–1090 (2019).
Xu, K. et al. Glycolysis fuels phosphoinositide 3-kinase signaling to bolster T cell immunity. Science 371, 405–410 (2021).
Suzuki, A. et al. Astrocyte–neuron lactate transport is required for long-term memory formation. Cell 144, 810–823 (2011).
Magistretti, P. J. & Allaman, I. Lactate in the brain: from metabolic end-product to signalling molecule. Nat. Rev. Neurosci. 19, 235–249 (2018).
Zeng, X. et al. Gut bacterial nutrient preferences quantified in vivo. Cell 185, 3441–3456 (2022).
Iatsenko, I., Boquete, J. P. & Lemaitre, B. Microbiota-derived lactate activates production of reactive oxygen species by the intestinal NADPH oxidase Nox and shortens Drosophila lifespan. Immunity 49, 929–942 (2018).
Dou, X. et al. PDK4-dependent hypercatabolism and lactate production of senescent cells promotes cancer malignancy. Nat. Metab. 5, 1887–1010 (2023).
Lund, J., Clemmensen, C. & Schwartz, T. W. Outrunning obesity with Lac-Phe? Cell Metab. 34, 1085–1087 (2022).
Li, V. L. et al. An exercise-inducible metabolite that suppresses feeding and obesity. Nature 606, 785–790 (2022).
Lin, Y. et al. Lactate is a key mediator that links obesity to insulin resistance via modulating cytokine production from adipose tissue. Diabetes 71, 637–652 (2022).
Watson, M. J. et al. Metabolic support of tumour-infiltrating regulatory T cells by lactic acid. Nature 591, 645–651 (2021).
Martinez-Reyes, I. & Chandel, N. S. Cancer metabolism: looking forward. Nat. Rev. Cancer 21, 669–680 (2021).
Wang, Y. et al. Saturation of the mitochondrial NADH shuttles drives aerobic glycolysis in proliferating cells. Mol. Cell 82, 3270–3283 (2022).
Gomez, H. & Kellum, J. A. Lactate in sepsis. J. Am. Med. Assoc. 313, 194–195 (2015).
Immke, D. C. & McCleskey, E. W. Lactate enhances the acid-sensing Na+ channel on ischemia-sensing neurons. Nat. Neurosci. 4, 869–870 (2001).
Zhang, J. et al. Endothelial lactate controls muscle regeneration from ischemia by inducing M2-like macrophage polarization. Cell Metab. 31, 1136–1153 (2020).
Cluntun, A. A. et al. The pyruvate–lactate axis modulates cardiac hypertrophy and heart failure. Cell Metab. 33, 629–648 (2021).
Pan, R. Y. et al. Positive feedback regulation of microglial glucose metabolism by histone H4 lysine 12 lactylation in Alzheimer’s disease. Cell Metab. 34, 634–648 (2022).
Glancy, B. et al. Mitochondrial lactate metabolism: history and implications for exercise and disease. J. Physiol. 599, 863–888 (2021).
Wan, N. et al. Cyclic immonium ion of lactyllysine reveals widespread lactylation in the human proteome. Nat. Methods 19, 854–864 (2022).
Li, X. et al. Ultrasensitive sensors reveal the spatiotemporal landscape of lactate metabolism in physiology and disease. Cell Metab. 35, 200–211 (2023).
Kraut, J. A. & Madias, N. E. Lactic acidosis. N. Engl. J. Med. 371, 2309–2319 (2014).
van der Windt, G. J. W., Chang, C. H. & Pearce, E. L. Measuring bioenergetics in T cells using a seahorse extracellular flux analyzer. Curr. Prot. Immunol. 113, 16B.11–16B.14 (2016).
Choe, M. & Titov, D. V. Genetically encoded tools for measuring and manipulating metabolism. Nat. Chem. Biol. 18, 451–460 (2022).
Zou, Y. et al. Analysis of redox landscapes and dynamics in living cells and in vivo using genetically encoded fluorescent sensors. Nat. Protoc. 13, 2362–2386 (2018).
Zhang, Z., Cheng, X., Zhao, Y. & Yang, Y. Lighting up live-cell and in vivo central carbon metabolism with genetically encoded fluorescent sensors. Annu. Rev. Anal. Chem. 13, 293–314 (2020).
Zhao, Y. et al. In vivo monitoring of cellular energy metabolism using SoNar, a highly responsive sensor for NAD+/NADH redox state. Nat. Protoc. 11, 1345–1359 (2016).
Zhao, Y. & Yang, Y. Profiling metabolic states with genetically encoded fluorescent biosensors for NADH. Curr. Opin. Biotechnol. 31, 86–92 (2015).
Zhao, Y. et al. Genetically encoded fluorescent sensors for intracellular NADH detection. Cell Metab. 14, 555–566 (2011).
