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An Efficient and Economical N-Glycome Sample Preparation Using Acetone Precipitation. Metabolites 2022; 12:metabo12121285. [PMID: 36557323 PMCID: PMC9786591 DOI: 10.3390/metabo12121285] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2022] [Revised: 12/09/2022] [Accepted: 12/15/2022] [Indexed: 12/23/2022] Open
Abstract
Due to the critical role of the glycome in organisms and its close connections with various diseases, much time and effort have been dedicated to glycomics-related studies in the past decade. To achieve accurate and reliable identification and quantification of glycans extracted from biological samples, several analysis methods have been well-developed. One commonly used methodology for the sample preparation of N-glycomics usually involves enzymatic cleavage by PNGase F, followed by sample purification using C18 cartridges to remove proteins. PNGase F and C18 cartridges are very efficient both for cleaving N-glycans and for protein removal. However, this method is most suitable for a limited quantity of samples. In this study, we developed a sample preparation method focusing on N-glycome extraction and purification from large-scale biological samples using acetone precipitation. The N-glycan yield was first tested on standard glycoprotein samples, bovine fetuin and complex biological samples, and human serum. Compared to C18 cartridges, most of the sialylated N-glycans from human serum were detected with higher abundance after acetone precipitation. However, C18 showed a slightly higher efficiency for protein removal. Using the unfiltered human serum as the baseline, around 97.7% of the proteins were removed by acetone precipitation, while more than 99.9% of the proteins were removed by C18 cartridges. Lastly, the acetone precipitation was applied to N-glycome extraction from egg yolks to demonstrate large-scale glycomics sample preparation.
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Yadav SPS, Yu A, Zhao J, Singh J, Kakkar S, Chakraborty S, Mechref Y, Molitoris B, Wagner MC. Glycosylation of a key cubilin Asn residue results in reduced binding to albumin. J Biol Chem 2022; 298:102371. [PMID: 35970386 PMCID: PMC9485058 DOI: 10.1016/j.jbc.2022.102371] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2022] [Revised: 08/09/2022] [Accepted: 08/10/2022] [Indexed: 10/28/2022] Open
Abstract
Kidney disease often manifests with an increase in proteinuria, which can result from both glomerular and/or proximal tubule injury. The proximal tubules are the major site of protein and peptide endocytosis of the glomerular filtrate, and cubilin is the proximal tubule brush border membrane glycoprotein receptor that binds filtered albumin and initiates its processing in proximal tubules. Albumin also undergoes multiple modifications depending upon the physiologic state. We previously documented that carbamylated albumin had reduced cubilin binding, but the effects of cubilin modifications on binding albumin remain unclear. Here, we investigate the cubilin-albumin binding interaction to define the impact of cubilin glycosylation and map the key glycosylation sites while also targeting specific changes in a rat model of proteinuria. We identified a key Asn residue, N1285, that when glycosylated reduced albumin binding. In addition, we found a pH-induced conformation change may contribute to ligand release. To further define the albumin-cubilin binding site, we determined the solution structure of cubilin's albumin-binding domain, CUB7,8, using small-angle X-ray scattering and molecular modeling. We combined this information with mass spectrometry crosslinking experiments of CUB7,8 and albumin that provides a model of the key amino acids required for cubilin-albumin binding. Together, our data supports an important role for glycosylation in regulating the cubilin interaction with albumin, which is altered in proteinuria and provides new insight into the binding interface necessary for the cubilin-albumin interaction.
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Affiliation(s)
- Shiv Pratap Singh Yadav
- Nephrology Division, Department of Medicine, Indiana University School of Medicine, Indianapolis, Indiana, USA
| | - Aiying Yu
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, Texas, USA
| | - Jingfu Zhao
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, Texas, USA
| | - Jasdeep Singh
- Department of Biochemical Engineering and Biotechnology, Indian Institute of Technology Delhi, New Delhi, India
| | - Saloni Kakkar
- CSIR-Institute of Microbial Technology, Chandigarh, India
| | | | - Yehia Mechref
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, Texas, USA
| | - Bruce Molitoris
- Nephrology Division, Department of Medicine, Indiana University School of Medicine, Indianapolis, Indiana, USA; Department of Cellular & Integrative Physiology, Indiana University School of Medicine, Indianapolis, Indiana, USA
| | - Mark C Wagner
- Nephrology Division, Department of Medicine, Indiana University School of Medicine, Indianapolis, Indiana, USA.
