Article
Biochemistry & Molecular Biology
Malwina Michalak, Martin Simon Kalteis, Aysel Ahadova, Matthias Kloor, Mark Kriegsmann, Katharina Kriegsmann, Uwe Warnken, Dominic Helm, Juergen Kopitz
Summary: Glycosylation is the most common form of post-translational protein modification, regulating various cellular functions. A new strategy has been described to compare membrane glycoproteomes and identify proteins with altered glycan structures and glycosites. The methodology can be applied not only to cell culture, but also to tissue samples or body fluids, making it a useful module in experimental settings targeting glycan functions.
Review
Biochemistry & Molecular Biology
Neetika Jaisinghani, Jessica C. Seeliger
Summary: Studying bacterial lipids poses challenges due to their differences from eukaryotic lipids, requiring specific methods for analysis. Recent research has made progress in this area but still faces challenges.
CURRENT OPINION IN CHEMICAL BIOLOGY
(2021)
Article
Biochemistry & Molecular Biology
Mingming Xu, Hong Jin, Wei Ge, Lingbo Zhao, Zhaoliang Liu, Zeyu Guo, Zhen Wu, Jing Chen, Chengjie Mao, Xumin Zhang, Chun-Feng Liu, Shuang Yang
Summary: Urine contains a wide range of glycoproteins, peptides, and free glycans, which can provide earlier and more sensitive molecular changes for biomarker discovery. Urine biomarkers have great diagnostic potential and are easy to collect and analyze non-invasively. The investigation of abnormal protein glycosylation in urine may shed light on the identification of disease-specific glycosylation biomarkers for Parkinson's disease.
ACS CHEMICAL NEUROSCIENCE
(2023)
Article
Biochemical Research Methods
J. B. S. K. Jayantha, Farshid Mashayekhy Rad, J. K. Vidanarachchi, Jonas Bergquist, S. J. Kumari A. Ubhayasekera
Summary: Phytosterols are important components of plant cell membranes and have health benefits such as reducing blood cholesterol levels. A new method using ultra-performance supercritical fluid chromatography hyphenated with atmospheric pressure chemical ionization tandem mass spectrometry was developed for fingerprint analysis of phytosterols. This method can separate seven phytosterols concurrently in 3 minutes, with a detection limit below 20 ng/mL, offering a faster, more sensitive, and more selective analytical process compared to previous methods.
JOURNAL OF CHROMATOGRAPHY B-ANALYTICAL TECHNOLOGIES IN THE BIOMEDICAL AND LIFE SCIENCES
(2023)
Article
Engineering, Chemical
Akos Kuki, Gergo Roth, Anna Nagy, Miklos Zsuga, Sandor Keki, Tibor Nagy
Summary: This article introduces a new data mining approach for simplifying copolymer mass spectra and determining their composition. By selecting the most abundant peak in the mass spectrum for calculation, the quantities and properties of the copolymer can be determined more efficiently.
Article
Multidisciplinary Sciences
Shin Morioka, Hiroki Nakanishi, Toshiyoshi Yamamoto, Junya Hasegawa, Emi Tokuda, Tomoya Hikita, Tomoko Sakihara, Yuuki Kugii, Chitose Oneyama, Masakazu Yamazaki, Akira Suzuki, Junko Sasaki, Takehiko Sasaki
Summary: A new method called PRMC-MS has been developed to analyze the dynamics of phosphoinositide acyl variants. The study reveals specific changes in acyl chains in prostate cancer tissues with PTEN deficiency and upon expression of oncogenic PIK3CA.
NATURE COMMUNICATIONS
(2022)
Article
Multidisciplinary Sciences
Haci Mehmet Kayili, Bekir Salih
Summary: Glycosylation is a crucial modification in proteins that affects drug efficacy. A method for qualitative and quantitative analysis of N-glycans in glycoproteins using HILIC-FLD-MS/MS has been proposed, which can be applied to glycoproteins from various species.
