Article
Chemistry, Multidisciplinary
Haizhen Wang, Di Liu, Haifeng Chen, Yuqing Jiao, Haixin Zhao, Zongcheng Li, Siyuan Hou, Yanli Ni, Rong Zhang, Jinyong Wang, Jie Zhou, Bing Liu, Yu Lan
Summary: During the development of mid-gestational mouse embryos, specialized endothelial cells called hemogenic endothelial cells (HECs) differentiate into hematopoietic stem and progenitor cells (HSPCs) through a process called endothelial-to-hematopoietic transition (EHT). This study reveals that the gene Nupr1, previously identified as a signature gene of HECs, negatively regulates the EHT process. Deletion of Nupr1 in endothelial cells leads to increased HSPC generation in the aorta-gonad-mesonephros region. The study also finds that the proinflammatory cytokine TNF-alpha is upregulated in Nupr1-deficient HECs, and neutralizing TNF-alpha partially reduces excessive HSPC generation. These findings suggest that Nupr1 could be a potential target for future research on hematopoietic stem cell regeneration.
Article
Developmental Biology
Yuki Sato, Mugiho Shigematsu, Maria Shibata-Kanno, Sho Maejima, Chie Tamura, Hirotaka Sakamoto
Summary: Endothelial-to-hematopoietic transition (EHT) is an important process for the generation of hematopoietic stem cells (HSCs). The change in morphology of hemogenic endothelial cells (HECs) from flat and adherent to spherical hematopoietic cells during EHT is regulated by water influx into vacuoles. Aquaporin 1 (AQP1) plays a role in this process, as its overexpression in non-HECs induces vacuole expansion, cell rounding, and detachment from the endothelium. These findings provide insights into cell/tissue morphogenesis through water-adoptive cellular responses.
Editorial Material
Cell Biology
Ann Sanoji Samarakkody, Alan B. Cantor
Summary: The study reveals the mechanism by which RUNX1 collaborates with TGF beta signaling transcription factors to drive chromatin accessibility changes that specify hemogenic endothelial cells (HECs). It also highlights interesting parallels between hematopoietic transition (EHT) and endothelial-to-mesenchymal transition (EndoMT) during cardiac development.
GENES & DEVELOPMENT
(2021)
Article
Multidisciplinary Sciences
Christina M. Termini, Amara Pang, Tiancheng Fang, Martina Roos, Vivian Y. Chang, Yurun Zhang, Nicollette J. Setiawan, Lia Signaevskaia, Michelle Li, Mindy M. Kim, Orel Tabibi, Paulina K. Lin, Joshua P. Sasine, Avradip Chatterjee, Ramachandran Murali, Heather A. Himburg, John P. Chute
Summary: Ionizing radiation and chemotherapy deplete hematopoietic stem cells and damage the vascular niche, leading to the secretion of SEMA3A from bone marrow endothelial cells. Inhibition of NRP1 promotes vascular and hematopoietic regeneration through increased expression of R spondin 2, suggesting a potential therapeutic target for improving hematopoietic recovery after myeloablation.
NATURE COMMUNICATIONS
(2021)
Article
Biochemical Research Methods
Iain B. H. Wilson, Shi Yan, Chunsheng Jin, Zuzanna Dutkiewicz, Dubravko Rendic, Dieter Palmberger, Ralf Schnabel, Katharina Paschinger
Summary: This study used Caenorhabditis elegans as a model organism to analyze the differences in N-glycans and O-glycans at different developmental stages and cultivation methods. It was found that the nematode synthesized a diverse glycome, but there was no clear correlation with transcript levels.
MOLECULAR & CELLULAR PROTEOMICS
(2023)
Article
Biochemistry & Molecular Biology
Chunqun Wang, Wenjie Gao, Shi Yan, Xing-Quan Zhu, Xun Suo, Xin Liu, Nishith Gupta, Min Hu
Summary: N-glycosylation is a physiologically vital post-translational modification in eukaryotic organisms, and Haemonchus contortus has exclusive chitobiose modifications in its N-glycans. Immunogenic proteins like peptidases are N-glycosylated in the parasite, with glycan-rich conjugates primarily located in the intestine and gonads of adult worms, evading host immune responses. This comprehensive atlas of N-glycosylation in the prevalent parasitic nematode highlights its importance for infection, immunity, and prevention.
