Professional Affiliations and Activities

  • Member, ASMS (2011 - Present)


All Publications

  • Succinate and its G-protein-coupled receptor stimulates osteoclastogenesis. Nature communications Guo, Y., Xie, C., Li, X., Yang, J., Yu, T., Zhang, R., Zhang, T., Saxena, D., Snyder, M., Wu, Y., Li, X. 2017; 8: 15621-?


    The mechanism underlying bone impairment in patients with diabetes mellitus, a metabolic disorder characterized by chronic hyperglycaemia and dysregulation in metabolism, is unclear. Here we show the difference in the metabolomics of bone marrow stromal cells (BMSCs) derived from hyperglycaemic (type 2 diabetes mellitus, T2D) and normoglycaemic mice. One hundred and forty-two metabolites are substantially regulated in BMSCs from T2D mice, with the tricarboxylic acid (TCA) cycle being one of the primary metabolic pathways impaired by hyperglycaemia. Importantly, succinate, an intermediate metabolite in the TCA cycle, is increased by 24-fold in BMSCs from T2D mice. Succinate functions as an extracellular ligand through binding to its specific receptor on osteoclastic lineage cells and stimulates osteoclastogenesis in vitro and in vivo. Strategies targeting the receptor activation inhibit osteoclastogenesis. This study reveals a metabolite-mediated mechanism of osteoclastogenesis modulation that contributes to bone dysregulation in metabolic disorders.

    View details for DOI 10.1038/ncomms15621

    View details for PubMedID 28561074

  • Pharmacological rescue of diabetic skeletal stem cell niches. Science translational medicine Tevlin, R., Seo, E. Y., Marecic, O., McArdle, A., Tong, X., Zimdahl, B., Malkovskiy, A., Sinha, R., Gulati, G., Li, X., Wearda, T., Morganti, R., Lopez, M., Ransom, R. C., Duldulao, C. R., Rodrigues, M., Nguyen, A., Januszyk, M., Maan, Z., Paik, K., Yapa, K., Rajadas, J., Wan, D. C., Gurtner, G. C., Snyder, M., Beachy, P. A., Yang, F., Goodman, S. B., Weissman, I. L., Chan, C. K., Longaker, M. T. 2017; 9 (372)


    Diabetes mellitus (DM) is a metabolic disease frequently associated with impaired bone healing. Despite its increasing prevalence worldwide, the molecular etiology of DM-linked skeletal complications remains poorly defined. Using advanced stem cell characterization techniques, we analyzed intrinsic and extrinsic determinants of mouse skeletal stem cell (mSSC) function to identify specific mSSC niche-related abnormalities that could impair skeletal repair in diabetic (Db) mice. We discovered that high serum concentrations of tumor necrosis factor-? directly repressed the expression of Indian hedgehog (Ihh) in mSSCs and in their downstream skeletogenic progenitors in Db mice. When hedgehog signaling was inhibited during fracture repair, injury-induced mSSC expansion was suppressed, resulting in impaired healing. We reversed this deficiency by precise delivery of purified Ihh to the fracture site via a specially formulated, slow-release hydrogel. In the presence of exogenous Ihh, the injury-induced expansion and osteogenic potential of mSSCs were restored, culminating in the rescue of Db bone healing. Our results present a feasible strategy for precise treatment of molecular aberrations in stem and progenitor cell populations to correct skeletal manifestations of systemic disease.

    View details for DOI 10.1126/scitranslmed.aag2809

    View details for PubMedID 28077677

  • Can heavy isotopes increase lifespan? Studies of relative abundance in various organisms reveal chemical perspectives on aging. BioEssays Li, X., Snyder, M. P. 2016; 38 (11): 1093-1101


    Stable heavy isotopes co-exist with their lighter counterparts in all elements commonly found in biology. These heavy isotopes represent a low natural abundance in isotopic composition but impose great retardation effects in chemical reactions because of kinetic isotopic effects (KIEs). Previous isotope analyses have recorded pervasive enrichment or depletion of heavy isotopes in various organisms, strongly supporting the capability of biological systems to distinguish different isotopes. This capability has recently been found to lead to general decline of heavy isotopes in metabolites during yeast aging. Conversely, supplementing heavy isotopes in growth medium promotes longevity. Whether this observation prevails in other organisms is not known, but it potentially bears promise in promoting human longevity.