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Wang J, Peng W, Yu A, Fokar M, Mechref Y. Glycome Profiling of Cancer Cell Lines Cultivated in Physiological and Commercial Media. Biomolecules 2022; 12:biom12060743. [PMID: 35740868 PMCID: PMC9221004 DOI: 10.3390/biom12060743] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2022] [Revised: 05/18/2022] [Accepted: 05/20/2022] [Indexed: 12/29/2022] Open
Abstract
A complex physiological culture medium (Plasmax) was introduced recently, composed of nutrients and metabolites at concentrations normally found in human plasma to mimic the in vivo environment for cell line cultivation. As glycosylation has been proved to be involved in cancer development, it is necessary to investigate the glycan expression changes in media with different nutrients. In this study, a breast cancer cell line, MDA-MB-231BR, and a brain cancer cell line, CRL-1620, were cultivated in Plasmax and commercial media to reveal cell line glycosylation discrepancies prompted by nutritional environments. Glycomics analyses of cell lines were performed using LC-MS/MS. The expressions of multiple fucosylated N-glycans, such as HexNAc4Hex3DeoxyHex1 and HexNAc5Hex3DeoxyHex1, derived from both cell lines exhibited a significant increase in Plasmax. Among the O-glycans, significant differences were also observed. Both cell lines cultivated in EMEM had the lowest amounts of O-glycans expressed. The original work described the development of Plasmax, which improves colony formation, and resulted in transcriptomic and metabolomic alterations of cancer cell lines, while our results indicate that Plasmax can significantly impact protein glycosylation. This study also provides information to guide the selection of media for in vitro cancer cell glycomics studies.
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Affiliation(s)
- Junyao Wang
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, TX 79409, USA; (J.W.); (W.P.); (A.Y.)
| | - Wenjing Peng
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, TX 79409, USA; (J.W.); (W.P.); (A.Y.)
| | - Aiying Yu
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, TX 79409, USA; (J.W.); (W.P.); (A.Y.)
| | - Mohamed Fokar
- Center of Biotechnology and Genomics, Texas Tech University, Lubbock, TX 79409, USA;
| | - Yehia Mechref
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, TX 79409, USA; (J.W.); (W.P.); (A.Y.)
- Center of Biotechnology and Genomics, Texas Tech University, Lubbock, TX 79409, USA;
- Correspondence: ; Tel.: +1-806-742-3059
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Laget J, Duranton F, Argilés À, Gayrard N. Renal insufficiency and chronic kidney disease – Promotor or consequence of pathological post-translational modifications. Mol Aspects Med 2022; 86:101082. [DOI: 10.1016/j.mam.2022.101082] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2021] [Revised: 01/27/2022] [Accepted: 02/03/2022] [Indexed: 12/12/2022]
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Yu A, Zhao J, Yadav SPS, Molitoris BA, Wagner MC, Mechref Y. Changes in the Expression of Renal Brush Border Membrane N-Glycome in Model Rats with Chronic Kidney Diseases. Biomolecules 2021; 11:1677. [PMID: 34827675 PMCID: PMC8616023 DOI: 10.3390/biom11111677] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2021] [Revised: 11/08/2021] [Accepted: 11/09/2021] [Indexed: 12/15/2022] Open
Abstract
Chronic kidney disease (CKD) is defined by a reduced renal function i.e., glomerular filtration rate (GFR), and the presence of kidney damage is determined by measurement of proteinuria or albuminuria. Albuminuria increases with age and can result from glomerular and/or proximal tubule (PT) alterations. Brush-border membranes (BBMs) on PT cells play an important role in maintaining the stability of PT functions. The PT BBM, a highly dynamic, organized, specialized membrane, contains a variety of glycoproteins required for the functions of PT. Since protein glycosylation regulates many protein functions, the alteration of glycosylation due to the glycan changes has attracted more interests for a variety of disease studies recently. In this work, liquid chromatography-tandem mass spectrometry was utilized to analyze the abundances of permethylated glycans from rats under control to mild CKD, severe CKD, and diabetic conditions. The most significant differences were observed in sialylation level with the highest present in the severe CKD and diabetic groups. Moreover, high mannose N-glycans was enriched in the CKD BBMs. Characterization of all the BBM N-glycan changes supports that these changes are likely to impact the functional properties of the dynamic PT BBM. Further, these changes may lead to the potential discovery of glycan biomarkers for improved CKD diagnosis and new avenues for therapeutic treatments.
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Affiliation(s)
- Aiying Yu
- Department of Chemistry and Biochemistry, Texas Tech University, Texas City, TX 79409, USA; (A.Y.); (J.Z.)
| | - Jingfu Zhao
- Department of Chemistry and Biochemistry, Texas Tech University, Texas City, TX 79409, USA; (A.Y.); (J.Z.)
| | - Shiv Pratap S. Yadav
- Nephrology Division, Department of Medicine, Indiana University, Indianapolis, IN 46202, USA; (S.P.S.Y.); (B.A.M.); (M.C.W.)
| | - Bruce A. Molitoris
- Nephrology Division, Department of Medicine, Indiana University, Indianapolis, IN 46202, USA; (S.P.S.Y.); (B.A.M.); (M.C.W.)
| | - Mark C. Wagner
- Nephrology Division, Department of Medicine, Indiana University, Indianapolis, IN 46202, USA; (S.P.S.Y.); (B.A.M.); (M.C.W.)
| | - Yehia Mechref
- Department of Chemistry and Biochemistry, Texas Tech University, Texas City, TX 79409, USA; (A.Y.); (J.Z.)
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