COMPUTATIONAL AND STRUCTURAL BIOTECHNOLOGY JOURNAL
(2021)
Article
Biochemistry & Molecular Biology
Leal Oburoglu, Els Mansell, Isaac Canals, Valgardur Sigurdsson, Carolina Guibentif, Shamit Soneji, Niels-Bjarne Woods
Summary: The emergence of blood lineages during human EHT is regulated by multiple metabolic pathways, steering the differentiation of HE cells towards specific hematopoietic lineages. Metabolism plays a key role in determining primitive versus definitive hematopoietic differentiation.
Article
Medicine, General & Internal
Panayiotis Louca, Tamara Stambuk, Azra Frkatovic-Hodzic, Ana Nogal, Massimo Mangino, Sarah E. Berry, Helena Deris, George Hadjigeorgiou, Jonathan Wolf, Martina Vinicki, Paul W. Franks, Ana M. Valdes, Tim D. Spector, Gordan Lauc, Cristina Menni
Summary: This study explores the relationship between plasma protein N-glycosylation and postprandial metabolism, and finds that certain glycans are significantly associated with postprandial triglycerides, glucose, and insulin levels. Furthermore, some glycans mediate the relationship between prediabetes and postprandial triglycerides.
Article
Developmental Biology
Laura F. Bennett, Melanie D. Mumau, Yan Li, Nancy A. Speck
Summary: The study reveals that MyD88-dependent toll like receptor (TLR) signaling regulates the numbers of lympho-myeloid biased progenitors (LMPs) and adult-repopulating hematopoietic stem cells (HSCs) in hemogenic endothelial cells and intra-arterial hematopoietic clusters.
Article
Biochemistry & Molecular Biology
Di Wang, Valeriia Kuzyk, Katarina Madunic, Tao Zhang, Oleg A. Mayboroda, Manfred Wuhrer, Guinevere S. M. Lageveen-Kammeijer
Summary: Colorectal cancer (CRC) is a common and deadly type of cancer. Studying the N-glycosylation of CRC cell lines can help identify potential therapeutic and diagnostic targets. The study found a diverse range of N-glycans among the examined CRC cell lines and discovered similarities between different platforms used for analysis.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Biochemistry & Molecular Biology
Akos Tiboldi, Johannes Fuehrer, Wolfgang Schaubmayr, Eva Hunyadi-Gulyas, Marie Louise Zach, Beatrix Hochreiter, Andreas Spittler, Roman Ullrich, Klaus Markstaller, Friedrich Altmann, Klaus Ulrich Klein, Verena Tretter
Summary: This study investigated the effects of different oxygen conditions on the glycobiology of the pulmonary endothelium, showing that oxygen can influence glycan structures which in turn affect cell interactions and signaling.
Article
Multidisciplinary Sciences
Leal Oburoglu, Els Mansell, Niels-Bjarne Woods
Summary: Glutamine metabolism plays an essential role in regulating the emergence and specification of hematopoietic cells during endothelial to hematopoietic transition (EHT), with different hematopoietic lineages requiring distinct derivatives of glutamine.
SCIENTIFIC REPORTS
(2021)
Article
Biochemistry & Molecular Biology
Helena Deris, Petra Tominac, Frano Vuckovic, Arne Astrup, Ellen E. Blaak, Gordan Lauc, Ivan Gudelj
Summary: The aberrant plasma protein glycosylation associated with various diseases was studied by analyzing glycomes from participants of the Diogenes study. Significant alterations in glycan structures were observed 8 weeks after the low-calorie diet, but these effects were nullified during the weight-maintenance diets period.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Biochemistry & Molecular Biology
Johannes Helm, Lena Hirtler, Friedrich Altmann
Summary: This study conducted an isomer-specific analysis of human brain N-glycome using standardized porous graphitic carbon LC-MS/MS technology, revealing structural differences and specific structures associated with neuronal diseases.