    View details for DOI 10.1002/bies.201600040

    View details for PubMedID 27554342

  • Yeast longevity promoted by reversing aging-associated decline in heavy isotope content npj Aging and Mechanisms of Disease Li, X., Snyder, M. P. 2016; 2 (16004)

    View details for DOI 10.1038/npjamd.2016.4

  • Metformin Improves Diabetic Bone Health by Re-Balancing Catabolism and Nitrogen Disposal PLOS ONE Li, X., Guo, Y., Yan, W., Snyder, M. P., Li, X. 2015; 10 (12)
  • Metabolomics as a robust tool in systems biology and personalized medicine: an open letter to the metabolomics community METABOLOMICS Snyder, M., Li, X. 2013; 9 (3): 532-534
  • Systematic investigation of protein-small molecule interactions IUBMB LIFE Li, X., Wang, X., Snyder, M. 2013; 65 (1): 2-8


    Cell signaling is extensively wired between cellular components to sustain cell proliferation, differentiation, and adaptation. The interaction network is often manifested in how protein function is regulated through interacting with other cellular components including small molecule metabolites. While many biochemical interactions have been established as reactions between protein enzymes and their substrates and products, much less is known at the system level about how small metabolites regulate protein functions through allosteric binding. In the past decade, study of protein-small molecule interactions has been lagging behind other types of interactions. Recent technological advances have explored several high-throughput platforms to reveal many "unexpected" protein-small molecule interactions that could have profound impact on our understanding of cell signaling. These interactions will help bridge gaps in existing regulatory loops of cell signaling and serve as new targets for medical intervention. In this review, we summarize recent advances of systematic investigation of protein-metabolite/small molecule interactions, and discuss the impact of such studies and their potential impact on both biological researches and medicine.

    View details for DOI 10.1002/iub.1111

    View details for Web of Science ID 000312886200002

    View details for PubMedID 23225626

  • Investigating metabolite-protein interactions: An overview of available techniques METHODS Yang, G. X., Li, X., Snyder, M. 2012; 57 (4): 459-466


    Metabolites comprise the molar majority of chemical substances in living cells, and metabolite-protein interactions are expected to be quite common. Many interactions have already been identified and have been shown to be involved in the regulation of different types of cellular processes including signaling events, enzyme activities, protein localizations and interactions. Recent technological advances have greatly facilitated the detection of metabolite-protein interactions at high sensitivity and some of these have been applied on a large scale. In this manuscript, we review the available in vitro, in silico and in vivo technologies for mapping small-molecule-protein interactions. Although some of these were developed for drug-protein interactions they can be applied for mapping metabolite-protein interactions. Information gained from the use of these approaches can be applied to the manipulation of cellular processes and therapeutic applications.

    View details for DOI 10.1016/j.ymeth.2012.06.013

    View details for Web of Science ID 000309625600009

    View details for PubMedID 22750303

    View details for PubMedCentralID PMC3448827

  • Metabolites as global regulators: A new view of protein regulation BIOESSAYS Li, X., Snyder, M. 2011; 33 (7): 485-489

    View details for DOI 10.1002/bies.201100026

    View details for Web of Science ID 000292710500002

    View details for PubMedID 21495048

  • mTOR-mediated dedifferentiation of the retinal pigment epithelium initiates photoreceptor degeneration in mice JOURNAL OF CLINICAL INVESTIGATION Zhao, C., Yasumura, D., Li, X., Matthes, M., Lloyd, M., Nielsen, G., Ahern, K., Snyder, M., Bok, D., Dunaief, J. L., LaVail, M. M., Vollrath, D. 2011; 121 (1): 369-383


    Retinal pigment epithelial (RPE) cell dysfunction plays a central role in various retinal degenerative diseases, but knowledge is limited regarding the pathways responsible for adult RPE stress responses in vivo. RPE mitochondrial dysfunction has been implicated in the pathogenesis of several forms of retinal degeneration. Here we have shown that postnatal ablation of RPE mitochondrial oxidative phosphorylation in mice triggers gradual epithelium dedifferentiation, typified by reduction of RPE-characteristic proteins and cellular hypertrophy. The electrical response of the retina to light decreased and photoreceptors eventually degenerated. Abnormal RPE cell behavior was associated with increased glycolysis and activation of, and dependence upon, the hepatocyte growth factor/met proto-oncogene pathway. RPE dedifferentiation and hypertrophy arose through stimulation of the AKT/mammalian target of rapamycin (AKT/mTOR) pathway. Administration of an oxidant to wild-type mice also caused RPE dedifferentiation and mTOR activation. Importantly, treatment with the mTOR inhibitor rapamycin blunted key aspects of dedifferentiation and preserved photoreceptor function for both insults. These results reveal an in vivo response of the mature RPE to diverse stressors that prolongs RPE cell survival at the expense of epithelial attributes and photoreceptor function. Our findings provide a rationale for mTOR pathway inhibition as a therapeutic strategy for retinal degenerative diseases involving RPE stress.

