Article
Chemistry, Analytical
Alaa Riezk, Vasin Vasikasin, Richard C. C. Wilson, Timothy M. M. Rawson, James G. G. McLeod, Rishi Dhillon, Jamie Duckers, Anthony E. G. Cass, Alison H. H. Holmes
Summary: This study aimed to establish and validate a rapid and reliable liquid chromatography-tandem mass spectrometry (LC/MS) method for the simultaneous quantification of cefiderocol and meropenem in human plasma of critically ill patients. The method involved protein precipitation using acetonitrile for sample clean-up, followed by reverse phase chromatography using triple quadrupole LC/MS. The developed method showed good linearity, accuracy, and sensitivity for both cefiderocol and meropenem, with stability at different temperatures and protein binding assessed in human plasma.
ANALYTICAL METHODS
(2023)
Article
Biochemistry & Molecular Biology
Simone Venz, Viola von Bohlen Und Halbach, Christian Hentschker, Heike Junker, Andreas Walter Kuss, Thomas Sura, Elke Krueger, Uwe Voelker, Oliver von Bohlen Und Halbach, Lars Riff Jensen, Elke Hammer
Summary: A workflow for tandem mass spectrometry-based protein profiling of immunohistochemistry specimens was established and applied to tissue sections. The CA1 region of the hippocampus was investigated using protein extraction and digestion methods followed by mass spectrometry measurement and data analysis. Literature searches and Gene Ontology annotation verified the applicability of this method for global protein profiling using formalin-fixed and embedded material and previously used immunohistochemistry slides.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Cell Biology
Devasahayam Arokia Balaya Rex, Yashwanth Subbannayya, Prashant Kumar Modi, Akhina Palollathil, Lathika Gopalakrishnan, Yashodhar P. Bhandary, Thottethodi Subrahmanya Keshava Prasad, Sneha M. Pinto
Summary: Interleukin-33 (IL-33) is an important cytokine involved in innate and adaptive immune responses. Aberrant IL-33 signaling has been shown to play a defensive role in infectious and inflammatory diseases. This study used quantitative phosphoproteomics analysis to investigate the temporal signaling dynamics of IL-33 in THP-1 monocytes, and identified differentially regulated proteins and pathways involved in IL-33 signaling.
Article
Chemistry, Analytical
Yunming Liu, Minghui Qu, Mengting Pan, Xiaofang Zheng, Yuwei Sheng, Yongqin Ji, Changjun You, Xiaoxia Dai
Summary: A chemical proteomic strategy was developed to identify over 70 potential UTP-binding proteins in the human proteome, revealing their involvement in multiple cellular processes. This high-throughput analysis provides a new method for the identification and quantification of UTP-binding proteins.
ANALYTICA CHIMICA ACTA
(2021)
Article
Chemistry, Multidisciplinary
Lin Bai, Guojian Yang, Zhaoyu Qin, Jiacheng Lyu, Yunzhi Wang, Jinwen Feng, Mingwei Liu, Tongqing Gong, Xianju Li, Zhengyang Li, Jixi Li, Jun Qin, Wenjun Yang, Chen Ding
Summary: This study used a novel method to analyze the binding activity of transcription factors under DNA modifications and identified potential readers for 5fC-modified DNA. By quantifying the modified DNA-binding activity of 1039 TFs, it revealed the hierarchical networks between the transcriptional protein machinery and modified DNA.
Article
Biochemical Research Methods
Philipp E. Geyer, Sebastian Porsdam Mann, Peter Treit, Matthias Mann
Summary: The goal of clinical proteomics is to assist in diagnosis, prognosis, and treatment by identifying, quantifying, and characterizing proteins in body fluids or tissues. However, ethical issues arise related to the privacy and sensitive information that can potentially be derived from proteomics data. Discussion and consideration of these ethical aspects are necessary for the development of guidelines in clinical proteomics.