Article
Biochemical Research Methods
Martina Zahradnikova, Ivana Ihnatova, Erika Lattova, Lukas Uhrik, Eliska Stuchlikova, Rudolf Nenutil, Dalibor Valik, Monika Nalezinska, Josef Chovanec, Zbynek Zdrahal, Borivoj Vojtesek, Lenka Hernychova, Milos Novotny
Summary: Investigating N-glycans in non-mucinous ovarian cancer patients may identify potential markers associated with resistance to platinum/taxane chemotherapy. Detection sensitivity to chemotherapy is crucial for these patients.
JOURNAL OF PROTEOMICS
(2021)
Article
Veterinary Sciences
Kira J. Noordwijk, Rui Qin, Maria E. Diaz-Rubio, Sheng Zhang, Jin Su, Lara K. Mahal, Heidi L. Reesink
Summary: This study identified differentially expressed metabolic and glycosylation pathways in synovial fluid from healthy horses and horses with naturally occurring carpal osteoarthritis. The results suggest potential diagnostic and therapeutic targets for equine osteoarthritis, and further targeted metabolomic and glycomic studies are recommended to verify these findings. Lectin microarrays could be a potential screening tool for the diagnosis and therapeutic monitoring of equine osteoarthritis.
EQUINE VETERINARY JOURNAL
(2022)
Article
Biochemistry & Molecular Biology
Daniel Bojar, Lawrence Meche, Guanmin Meng, William Eng, David F. Smith, Richard D. Cummings, Lara K. Mahal
Summary: Glycans play critical roles in biology and medicine, but the specificity of lectins, which are key proteins in glycans binding, has not been well-defined. In this study, machine learning algorithms and expert annotation were used to define the lectin specificity for 57 unique lectins. This research provides important insights into the complex binding features of commercially available lectins.
ACS CHEMICAL BIOLOGY
(2022)
Article
Biochemistry & Molecular Biology
Linh Nguyen, Kelli A. McCord, Duong T. Bui, Kim M. Bouwman, Elena N. Kitova, Mohamed Elaish, Dhanraj Kumawat, Gour C. Daskhan, Ilhan Tomris, Ling Han, Pradeep Chopra, Tzu-Jing Yang, Steven D. Willows, Andrew L. Mason, Lara K. Mahal, Todd L. Lowary, Lori J. West, Shang-Te Danny Hsu, Tom Hobman, Stephen M. Tompkins, Geert-Jan Boons, Robert P. de Vries, Matthew S. Macauley, John S. Klassen
Summary: Evidence suggests that host glycans, specifically glycolipids containing sialic acid, play a role in facilitating the entry of SARS-CoV-2 virus into host cells by binding to the receptor-binding domain (RBD) of the spike protein. Depletion of cell surface sialic acid levels through various methods decreases RBD binding and infection of the virus, indicating the importance of sialylated glycans in viral entry.
NATURE CHEMICAL BIOLOGY
(2022)
Article
Medicine, Research & Experimental
Lingjuan Hong, Na Li, Victor Gasque, Sameet Mehta, Lupeng Ye, Yinyu Wu, Jinyu Li, Andreas Gewies, Juergen Ruland, Karen K. Hirschi, Anne Eichmann, Caroline Hendry, David van Dijk, Arya Mani
Summary: The study identified Prdm6 as an epigenetic modifier that regulates the fate of migrating cardiac NCCs (CNCCs) by controlling the expression of CNCC specification genes. Loss of Prdm6 resulted in impaired CNCC differentiation and migration, leading to congenital heart diseases.