    View details for DOI 10.1172/JCI44303

    View details for Web of Science ID 000285892300039

    View details for PubMedID 21135502

  • Analyzing In Vivo Metabolite-Protein Interactions By Large-Scale Systematic Analyses. Current protocols in chemical biology Li, X., Snyder, M. 2011; 3 (4): 181-196


    Metabolites interact with proteins in vivo in various ways other than enzymatic reactions. Profiling of such interactions may help disclose unknown molecular mechanisms that regulate protein functions, and provide potential targets for disease treatment. Here we describe a procedure for systematic analyses of metabolite-protein interactions in vivo. This procedure couples protein affinity purification and mass spectrometry to identify metabolite-protein interactions. The primary effort can be completed within one day and scaled to process hundreds of samples in a batch. Originally developed in yeast, the same principle and protocol can be adapted to other organisms.

    View details for PubMedID 22846927

  • Extensive In Vivo Metabolite-Protein Interactions Revealed by Large-Scale Systematic Analyses CELL Li, X., Gianoulis, T. A., Yip, K. Y., Gerstein, M., Snyder, M. 2010; 143 (4): 639-650


    Natural small compounds comprise most cellular molecules and bind proteins as substrates, products, cofactors, and ligands. However, a large-scale investigation of in vivo protein-small metabolite interactions has not been performed. We developed a mass spectrometry assay for the large-scale identification of in vivo protein-hydrophobic small metabolite interactions in yeast and analyzed compounds that bind ergosterol biosynthetic proteins and protein kinases. Many of these proteins bind small metabolites; a few interactions were previously known, but the vast majority are new. Importantly, many key regulatory proteins such as protein kinases bind metabolites. Ergosterol was found to bind many proteins and may function as a general regulator. It is required for the activity of Ypk1, a mammalian AKT/SGK kinase homolog. Our study defines potential key regulatory steps in lipid biosynthetic pathways and suggests that small metabolites may play a more general role as regulators of protein activity and function than previously appreciated.

    View details for DOI 10.1016/j.cell.2010.09.048

    View details for Web of Science ID 000284149100020

    View details for PubMedID 21035178

  • A distinct endosomal Ca2+/Mn2+ pump affects root growth through the secretory process PLANT PHYSIOLOGY Li, X., Chanroj, S., Wu, Z., Romanowsky, S. M., Harper, J. F., Sze, H. 2008; 147 (4): 1675-1689


    Ca(2+) is required for protein processing, sorting, and secretion in eukaryotic cells, although the particular roles of the transporters involved in the secretory system of plants are obscure. One endomembrane-type Ca-ATPase from Arabidopsis (Arabidopsis thaliana), AtECA3, diverges from AtECA1, AtECA2, and AtECA4 in protein sequence; yet, AtECA3 appears similar in transport activity to the endoplasmic reticulum (ER)-bound AtECA1. Expression of AtECA3 in a yeast (Saccharomyces cerevisiae) mutant defective in its endogenous Ca(2+) pumps conferred the ability to grow on Ca(2+)-depleted medium and tolerance to toxic levels of Mn(2+). A green fluorescent protein-tagged AtECA3 was functionally competent and localized to intracellular membranes of yeast, suggesting that Ca(2+) and Mn(2+) loading into internal compartment(s) enhanced yeast proliferation. In mesophyll protoplasts, AtECA3-green fluorescent protein associated with a subpopulation of endosome/prevacuolar compartments based on partial colocalization with the Ara7 marker. Interestingly, three independent eca3 T-DNA disruption mutants showed severe reduction in root growth normally stimulated by 3 mm Ca(2+), indicating that AtECA3 function cannot be replaced by an ER-associated AtECA1. Furthermore, root growth of mutants is sensitive to 50 microm Mn(2+), indicating that AtECA3 is also important for the detoxification of excess Mn(2+). Curiously, Ateca3 mutant roots produced 65% more apoplastic protein than wild-type roots, as monitored by peroxidase activity, suggesting that the secretory process was altered. Together, these results demonstrate that the role of AtECA3 is distinct from that of the more abundant ER AtECA1. AtECA3 supports Ca(2+)-stimulated root growth and the detoxification of high Mn(2+), possibly through activities mediated by post-Golgi compartments that coordinate membrane traffic and sorting of materials to the vacuole and the cell wall.