MOLECULAR & CELLULAR PROTEOMICS
(2021)
Article
Chemistry, Multidisciplinary
Xiaoyun Zhang, Jochen Spiegel, Sergio Martinez Cuesta, Santosh Adhikari, Shankar Balasubramanian
Summary: The CMPP strategy allows for the investigation of DNA G-quadruplex (G4) interactions with proteins in native chromatin. This approach enables the identification of G4-interacting proteins in live cells, providing a chemical strategy to study molecular interactions in cellular chromatin.
Review
Biochemistry & Molecular Biology
Hans H. Wandall, Mathias A. I. Nielsen, Sarah King-Smith, Noortje de Haan, Ieva Bagdonaite
Summary: O-glycosylation, particularly O-GalNAc glycans, plays crucial roles in tissue development, homeostasis, and host-microbe interactions. Technological advancements, such as mass spectrometry and genetic engineering, have allowed for a better understanding of O-glycosylation profiles and functions, with high-throughput O-glycoproteomics providing comprehensive insights. However, there is still much to explore, especially in understanding the context-dependent functions of O-glycans in different cellular processes and disease states.
Article
Oncology
Xinyan Wu, Li Wang, Nicole A. Pearson, Santosh Renuse, Ran Cheng, Ye Liang, Dong-Gi Mun, Anil K. Madugundu, Yaoyu Xu, Parkash S. Gill, Akhilesh Pandey
Summary: This study utilized mass spectrometry-based proteomics to quantify cancer signaling regulated by AXL activation, identifying over 1000 phosphotyrosine sites and upregulation of cancer-promoting and cell migration pathways. Rapid phosphorylation of multiple receptor tyrosine kinases and protein tyrosine phosphatases was observed upon GAS6 stimulation. The study provides insights into AXL's oncogenic role and potential therapeutic targets.
Article
Chemistry, Analytical
Na Wu, Lingyi Jiao, Matthias Butikofer, Zhihui Zeng, Renato Zenobi
Summary: This study successfully utilized commercially available purified proteins as internal standards for high-mass MALDI-MS analysis, achieving absolute quantification of various high-mass analytes. By systematically evaluating four sample deposition methods and using a sandwich deposition method with saturated sinapinic acid, robust quantitative analysis by high-mass MALDI-MS was performed. Furthermore, combining this quantitative strategy with chemical cross-linking allowed for evaluation of the affinity of protein-protein interactions, providing dissociation constants between 10 nM and 5 mu M for the protein complexes formed.
ANALYTICAL CHEMISTRY
(2021)
Article
Biology
Ruben Rosas, Rhiannon R. Aguilar, Nina Arslanovic, Anna Seck, Duncan J. Smith, Jessica K. Tyler, Mair E. A. Churchill
Summary: The histone chaperone CAF-1 deposits histone H3/H4 dimers onto newly replicated DNA to form the central core of the nucleosome tetrasome. The KER SAH region of CAF-1 plays a crucial role in ensuring the assembly of tetrasomes by linking functional domains within CAF-1 with structural precision.
Article
Multidisciplinary Sciences
Jing Kai Chang, Guoshou Teo, Yael Pewzner-Jung, Daniel J. Cuthbertson, Anthony H. Futerman, Markus R. Wenk, Hyungwon Choi, Federico Torta
Summary: In this study, an untargeted lipidomics workflow using Q-RAI DIA approach was proposed, which enables simultaneous identification and reproducible relative quantification of lipids. This method was validated using lipid extracts from human plasma and serum samples from CerS2 null mice, and several lipid species significantly different between groups were identified.
SCIENTIFIC REPORTS
(2023)
Article
Biochemical Research Methods
Cathrin Grawe, Miguel Hernandez-Quiles, Pascal W. T. C. Jansen, Annika Brimmers, Michiel Vermeulen
Summary: In recent years, quantitative mass spectrometry-based interaction proteomics technology has been effective in identifying specific DNA-protein interactions. The PASMAN method was developed using a SILAC/TMT-based higher-order multiplexing approach, allowing the determination of specific DNA-protein interactions and their apparent binding affinities. This method was applied to study two CGCG-containing consensus DNA motifs and revealed distinct affinities of two BEN domain-containing proteins, BANP and BEND3, towards these motifs.