Zhao, Y. et al. SoNar, a highly responsive NAD+/NADH sensor, allows high-throughput metabolic screening of anti-tumor agents. Cell Metab. 21, 777–789 (2015).
Tao, R. et al. Genetically encoded fluorescent sensors reveal dynamic regulation of NADPH metabolism. Nat. Methods 14, 720–728 (2017).
Zou, Y. et al. Illuminating NAD+ metabolism in live cells and in vivo using a genetically encoded fluorescent sensor. Dev. Cell 53, 240–252 (2020).
San Martin, A. et al. A genetically encoded FRET lactate sensor and its use to detect the Warburg effect in single cancer cells. PloS ONE 8, e57712 (2013).
Harada, K. et al. Green fluorescent protein-based lactate and pyruvate indicators suitable for biochemical assays and live cell imaging. Sci. Rep. 10, 19562 (2020).
Nasu, Y. et al. A genetically encoded fluorescent biosensor for extracellular l-lactate. Nat. Commun. 12, 7058 (2021).
Bekdash, R. et al. GEM-IL: a highly responsive fluorescent lactate indicator. Cell Rep. Methods 1, 100092 (2021).
Koveal, D. et al. A high-throughput multiparameter screen for accelerated development and optimization of soluble genetically encoded fluorescent biosensors. Nat. Commun. 13, 2919 (2022).
Aburto, C. et al. Single-fluorophore indicator to explore cellular and subcellular lactate dynamics. ACS Sens. 7, 3278–3286 (2022).
Aguilera, L. et al. Dual role of LldR in regulation of the lldPRD operon, involved in l-lactate metabolism in Escherichia coli. J. Bacteriol. 190, 2997–3005 (2008).
Li, Z. & Ai, H. W. Illuminating lactate in cells, mice, and patient samples. Cell Metab. 35, 5–7 (2023).
Wishart, D. S. et al. HMDB 5.0: the human metabolome database for 2022. Nucleic Acids Res. 50, D622–d631 (2022).
Chen, W. W., Freinkman, E., Wang, T., Birsoy, K. & Sabatini, D. M. Absolute quantification of matrix metabolites reveals the dynamics of mitochondrial metabolism. Cell 166, 1324–1337.e1311 (2016).
Zhao, Y. et al. An expanded palette of genetically encoded Ca2+ indicators. Science 333, 1888–1891 (2011).
Wiederkehr, A. & Demaurex, N. Illuminating redox biology using NADH- and NADPH-specific sensors. Nat. Methods 14, 671–672 (2017).
Gu, W. et al. Glycolytic metabolism plays a functional role in regulating human pluripotent stem cell state. Cell Stem Cell 19, 476–490 (2016).
Hernández, G. et al. Effect of a resuscitation strategy targeting peripheral perfusion status vs serum lactate levels on 28-day mortality among patients with septic shock: the ANDROMEDA-SHOCK randomized clinical trial. J. Am. Med. Assoc. 321, 654–664 (2019).
Larsen, T. Fluorometric determination of d-lactate in biological fluids. Anal. Biochem. 539, 152–157 (2017).
Belousov, V. V. et al. Genetically encoded fluorescent indicator for intracellular hydrogen peroxide. Nat. Methods 3, 281–286 (2006).
Berg, J., Hung, Y. P. & Yellen, G. A genetically encoded fluorescent reporter of ATP:ADP ratio. Nat. Methods 6, 161–166 (2009).
Tantama, M., Hung, Y. P. & Yellen, G. Imaging intracellular pH in live cells with a genetically encoded red fluorescent protein sensor. J. Am. Chem. Soc. 133, 10034–10037 (2011).
Xue, S. et al. A synthetic-biology-inspired therapeutic strategy for targeting and treating hepatogenous diabetes. Mol. Ther. 25, 443–455 (2017).
Zhou, Y. et al. A small and highly sensitive red/far-red optogenetic switch for applications in mammals. Nat. Biotechnol. 40, 262–272 (2022).
Wu, Z., Asokan, A. & Samulski, R. J. Adeno-associated virus serotypes: vector toolkit for human gene therapy. Mol. Ther. 14, 316–327 (2006).
Fripont, S., Marneffe, C., Marino, M., Rincon, M. Y. & Holt, M. G. Production, purification, and quality control for adeno-associated virus-based vectors. J. Vis. Exp. https://doi.org/10.3791/58960 (2019).
Gutscher, M. et al. Real-time imaging of the intracellular glutathione redox potential. Nat. Methods 5, 553–559 (2008).

Comprehensive multiscale analysis of lactate metabolic dynamics in vitro and in vivo using highly responsive biosensors

Supplementary information

推荐阅读