    View details for DOI 10.1104/pp.108.119909

    View details for Web of Science ID 000258184800021

    View details for PubMedID 18567829

  • Participation of endomembrane cation/H+ exchanger AtCHX20 in osmoregulation of guard cells PLANT PHYSIOLOGY Padmanaban, S., Chanroj, S., Kwak, J. M., Li, X., Ward, J. M., Sze, H. 2007; 144 (1): 82-93


    Guard cell movement is induced by environmental and hormonal signals that cause changes in turgor through changes in uptake or release of solutes and water. Several transporters mediating these fluxes at the plasma membrane have been characterized; however, less is known about transport at endomembranes. CHX20, a member of a poorly understood cation/H+ exchanger gene family in Arabidopsis (Arabidopsis thaliana), is preferentially and highly expressed in guard cells as shown by promoterbeta-glucuronidase activity and by whole-genome microarray. Interestingly, three independent homozygous mutants carrying T-DNA insertions in CHX20 showed 35% reduction in light-induced stomatal opening compared to wild-type plants. To test the biochemical function of CHX20, cDNA was expressed in a yeast (Saccharomyces cerevisiae) mutant that lacks Na+(K+)/H+ antiporters (Deltanhx1 Deltanha1 Deltakha1) and plasma membrane Na+ pumps (Deltaena1-4). Curiously, CHX20 did not enhance tolerance of mutants to moderate Na+ or high K+ stress. Instead, it restored growth of the mutant on medium with low K+ at slightly alkaline pH, but had no effect on growth at acidic pH. Green fluorescent protein-tagged CHX20 expressed in mesophyll protoplasts was localized mainly to membranes of the endosomal system. Furthermore, light-induced stomatal opening of the Arabidopsis mutants was insensitive to external pH and was impaired at high KCl. The results are consistent with the idea that, in exchanging K+ for H+, CHX20 maintains K+ homeostasis and influences pH under certain conditions. Together, these results provide genetic and biochemical evidence that one CHX protein plays a critical role in osmoregulation through K+ fluxes and possibly pH modulation of an active endomembrane system in guard cells.

    View details for DOI 10.1104/pp.106.092155

    View details for Web of Science ID 000246356300009

    View details for PubMedID 17337534

  • Expression patterns of a novel AtCHX gene family highlight potential roles in osmotic adjustment and K+ homeostasis in pollen development PLANT PHYSIOLOGY Sze, H., Padmanaban, S., Cellier, F., Honys, D., Cheng, N. H., Bock, K. W., Conejero, G., Li, X. Y., Twell, D., Ward, J. M., Hirschi, K. D. 2004; 136 (1): 2532-2547


    A combined bioinformatic and experimental approach is being used to uncover the functions of a novel family of cation/H(+) exchanger (CHX) genes in plants using Arabidopsis as a model. The predicted protein (85-95 kD) of 28 AtCHX genes after revision consists of an amino-terminal domain with 10 to 12 transmembrane spans (approximately 440 residues) and a hydrophilic domain of approximately 360 residues at the carboxyl end, which is proposed to have regulatory roles. The hydrophobic, but not the hydrophilic, domain of plant CHX is remarkably similar to monovalent cation/proton antiporter-2 (CPA2) proteins, especially yeast (Saccharomyces cerevisiae) KHA1 and Synechocystis NhaS4. Reports of characterized fungal and prokaryotic CPA2 indicate that they have various transport modes, including K(+)/H(+) (KHA1), Na(+)/H(+)-K(+) (GerN) antiport, and ligand-gated ion channel (KefC). The expression pattern of AtCHX genes was determined by reverse transcription PCR, promoter-driven beta-glucuronidase expression in transgenic plants, and Affymetrix ATH1 genome arrays. Results show that 18 genes are specifically or preferentially expressed in the male gametophyte, and six genes are highly expressed in sporophytic tissues. Microarray data revealed that several AtCHX genes were developmentally regulated during microgametogenesis. An exciting idea is that CHX proteins allow osmotic adjustment and K(+) homeostasis as mature pollen desiccates and then rehydrates at germination. The multiplicity of CHX-like genes is conserved in higher plants but is not found in animals. Only 17 genes, OsCHX01 to OsCHX17, were identified in rice (Oryza sativa) subsp. japonica, suggesting diversification of CHX in Arabidopsis. These results reveal a novel CHX gene family in flowering plants with potential functions in pollen development, germination, and tube growth.

    View details for DOI 10.1104/pp.104.046003

    View details for Web of Science ID 000223962100012

    View details for PubMedID 15347787

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