JOURNAL OF PROTEOME RESEARCH
(2023)
Article
Biochemistry & Molecular Biology
Kaixuan Luo, Jianling Zhong, Alexias Safi, Linda K. Hong, Alok K. Tewari, Lingyun Song, Timothy E. Reddy, Li Ma, Gregory E. Crawford, Alexander J. Hartemink
Summary: In this study, we developed a method called TF Occupancy Profiler (TOP) that allows comprehensive observation and quantification of the binding of multiple transcription factors (TFs) in the genome using data from chromatin accessibility experiments. TOP enables the study of how TF occupancy changes across different cell types, exposure to hormones, and genetic backgrounds of individuals.
Review
Biochemistry & Molecular Biology
Ilka Wittig, Pedro Felipe Malacarne
Summary: Complexome profiling is a mass spectrometry-based method that can provide insights into protein assembly, stability, and remodeling in health and disease. It combines various separation and sequencing techniques to generate detailed inventories of protein assemblies within cells.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Biochemical Research Methods
Irene Santos-Barriopedro, Guido van Mierlo, Michiel Vermeulen
Summary: This article introduces a proximity biotinylation method in cells without transfection or transduction, which utilizes a recombinant enzyme to identify proteins near a specific protein of interest. The method can be completed within 3 days and can be adapted to study different subcellular regions.
Article
Oncology
Jennifer Eymael, Martijn van den Broek, Laura Miesen, Valerie Villacorta Monge, Bartholomeus T. van den Berge, Fieke Mooren, Vicky Luna Velez, Jelmer Dijkstra, Meyke Hermsen, Peter Bandi, Michiel Vermeulen, Saskia de Wildt, Brigith Willemsen, Sandrine Florquin, Roy Wetzels, Eric Steenbergen, Rafael Kramann, Marcus Moeller, Michiel F. Schreuder, Jack Fm Wetzels, Johan van der Vlag, Jitske Jansen, Bart Smeets
Summary: Scattered tubular cells (STCs) in the proximal tubule increase in number after acute kidney injury. STCs are preferentially located within the inner bends of the tubule and their number increases with age. STCs represent a transient state of dedifferentiated proximal tubule epithelial cells (PTECs) showing metabolic shift towards glycolysis, facilitating cellular survival after kidney injury.
JOURNAL OF PATHOLOGY
(2023)
Article
Biochemical Research Methods
Jelmer J. Dijkstra, Hannah K. Neikes, Somayeh Rezaeifard, Xuhui Ma, Emile E. Voest, Daniele V. F. Tauriello, Michiel Vermeulen
Summary: Loss of SMAD4 in colorectal cancer leads to changes in biological processes, including decreased differentiation and activation of pro-migratory and cell proliferation processes, disruption of key oncogenic pathways, and increased secretion of proteins involved in pro-metastatic processes. SMAD4-mutant organoids specifically secrete DKK3, which reduces the antitumor effects of natural killer cells.
JOURNAL OF PROTEOME RESEARCH
(2023)
Article
Biochemistry & Molecular Biology
Maria V. Luna Velez, Hannah K. Neikes, Rebecca R. Snabel, Yarah Quint, Chen Qian, Aniek Martens, Gert Jan C. Veenstra, Michael R. Freeman, Simon J. van Heeringen, Michiel Vermeulen
Summary: In this study, a multi-omics approach was used to investigate the molecular mechanisms driving M cell differentiation in mouse small intestinal organoids. Cell type-specific regulatory elements and associated transcription factors were identified through chromatin accessibility changes and transcription factor dynamics. The transcription factor ONECUT2 was found to play a role in enterocyte differentiation and restrict M cell lineage specification.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Cell Biology
Gaurav Kumar Pandey, Nick Landman, Hannah K. Neikes, Danielle Hulsman, Cor Lieftink, Roderick Beijersbergen, Krishna Kalyan Kolluri, Sam M. Janes, Michiel Vermeulen, Jitendra Badhai, Maarten van Lohuizen
Summary: More than half of patients with malignant mesothelioma have alterations in the BAP1 tumor-suppressor gene. CRISPR-Cas9 kinome screening in mesothelioma cells identified two kinases in the mevalonate/cholesterol biosynthesis pathway. Inhibition of PRC2 and the mevalonate pathway showed a potent anti-tumor effect in Bap1-deficient mesothelioma, suggesting a targeted combination therapy.
