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Correlations Between LC-MS/MS-Detected Glycomics and NMR-Detected Metabolomics in Caenorhabditis Elegans Development

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Correlations Between LC-MS/MS-Detected Glycomics and NMR-Detected Metabolomics in Caenorhabditis Elegans Development ORIGINAL RESEARCH published: 28 June 2019 doi: 10.3389/fmolb.2019.00049 Correlations Between LC-MS/MS-Detected Glycomics and NMR-Detected Metabolomics in Caenorhabditis elegans Development M. Osman Sheikh 1†, Fariba Tayyari 1†, Sicong Zhang 1,2†, Michael T. Judge 1,3, D. Brent Weatherly 1, Francesca V. Ponce 1, Lance Wells 1,2* and Arthur S. Edison 1,2,3,4* 1 Complex Carbohydrate Research Center, University of Georgia, Athens, GA, United States, 2 Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA, United States, 3 Department of Genetics, University of Georgia, Athens, GA, United States, 4 Institute of Bioinformatics, University of Georgia, Athens, GA, United States Edited by: Reza M. Salek, International Agency for Research On This study examined the relationship between glycans, metabolites, and development in Cancer (IARC), France C. elegans. Samples of N2 animals were synchronized and grown to five different time Reviewed by: points ranging from L1 to a mixed population of adults, gravid adults, and offspring. Benedicte Elena-Herrmann, INSERM U1209 Institut pour Each time point was replicated seven times. The samples were each assayed by a l’Avancée des Biosciences large particle flow cytometer (Biosorter) for size distribution data, LC-MS/MS for targeted (IAB), France Atsushi Fukushima, N- and O-linked glycans, and NMR for metabolites. The same samples were utilized for RIKEN, Japan all measurements, which allowed for statistical correlations between the data. A new *Correspondence: protocol was developed to correlate Biosorter developmental data with LC-MS/MS data Lance Wells to obtain stage-specific information of glycans. From the five time points, four distinct [email protected] Arthur S. Edison sizes of worms were observed from the Biosorter distributions, ranging from the smallest [email protected] corresponding to L1 to adult animals. A network model was constructed using the †These authors have contributed four binned sizes of worms as starting nodes and adding glycans and metabolites that equally to this work had correlations with r ≥ 0.5 to those nodes. The emerging structure of the network showed distinct patterns of N- and O-linked glycans that were consistent with previous Specialty section: This article was submitted to studies. Furthermore, some metabolites that were correlated to these glycans and Metabolomics, worm sizes showed interesting interactions. Of note, UDP-GlcNAc had strong positive a section of the journal correlations with many O-glycans that were expressed in the largest animals. Similarly, Frontiers in Molecular Biosciences phosphorylcholine correlated with many N-glycans that were expressed in L1 animals. Received: 12 January 2019 Accepted: 11 June 2019 Keywords: C. elegans, glycomics, mass spectrometry, NMR, metabolomics, development, biosorter Published: 28 June 2019 Citation: Sheikh MO, Tayyari F, Zhang S, INTRODUCTION Judge MT, Weatherly DB, Ponce FV, Wells L and Edison AS (2019) This paper presents a new approach to evaluate the relationship between Caenorhabditis elegans Correlations Between development, glycan abundance, and metabolites. Regardless of the organism, glycomics and LC-MS/MS-Detected Glycomics and NMR-Detected Metabolomics in metabolomics are generally conducted independently, but metabolism and glycan biosynthesis Caenorhabditis elegans Development. are intimately related (Freeze et al., 2015). For example, O-linked β-N-acetylglucosamine Front. Mol. Biosci. 6:49. (O-GlcNAc)—a type of posttranslational glycosylation of nuclear and cytoplasmic proteins—acts doi: 10.3389/fmolb.2019.00049 as a sensor of nutrition and cellular stress (Zachara and Hart, 2004; Zachara, 2018). The addition Frontiers in Molecular Biosciences | www.frontiersin.org 1 June 2019 | Volume 6 | Article 49 Sheikh et al. Worm Glycomics, Metabolomics, and Development of O-GlcNAc to proteins is catalyzed by a single enzyme, statistically correlate LC-MS/MS glycomics data with Biosorting O-GlcNAc transferase (OGT), which relies on the availability data, which provides a population distribution of the samples. of the sugar-nucleotide donor substrate, UDP-GlcNAc via the To our knowledge, until now nobody has statistically associated hexosamine biosynthetic pathway (HBP) (Vaidyanathan and molecular data such as glycans and metabolites with population Wells, 2014). Through the HBP, concentrations of UDP-GlcNAc distribution data through a large-particle flow cytometer. This are modulated by the metabolism of glucose, fatty acids, amino allows a direct and unbiased association between glycans and acids, and nucleotides. This vital glycosylation