Article
Immunology
Jiangbei Yuan, Zhangfu Li, Zewei Lin, Siyu Yao, Yuewen Han, Qihuan Fu, Jikui Liu
Summary: The Steap3-Gm2a axis restricts the phagosomal escape of L. monocytogenes and may serve as a potential molecular drug target for antibacterial treatment.
MICROBES AND INFECTION
(2022)
Article
Chemistry, Analytical
Madisson Chabas, Olivier Pible, Jean Armengaud, Beatrice Alpha-Bazin
Summary: To accurately and rapidly identify microorganisms from complex microbiota for clinical diagnostic purposes, an innovative label-free multiplexing method for the identification of microorganisms using tandem mass spectrometry is proposed in this paper. The method involves offline reversed-phase fractionation of individual peptidomes and achieves multiplexing by mixing fractions of staged hydrophobicity. This approach enables the identification of up to 21 microorganisms in a single 60-minute run without the use of labeling reagents, providing new perspectives for high-throughput proteotyping of bacteria in large culturomics projects.
ANALYTICAL CHEMISTRY
(2023)
Article
Chemistry, Analytical
Yuming Jiang, Alexandre Hutton, Caleb W. Cranney, Jesse G. Meyer
Summary: This article introduces an improved direct infusion and ion mobility method for proteome analysis, and proposes a label-free quantification method DISPA-LFQ, which can rapidly identify and quantify proteins in complex mixtures. This technology has important applications in drug screening, biomarker discovery, and clinical analysis.
ANALYTICAL CHEMISTRY
(2022)
Review
Chemistry, Medicinal
Jichao Sun, Nayana Prabhu, Jun Tang, Fan Yang, Lin Jia, Jinan Guo, Kefeng Xiao, Wai Leong Tam, Par Nordlund, Lingyun Dai
Summary: Assessing drug-target engagement on a proteome-wide scale is crucial for understanding molecular mechanisms and developing more effective drugs. Label-free target deconvolution approaches have gained attention as they avoid chemical modification and offer insights into drug action mechanisms.
MEDICINAL RESEARCH REVIEWS
(2021)
Article
Cell Biology
Tian-Yi Zhu, Shang-Tong Li, Dan-Dan Liu, Xiajun Zhang, Lianqi Zhou, Rong Zhou, Bing Yang
Summary: This study quantifies protein changes during aging in different individuals using single-worm mass spectrometry, and reveals the heterogeneity of aging by reconstructing the aging trajectory and proteomic landscape of C. elegans.
Article
Biochemical Research Methods
Kailin Yu, Tianyu F. Qi, Weili Miao, Xiaochuan Liu, Yinsheng Wang
Summary: This study revealed the impact of ALKBH4 gene depletion on protein expression in HEK293T cells through a quantitative proteomic experiment. The results showed that depletion of ALKBH4 led to decreased levels of GSTP1 and HSPB1 proteins, which were associated with an increased expression level of DNMT1 and elevated cytosine methylation in the promoter regions of GSTP1 and HSPB1 genes.
Article
Agriculture, Dairy & Animal Science
Andrzej Gawor, Anna Ruszczynska, Anna Konopka, Grzegorz Wryk, Marian Czauderna, Ewa Bulska
Summary: This study investigated the effects of different dietary supplements, including selenium, on protein expression in animal tissues using global differential proteomic experiments and protein-protein interaction network analysis. Selenium was found to play a significant role in regulating important biological functions such as cell adhesion and heart development.
Article
Multidisciplinary Sciences
Rodolfo Ciuffa, Federico Uliana, Jonathan Mannion, Martin Mehnert, Tencho Tenev, Cathy Marulli, Ari Satanowski, Lena Maria Leone Keller, Pilar Natalia Rodilla Ramirez, Alessandro Ori, Matthias Gstaiger, Pascal Meier, Ruedi Aebersold
Summary: Protein-protein interactions (PPIs) are the main mode of proteome organization in cells. Traditional PPI networks lack contextual information. Generating context-dependent PPI networks is necessary for structural and systems-level modeling, but remains challenging. In this study, an experimental/computational strategy is described to achieve contextual modeling of PPIs.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
Article
Biology
Giorgio Oliviero, Sergey Kovalchuk, Adelina Rogowska-Wrzesinska, Veit Schwammle, Ole N. Jensen
Summary: In this study, the chromatin proteomes of various mouse organs were analyzed using quantitative proteomics. The results showed distinct and organ-specific temporal protein expression profiles and regulation at the post-translational level. The spleen exhibited a static chromatin proteome, reflecting its important role in physiological defense and immunity. These findings support the hypothesis that chromatin-associated proteins are involved in distinct and specific physiological functions in ageing organs.