CELL REPORTS MEDICINE
(2023)
Article
Biochemistry & Molecular Biology
Dieuwke L. Marvin, Jelmer Dijkstra, Rabia M. Zulfiqar, Michiel Vermeulen, Peter ten Dijke, Laila Ritsma
Summary: Melanoma patients with liver metastasis have a poor prognosis. The cytokine Transforming Growth Factor beta (TGF-beta) plays a role in melanoma cells and acts on cells in the liver. We hypothesized that this cytokine influences the metastatic outgrowth of melanoma in liver. To investigate this, we generated a model to turn on and off TGF-beta signaling in the B16F10 melanoma cells, and found that TGF-beta activation repressed cell growth and migration in vitro, while it increased outgrowth in liver in vivo.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Biochemistry & Molecular Biology
Eleanor Glancy, Cheng Wang, Ellen Tuck, Evan Healy, Simona Amato, Hannah K. Neikes, Andrea Mariani, Marlena Mucha, Michiel Vermeulen, Diego Pasini, Adrian P. Bracken
Summary: Polycomb repressive complex 2 (PRC2) mediates H3K27me3 deposition and recruits cPRC1 for repression of developmental genes. PRC2 forms two subcomplexes, PRC2.1 and PRC2.2, which have distinct roles in recruiting different forms of cPRC1. PRC2.1 catalyzes H3K27me3 and recruits CBX2/4-cPRC1, while PRC2.2 recruits CBX7-cPRC1 through its accessory protein JARID2.
Article
Biotechnology & Applied Microbiology
Hannah K. Neikes, Katarzyna W. Kliza, Cathrin Grawe, Roelof A. Wester, Pascal W. T. C. Jansen, Lieke A. Lamers, Marijke P. Baltissen, Simon J. van Heeringen, Colin Logie, Sarah A. Teichmann, Rik G. H. Lindeboom, Michiel Vermeulen
Summary: BANC-seq is a method to determine the absolute binding affinities of transcription factors to native DNA across the genome. It adds a quantitative dimension to transcription factor biology and allows prediction of binding sites under non-physiological conditions.
NATURE BIOTECHNOLOGY
(2023)
Article
Multidisciplinary Sciences
Bob J. Ignacio, Jelmer Dijkstra, Natalia Mora, Erik F. J. Slot, Margot J. van Weijsten, Erik Storkebaum, Michiel Vermeulen, Kimberly M. Bonger
Summary: THRONCAT is a threonine-derived non-canonical amino acid tagging method based on bioorthogonal threonine analog beta-ethynylserine (beta ES), which enables efficient labeling of the nascent proteome in complete growth media within minutes. It can be used in bacteria, mammalian cells, and Drosophila melanogaster, and has the potential to address diverse biological questions.
NATURE COMMUNICATIONS
(2023)
Article
Genetics & Heredity
Diana A. Llerena Schiffmacher, Katarzyna W. Kliza, Arjan F. Theil, Gert-Jan Kremers, Jeroen A. A. Demmers, Tomoo Ogi, Michiel Vermeulen, Wim Vermeulen, Alex Pines
Summary: Transcription-coupled nucleotide excision repair (TC-NER) is a highly specific process that prevents cellular toxicity caused by DNA damage and maintains proper transcription. This study used a knock-in cell line to investigate the molecular dynamics of the TC-NER protein CSB in response to physiologically relevant UV doses. The researchers discovered the tightly regulated association of CSB with chromatin, controlled by the CSA-containing ubiquitin-ligase CRL complex (CRL4CSA), and identified novel CSB interactors and variations in complex composition during TC-NER progression.