precursor is not developmental stage. We also collected untargeted NMR data on only utilized by OGT to modify thousands of proteins with the same samples used for glycomics and Biosorting. Statistical O-GlcNAc (Zachara and Hart, 2004; Zachara, 2018), but also correlations between LC-MS/MS glycomics and NMR data by many other glycosyltransferases to generate more elaborate provided links between specific resonances in the NMR data types of N- and O-linked glycans (Brockhausen and Stanley, with specific groups of glycans, which allowed us to begin to 2015; Stanley et al., 2015). Better approaches of associating interpret the interplay between metabolites and glycans through glycomics and metabolomics would be valuable to gain a deeper development in C. elegans. Finally, we constructed a correlation understanding of their interactions. network of binned sizes of worms from Biosorter distributions, C. elegans has become an important model organism for LC-MS/MS glycomics, and NMR metabolomics data, which chemical signaling (Srinivasan et al., 2008; von Reuss et al., 2012; exposes some unique interactions between these three distinct Ludewig and Schroeder, 2013), metabolism (Srinivasan et al., types of data. 2012; von Reuss and Schroeder, 2015; Witting et al., 2018), and glycomics (Paschinger et al., 2008). C. elegans has a surprising MATERIALS AND METHODS diversity of many of these groups. Both ascaroside (Srinivasan et al., 2012; von Reuss and Schroeder, 2015) and O-GlcNAc All data reported in this study have been deposited in (Zachara and Hart, 2004) biosynthesis incorporate many of the the Metabolomics Workbench (doi: 10.21228/M8240W) same primary metabolic pathways in C. elegans. Therefore, C. (Sud et al., 2016). elegans is a good model organism to study the interactions between glycomics and metabolomics. C. elegans develops from Reagents egg to adult in about 3 days through 4 distinct larval stages PNGase A (Protein N-Glycosidase A, Calbiochem) was (L1-L4), young adult, adult. When resources are limited or the purchased from MilliporeSigma (St. Louis, MO, USA). Sodium population of worms too high, C. elegans enters the dauer stage, hydroxide (50%) was purchased from Fisher Scientific. Sep- which can persist for several months and is specialized for Pak C18 disposable extraction columns were obtained from dispersal (Hu, 2007). C. elegans development has been studied Waters Corporation (Milford, MA, USA). AG-50W-X8 cation for decades, including the seminal study that mapped the entire exchange resin (H+ form) was purchased from Bio-Rad and cell lineage of post-embryonic animals and led to the discovery trifluoroacetic acid from Pierce. Ultra Pure UDP-GlcNAc was of apoptosis (Sulston and Horvitz, 1977). Gene expression has purchased from Promega Corporation (Madison, WI, USA). been linked with development in C. elegans through the use Trypsin, Chymotrypsin, and all other chemical reagents were of green fluorescent protein (GFP), the first application of this purchased from Sigma-Aldrich/MilliporeSigma (St. Louis, important technique in animals (Chalfie et al., 1994). Metabolites MO, USA). (Srinivasan et al., 2008; Kaplan et al., 2009, 2011) and glycans (Morio et al., 2003; Cipollo et al., 2005; Kanaki et al., 2018) C. elegans Sample Preparation have been implicated in playing major roles in different stages This study used N2, the laboratory reference strain of C. elegans, of development. However, because there are no simple tools which was obtained from the Caenorhabditis Genetics Center such as the use of a fluorescent reporter of gene expression, (CGC). We followed the general protocol published previously it is still extremely difficult to relate metabolites and glycans for obtaining liquid cultures of synchronized worms (Srinivasan to development. et al., 2008; Kaplan et al., 2009). This defines our biological In this study, we used LC-MS/MS to quantify the expression replicate: A single L1 animal from a synchronized culture was profiles of both N- and O-linked glycans in C. elegans as a placed onto an agar plate seeded with E. coli MG1655. This plate function of development. We developed a novel approach to was grown until there were a large number of young gravid adult hermaphrodites (about 48 h at ∼24◦C). The plate was then Abbreviations: C. elegans, Caenorhabditis elegans; dHex, deoxyhexose, washed into a 15 mL tube with M9 buffer, rinsed 3x with M9, namely Fuc, fucose; Gal, galactose; GalNAc, N-acetylgalactosamine; GDP- and lysed with an alkaline hypochlorite solution until about 50% Fucose, Guanosine diphosphate fucose; Glc, glucose; GlcA, glucuronic acid; of the worms were dissolved (no more than 5 min). Then, M9 GlcNAc, N-acetylglucosamine; HBP, Hexosamine Biosynthetic Pathway; HCA, Hierarchical Clustering Analysis; Hex, hexose, either Glc, Gal, or Man; HexA, buffer was added to dilute the lysing solution, and the liquid was hexuronic acid,
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