JOVE-JOURNAL OF VISUALIZED EXPERIMENTS
(2021)
Article
Chemistry, Analytical
Luyao Liu, Bin Zhu, Zheng Fang, Na Zhang, Hongqiang Qin, Zhimou Guo, Xinmiao Liang, Zhenzhen Yao, Mingliang Ye
Summary: Bottom-up proteomics is increasingly used in clinical research, but glycoproteomic analysis has been a bottleneck. An automated glycopeptide enrichment method was developed for site-specific N-glycoproteome analysis, showing higher efficiency and reliability.
ANALYTICAL CHEMISTRY
(2021)
Article
Engineering, Biomedical
Hebatullah Hussein, Anil Kishen
Summary: This study found that engineered bioactive chitosan-based nanoparticles can modulate the protein and cytokine profiles of macrophages, reducing inflammation caused by apical periodontitis and promoting the migration of periodontal ligament fibroblasts.
BIOACTIVE MATERIALS
(2022)
Article
Environmental Sciences
Fengkai Liu, Darong Huang, Xinrong Guo, Cunqian Feng
Summary: In this paper, a novel ISAR imaging method is proposed to improve the imaging quality by removing the Doppler ambiguity and compensating for the MTRC. The proposed method accurately estimates the rotational parameters and achieves high-quality ISAR images for group targets with complex maneuvers without Doppler ambiguity.
Article
Genetics & Heredity
Farhana Taher Sumya, Irina D. Pokrovskaya, Vladimir Lupashin
Summary: Researchers successfully developed cellular models for COG4 mutations in RPE1 and HEK293T cell lines, thoroughly characterizing them using various methods and revealing specific defects in glycosylation and protein secretion in mutant cells. The study suggests that cellular models with COG mutations may aid in further investigating the molecular mechanisms of the disease and potentially provide guidance for the treatment of COG-CDGs.
FRONTIERS IN GENETICS
(2021)
Article
Oncology
Iiris Ukkola, Pirjo Nummela, Annamari Heiskanen, Matilda Holm, Sadia Zafar, Mia Kero, Caj Haglund, Tero Satomaa, Soili Kytola, Ari Ristimaki
Summary: All human cells have a complex glycan coating, and alterations in cell surface glycans are related to cancer progression and immune suppression. Colorectal cancer is a heterogeneous disease with different molecular subtypes, which have varying prognosis and therapy responses. Microsatellite instability and BRAF gene mutation, two important molecular markers, have been ignored in previous glycomics studies. Our analysis of the N-glycan profiles of colorectal cancers with different molecular subtypes revealed characteristic glycan profiles that may explain their tumorigenic properties.
Article
Biochemical Research Methods
Amy L. George, Frances R. Sidgwick, Jessica E. Watt, Mathew P. Martin, Matthias Trost, Jose Luis Marin-Rubio, Maria Emilia Duenas
Summary: Thermal proteome profiling (TPP) is a powerful approach to studying the interactions of therapeutic molecules with proteins. Isobaric tandem mass tags (TMTs) are commonly used in TPP analysis, but data-independent acquisition (DIA) approaches offer higher sensitivity and protein coverage with reduced costs. In this study, different DIA-based label-free quantification approaches were compared to TMT-DDA for thermal shift quantitation, and it was found that DIA approaches are a cost-effective alternative.
JOURNAL OF PROTEOME RESEARCH
(2023)
Article
Biochemistry & Molecular Biology
Jialin Liu, Yi Hao, Chunting Wang, Yangya'nan Jin, Yong Yang, Jin Gu, Xing Chen
Summary: O-GlcNAc glycosylation is a significant protein post-translational modification in metazoans, and isoPTOP is an optimized strategy enabling quantitative and site-specific profiling of O-GlcNAcylation. The research has identified a large number of O-GlcNAcylation sites in CRC cells and demonstrated the applicability of isoPTOP for studying O-GlcNAcylation dynamics in various pathophysiological processes.