Article
Biochemistry & Molecular Biology
Glenn F. van Wigcheren, Jorge Cuenca-Escalona, Suzan Stelloo, Julia Brake, Eline Peeters, Sophie. K. Horrevorts, Siebren Frolich, Ivan Ramos-Tomillero, Yvonne Wesseling-Rozendaal, Carla M. L. van Herpen, Anja van de Stolpe, Michiel Vermeulen, I. Jolanda M. de Vries, Carl G. Figdor, Georgina Florez-Grau
Summary: Imbalanced immune responses characterized by suppressive myeloid cells are significant in cancer and autoimmunity. Understanding the induction mechanisms of myeloid-derived suppressor cells (MDSCs) and tolerogenic dendritic cells (TolDCs) can aid in developing immune-restoring therapies.
JOURNAL OF BIOLOGICAL CHEMISTRY
(2023)
Article
Biochemistry & Molecular Biology
Joep Joosten, Bob van Sluijs, Wilma Vree Egberts, Martin Emmaneel, Pascal W. T. C. Jansen, Michiel Vermeulen, Wilbert Boelens, Kimberly M. Bonger, Evan Spruijt
Summary: This study investigates the effects of altering the relative expression levels of HspB2 and HspB3 on the phase behavior of cellular proteins. The results show that co-expression of HspB2 and HspB3 forms soluble complexes, while expression of HspB2 alone forms liquid nuclear condensates, and expression biased towards HspB3 forms solid-like aggregates. These findings have important implications for understanding the regulation of protein phase behavior.
JOURNAL OF MOLECULAR BIOLOGY
(2023)
Article
Biochemical Research Methods
Cathrin Grawe, Miguel Hernandez-Quiles, Pascal W. T. C. Jansen, Annika Brimmers, Michiel Vermeulen
Summary: In recent years, quantitative mass spectrometry-based interaction proteomics technology has been effective in identifying specific DNA-protein interactions. The PASMAN method was developed using a SILAC/TMT-based higher-order multiplexing approach, allowing the determination of specific DNA-protein interactions and their apparent binding affinities. This method was applied to study two CGCG-containing consensus DNA motifs and revealed distinct affinities of two BEN domain-containing proteins, BANP and BEND3, towards these motifs.
JOURNAL OF PROTEOME RESEARCH
(2023)
Article
Biology
Leonhard A. Karl, Lorenzo Galanti, Susanne C. S. Bantele, Felix Metzner, Barbara Safaric, Lional Rajappa, Benjamin Foster, Vanessa Borges Pires, Priyanka Bansal, Erika Chacin, Jerome Basquin, Karl E. Duderstadt, Christoph F. Kurat, Till Bartke, Karl-Peter Hopfner, Boris Pfander
Summary: Fun30 is a prototype of nucleosome remodelers involved in DNA repair and gene silencing. It acts as a single-subunit nucleosome remodeler, but its molecular mechanisms are poorly understood. Through structural analysis, a conserved domain termed SAM-key is identified, and its deletion leads to defects in DNA repair and gene silencing. The SAM-key helix interacts with a critical subdomain to regulate ATPase activity, highlighting the importance of allosteric activation for Fun30 enzymes.
LIFE SCIENCE ALLIANCE
(2023)
Meeting Abstract
Transplantation
Nils Rother, Cansu Yanginlar, Tomas Post, Maaike Jacobs, Inge Jonkman, Montsy Brouns, Maarten van der Sande, Sybren Rinzema, Joost Martens, Michiel Vermeulen, Leo Joosten, Mihai Netea, Luuk Hilbrands, Zaheeb Choudry, Johan Van Der Vlag, Raphael Duivenvoorden
NEPHROLOGY DIALYSIS TRANSPLANTATION
(2023)