Article
Chemistry, Analytical
Duong T. Bui, Jaesoo Jung, Elena N. Kitova, Zhixiong Li, Steven D. Willows, Marie E. Boddington, Pavel Kitov, Andrew L. Mason, Chantelle J. Capicciotti, Lara K. Mahal, Matthew S. Macauley, John S. Klassen
Summary: Mass spectrometry-based shotgun glycomics (MS-SG) is a rapid and sensitive method for discovering natural ligands of glycan-binding proteins (GBPs). By combining CaR-ESI-MS data with HILIC quantification, relative affinities can be ranked. The study suggests that the 2-AB(CaR-ESI-MS)/2-AB(HILIC) combination provides the most reliable description of GBP binding specificities for N-glycans.
ANALYTICAL CHEMISTRY
(2022)
Article
Chemistry, Medicinal
Daniel W. Heindel, Shuhui Chen, Peter Aziz, Jonathan Y. Chung, Jamey D. Marth, Lara K. Mahal
Summary: Sepsis causes changes in the glycome of the blood sera, regardless of the Gram-positive or Gram-negative nature of the bacteria. It leads to a decrease in bisecting GlcNAc and an increase in core 1/3 O-glycans. The major cause of this glycan shift is a high molecular weight protein induced by the four bacterial pathogens, which include ITIHs and fibronectin.
ACS INFECTIOUS DISEASES
(2022)
Article
Chemistry, Analytical
Richard Lauman, Hee Jong Kim, Lindsay K. Pino, Alessandro Scacchetti, Yixuan Xie, Faith Robison, Simone Sidoli, Roberto Bonasio, Benjamin A. Garcia
Summary: Post-transcriptional modifications greatly affect the structure and function of RNA. Current sequencing and mass spectrometry methods have limitations in accurately identifying and cataloging RNA modifications. We have developed a new approach that combines high-field asymmetric ion mobility separation and electrochemically modulated liquid chromatography, which significantly improves the coverage and throughput of RNA sequencing while allowing for precise identification and localization of RNA modifications.
ANALYTICAL CHEMISTRY
(2023)
Article
Oncology
Michael Russelle Alvarez, Qingwen Zhou, Jennyfer Tena, Mariana Barboza, Maurice Wong, Yixuan Xie, Carlito B. Lebrilla, Michelle Cabanatan, Ma. Teresa Barzaga, Nelia Tan-Liu, Francisco M. Heralde, Luster Serrano, Ruel C. Nacario, Gladys Cherisse Completo
Summary: Protein glycosylation is a modification that affects a protein's function and has been correlated with cancer progression. This study aims to find unique protein glycosylation cancer biomarkers in a Philippine population, as previous research has focused on Caucasian populations. Lung cancer, particularly NSCLC, is a major cause of cancer death, and identifying potential biomarkers is crucial for diagnosis. The study analyzed the glycosylation patterns and protein expression profiles of Filipino lung cancer patients, and found specific trends that support the role of aberrant glycosylation in cancer progression.
Article
Biochemistry & Molecular Biology
Joseph Wayne M. Fowler, Nabil E. Boutagy, Rong Zhang, Daiki Horikami, Michael B. Whalen, Casey E. Romanoski, William C. Sessa
Summary: The transcription factor SREBP2 is the main regulator of cholesterol homeostasis and has been implicated in leukocyte immune responses. In this study, the role of SREBP2 in endothelial cells was investigated, revealing its impact on inflammatory chemokine production and interferon response genes.
JOURNAL OF LIPID RESEARCH
(2023)
Article
Biochemical Research Methods
Zongtao Lin, Joanna Gongora, Xingyu Liu, Yixuan Xie, Chenfeng Zhao, Dongwen Lv, Benjamin A. Garcia
Summary: Chemical proteomics utilizes small-molecule probes to study protein interactions. The application of automated robotic systems in sample preparation can accelerate research progress and expand the future of chemical biology.