ACS CHEMICAL BIOLOGY
(2022)
Article
Chemistry, Analytical
Susan C. Scott, Nicole M. Anders, Morgan Scardina, Christine L. Hann, Michelle A. Rudek
Summary: Vistusertib, an orally bioavailable mTOR inhibitor under clinical trials, was quantitated using a novel LC-MS/MS method to explore exposure-response relationships accurately. The method allowed accurate quantitation of high-concentration samples through dilution, and maintained long-term frozen stability.
JOURNAL OF PHARMACEUTICAL AND BIOMEDICAL ANALYSIS
(2022)
Article
Hematology
Kayleigh M. Voos, Wenpeng Cao, Nicholas A. Arce, Emily R. Legan, Yingchun Wang, Asif Shajahan, Parastoo Azadi, Pete Lollar, Xiaohui Frank Zhang, Renhao Li
Summary: Desialylation of O-glycans around A1 increases its activity by destabilizing the AIM, leading to enhanced binding activity and platelet aggregation.
JOURNAL OF THROMBOSIS AND HAEMOSTASIS
(2022)
Article
Biochemistry & Molecular Biology
Emma G. Jackson, Giuliano Cutolo, Bo Yang, Nageswari Yarravarapu, Mary W. N. Burns, Ganka Bineva-Todd, Chloe Roustan, James B. Thoden, Halley M. Lin-Jones, Toin H. van Kuppevelt, Hazel M. Holden, Benjamin Schumann, Jennifer J. Kohler, Christina M. Woo, Matthew R. Pratt
Summary: Bio-orthogonal chemistries have revolutionized various fields, with metabolic chemical reporters (MCRs) playing a crucial role in incorporating bio-orthogonal functionalities into biomolecules. Research on selective MCRs provides insights into understanding intracellular glycosylation modifications.
ACS CHEMICAL BIOLOGY
(2022)
Article
Biochemistry & Molecular Biology
Daniela J. Carroll, Mary W. N. Burns, Lynda Mottrarn, Daniel C. Propheterl, Andrew Boucher, Gabrielle M. Lessen, Ashwani Kumar, Stacy A. Malaker, Chao Xing, Lora Hooper, Ulf Yrlid, Jennifer J. Kohler
Summary: IL-22 signaling regulates fucosylation of glycoproteins in intestinal epithelial cells by regulating the expression of B3GNT7, which is involved in the synthesis of polyLacNAc chains. This study uncovers a novel role for B3GNT7 in intestinal fucosylation.
JOURNAL OF BIOLOGICAL CHEMISTRY
(2022)
Article
Biochemical Research Methods
Nageswari Yarravarapu, Rohit Sai Reddy Konada, Narek Darabedian, Nichole J. Pedowitz, Soumya N. Krishnamurthy, Matthew R. Pratt, Jennifer J. Kohler
Summary: Glycan binding is crucial in extracellular recognition events. This method utilizes exoenzymatic labeling to add a modified sialic acid to cell surface glycoconjugates, enabling UV-induced crosslinking of glycan-mediated binding interactions.
BIOCONJUGATE CHEMISTRY
(2022)
Article
Cell Biology
Paulina Sosicka, Bobby G. Ng, Lauren E. Pepi, Asif Shajahan, Maurice Wong, David A. Scott, Kenjiroo Matsumoto, Zhi-Jie Xia, Carlito B. Lebrilla, Robert S. Haltiwanger, Parastoo Azadi, Hudson H. Freeze
Summary: Cells selectively use activated GDP-fucose from multiple, separate pools for glycosylation, dispelling the concept of a single, homogenous precursor pool. This discovery provides novel perspectives on monosaccharide metabolism.
JOURNAL OF CELL BIOLOGY
(2022)
Review
Chemistry, Multidisciplinary
Mary W. N. Burns, Jennifer J. Kohler
Summary: Glycoconjugates are assembled by the coordinated actions of glycosyltransferases and glycosidases. Mutagenesis can be used to introduce unnatural sugar analogs for labeling and isolating substrates, and engineering enzymes can help determine the roles of specific glycosylation events. The engineering of glycosidases can also be used to target specific substrates, with applications in both basic science and translational research.