Article
Plant Sciences
Chuanfa Liu, Guanting Niu, Xiaowen Li, Huchen Zhang, Huawei Chen, Dongxia Hou, Ping Lan, Zhi Hong
Summary: This study identified salt-responsive glycoproteins critical for plant adaptation to salt stress and highlighted the importance of N-glycan in regulating stress-responsive protein levels. A total of 97 differentially abundant glycoproteins were identified, showing differences in substrate preferences and regulatory networks between mutant types. The study further confirmed the involvement of two N-glycosylation clients in salt stress response and provided novel insights into salt stress tolerance mechanisms in Arabidopsis.
FRONTIERS IN PLANT SCIENCE
(2021)
Article
Biochemical Research Methods
Meng Wang, Lihua Jiang, Ruiqi Jian, Joanne Y. Chan, Qing Liu, Michael P. Snyder, Hua Tang
Summary: The study focused on improving normalization methods in highly heterogeneous samples, developing a novel data-driven approach to correct systematic bias while maintaining biological heterogeneity. The results showed that this method achieved the greatest reduction in bias while preserving variation across samples.
Article
Biology
Shubham Gupta, Justin C. Sing, Hannes L. Rost
Summary: DIA is a quantitative proteomics method, but consistent quantification across different LC-MS/MS instruments is challenging. To address this issue, multirun chromatogram alignment strategies have been proposed, including reference-based, MST, and Progressive alignment methods. These strategies can reduce quantitation errors and improve precision in protein measurements in multi-species datasets.
COMMUNICATIONS BIOLOGY
(2023)
Article
Multidisciplinary Sciences
Julia P. Schessner, Vincent Albrecht, Alexandra K. Davies, Pavel Sinitcyn, Georg H. H. Borner
Summary: The Dynamic Organellar Maps (DOMs) approach combines cell fractionation and shotgun-proteomics to analyze protein subcellular localization. By using data-independent acquisition (DIA) mass spectrometry, DIA-DOMs achieve deeper coverage and improve precision and reproducibility compared to previous methods. A software tool called DOM-ABC is introduced for analyzing profiling data. DIA-DOMs are applied to identify subcellular localization changes in HeLa cells, revealing cycles of Golgi proteins through endosomes. This workflow offers a superior label-free spatial proteomics approach for systematic phenotype discovery.
NATURE COMMUNICATIONS
(2023)
Article
Chemistry, Multidisciplinary
Jan Leipert, Philipp T. Kaulich, Max K. Steinbach, Britta Steer, Konrad Winkels, Christine Blurton, Matthias Leippe, Andreas Tholey
Summary: Researchers have developed a sample preparation method based on protein aggregation and acidic elution, allowing for sensitive protein identification analysis of single nematodes on a digital microfluidics device. Compared to in-tube sample preparation, this method increases proteoform identifications by 46%. Label-free quantification also reveals changes in proteoform abundance that cannot be distinguished by bottom-up proteomics. This workflow facilitates proteoform-focused analysis on limited availability samples.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2023)
Review
Genetics & Heredity
Xiulan Chen, Yaping Sun, Tingting Zhang, Lian Shu, Peter Roepstorff, Fuquan Yang
Summary: Isobaric labeling technology has become a key tool for comparing protein expression in biological samples, although challenges remain in terms of quantitative accuracy and precision. The different types of isobaric mass tags and advantages and disadvantages of the labeling method are detailed, along with precautions needed at each step of the workflow for reliable quantification results. The broad applications of isobaric labeling technology in biological and clinical studies, with a focus on thermal proteome profiling and proteogenomics, are also discussed.
GENOMICS PROTEOMICS & BIOINFORMATICS
(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
Biochemistry & Molecular Biology
Lotte E. E. Tholen, Heidi Schigt, Sanne G. E. Kleuskens, Caro Bos, Cornelia G. G. Spruijt, Brigith Willemsen, Michiel Vermeulen, Joost G. J. Hoenderop, Jeroen H. F. de Baaij
Summary: We identified BAIAP2L2 as a novel transcriptional target of HNF1 beta, which plays a role in maintaining epithelial cell integrity in the kidney.
Article
Biochemistry & Molecular Biology
Dirk J. W. den Braanker, Rutger J. H. Maas, Guido van Mierlo, Naomi M. J. Parr, Marinka Bakker-van Bebber, Jeroen K. J. Deegens, Pascal W. T. C. Jansen, Jolein Gloerich, Brigith Willemsen, Henry B. B. Dijkman, Alain J. J. van Gool, Jack F. M. Wetzels, Markus M. M. Rinschen, Michiel Vermeulen, Tom Nijenhuis, Johan van der Vlag
Summary: This study aimed to investigate the possible factors and mechanisms leading to recurrence of focal segmental glomerulosclerosis (FSGS) after kidney transplantation. It was found that a protein called perilipin-2 was significantly increased in infiltrating cells of patients' glomeruli and was associated with lipid droplet accumulation, suggesting it as a potential biomarker. Further research should focus on understanding how these factors alter lipid metabolism in podocytes and provide new treatment strategies.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(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)
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)