JOURNAL OF PROTEOME RESEARCH
(2023)
Article
Multidisciplinary Sciences
William J. Lu-Culligan, Leah J. Connor, Yixuan Xie, Babatunde E. Ekundayo, Brendan T. Rose, Martin Machyna, Andreas P. Pintado-Urbanc, Joshua T. Zimmer, Isaac W. Vock, Natarajan V. Bhanu, Megan C. King, Benjamin A. Garcia, Franziska Bleichert, Matthew D. Simon
Summary: Lysine residues can be modified by both methylation and acetylation to form N epsilon-acetyl-N epsilon-methyllysine (Kacme). Kacme is found on histone H4 across species and mammalian tissues and is associated with active chromatin.
Article
Cell Biology
Joey J. Ghersi, Gabriel Baldissera, Jared Hintzen, Stephanie A. Luff, Siyuan Cheng, Ivan Fan Xia, Christopher M. Sturgeon, Stefania Nicoli
Summary: Ghersi et al. have found that the diversity of haematopoietic stem and progenitor cells is established at the haemogenic endothelium level and is regulated by microRNA-128-mediated modulation of Wnt and Notch signalling. Haematopoietic stem and progenitor cells (HSPCs) generate different lineages and are produced in the embryo through the transformation of haemogenic endothelial cells in the aorta-gonad-mesonephros (AGM). The researchers discovered that loss of microRNA-128 leads to an expansion of HSPCs in the AGM with different cell cycle states and a bias towards erythroid and lymphoid progenitors.
NATURE CELL BIOLOGY
(2023)
Article
Multidisciplinary Sciences
Wenping Zhou, Wenxue Li, Shisheng Wang, Barbora Salovska, Zhenyi Hu, Bo Tao, Yi Di, Ujwal Punyamurtula, Benjamin E. E. Turk, William C. C. Sessa, Yansheng Liu
Summary: The authors used optogenetics and mass spectrometry-based phosphoproteomics to study the effects of different intensities, durations, and patterns of Akt1 activation on phosphorylation circuits, revealing downstream signaling outcomes of Akt1. The study showed that different intensities, durations, and patterns of Akt1 activation lead to distinct phosphorylation profiles in vascular endothelial cells, and also revealed the interaction between Akt1 signaling and growth factor signaling in these cells. The resulting dataset provides an important resource for future studies on AKT signaling and dynamics.
NATURE COMMUNICATIONS
(2023)
Article
Chemistry, Multidisciplinary
Yixuan Xie, Francisca N. De Luna Vitorino, Ye Chen, Joanna K. Lempiainen, Chenfeng Zhao, Robert T. Steinbock, Zongtao Lin, Xingyu Liu, Emily Zahn, Arabella L. Garcia, Matthew D. Weitzman, Benjamin A. Garcia
Summary: The interest in MS-based analysis of modified nucleic acids is increasing due to the application of nucleic acids in therapeutics. However, there are few available integrated platforms for characterizing nucleic acid modifications. Herein, we report a general mass spectrometry-based SWATH platform to identify and quantify both RNA and DNA modifications, which we call SWATH analysis of modified nucleic acids (SWAMNA). SWAMNA incorporates the search engine, NuMo finder, enabling the analysis of modifications in native and permethylated form. SWAMNA will aid discoveries that provide new insights into nucleic acid modifications. A comprehensive platform, SWAMNA, is reported, enabling general researchers to obtain information about nucleoside modifications.
CHEMICAL COMMUNICATIONS
(2023)
Review
Gastroenterology & Hepatology
Michele A. Rodrigues, Dawidson A. Gomes, Romina Fiorotto, Mateus T. Guerra, Jittima Weerachayaphorn, Tao Bo, William C. Sessa, Mario Strazzabosco, Michael H. Nathanson
Summary: Fluid and bicarbonate secretion in cholangiocytes is regulated by ITPR3, which localizes to the apical region. This localization is dependent on intact lipid rafts and interactions with CAV1 and MYH9. Disruption of lipid rafts or knockdown of CAV1 or MYH9 impairs ITPR3 localization and secretion.
HEPATOLOGY COMMUNICATIONS
(2022)