ISRAEL JOURNAL OF CHEMISTRY
(2023)
Article
Biology
M. Kristen Hall, Asif Shajahan, Adam P. Burch, Cody J. Hatchett, Parastoo Azadi, Ruth A. Schwalbe
Summary: Glycosylation plays a crucial role in cancer progression and the expression of endoplasmic reticulum proteins. Altered N-glycosylation influences cellular properties and the behavior of aggressive neuroblastoma cells. Oligomannose N-glycans contribute to neuroblastoma progression and perturbations in the N-glycosylation pathway impact chaperone systems.
Article
Oncology
Jingyu Zhan, Dong Lin, Nathan Watson, Lothar Esser, Wai Kwan Tang, Alex Zhang, Xiufen Liu, Raffit Hassan, Anne Gleinich, Asif Shajahan, Parastoo Azadi, Ira Pastan, Di Xia
Summary: Mesothelin, a tumor-associated antigen, is highly expressed on the cell surface of many human cancers and has limited expression in normal tissues. Binding of mesothelin to CA-125 can facilitate cell adhesion and tumor metastasis. Immunotherapeutic strategies targeting mesothelin are actively being studied.
CANCER RESEARCH COMMUNICATIONS
(2023)
Letter
Biochemistry & Molecular Biology
Michael Boyce, Stacy A. Malaker, Nicholas M. Riley, Jennifer J. Kohler
Article
Biochemistry & Molecular Biology
Akshi Singla, Andrew Boucher, Kerri-Lee Wallom, Michael Lebens, Jennifer J. Kohler, Frances M. Platt, Ulf Yrlid
Summary: Prior research on cholera toxin (CT) binding and intoxication has relied on human colonic cancer derived epithelial cells. However, this study used human enteroids derived from jejunal biopsies to study CT binding and intoxication of human non-transformed small intestinal epithelial cells. The study found that inhibition of fucosylation or O-glycosylation sensitized enteroids to CT intoxication. Furthermore, simultaneous inhibition of fucosylation and O-glycosylation increased the availability of additional glycoconjugates, but counteracted the sensitization in CT intoxication caused by inhibiting O-glycosylation due to reduction in fucose. This suggests a dual role of fucose in influencing CT binding and intoxication. Additionally, the study revealed a role for human genetic variation in determining sensitivity to CT.
Article
Biochemistry & Molecular Biology
Bartlomiej M. Kolaczkowski, Christian Jorgensen, Nikolaj Spodsberg, Mary A. Stringer, Nitin T. Supekar, Parastoo Azadi, Peter Westh, Kristian B. R. M. Krogh, Kenneth Jensen
Summary: Glycoengineering allows control over glycosylation patterns to generate new glycoprotein variants with desired properties. Challenges include glycan heterogeneity and nonnative glycan chains introduced by heterologous protein expression. Partial trimming or complete removal of glycan chains can address these challenges.
Article
Biochemistry & Molecular Biology
Han Wu, Asif Shajahan, Jeong-Yeh Yang, Emanuela Capota, Amberlyn M. Wands, Connie M. Arthur, Sean R. Stowell, Kelley W. Moremen, Parastoo Azadi, Jennifer J. Kohler
Summary: This study describes a metabolic method to introduce a photo-cross-linker onto GlcNAc residues of cell-surface N-linked glycoproteins, which can be used to discover and characterize binding interactions that depend on N-glycans.
CELL CHEMICAL BIOLOGY
(2022)
Meeting Abstract
Biochemistry & Molecular Biology
Grace Lu, Stephanie Archer-Hartmann, Christian Heiss, Artur Muszynski, Ian Black, Asif Shajahan, Ikenna Ndukwe, Lauren Pepi, Jiri Vlach, Li Tan, Varughese Mulamoottil, Nicholas Miller, Parastoo Azadi
Meeting Abstract
Biochemistry & Molecular Biology
Lauren Pepi, Leonardo Molina, Asif Shajahan, David J. Miller, Parastoo Azadi