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.
Review
Cardiac & Cardiovascular Systems
Jared S. Kushner, Guoxia Liu, Robyn J. Eisert, Gary A. Bradshaw, Geoffrey S. Pitt, J. Travis Hinson, Marian Kalocsay, Steven O. Marx
Summary: This review outlines the application of proximity proteomics in cardiovascular research, discussing its principles, concepts, and potential for future research.
CIRCULATION RESEARCH
(2022)
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
Biochemistry & Molecular Biology
Mariela Gonzalez-Avendano, Simon Zuniga-Almonacid, Ian Silva, Boris Lavanderos, Felipe Robinson, Roberto Rosales-Rojas, Fabio Duran-Verdugo, Wendy Gonzalez, Monica Caceres, Oscar Cerda, Ariela Vergara-Jaque
Summary: The PPI-MASS web server provides an interactive platform for filtering protein sets based on biological features to identify protein-protein interactions with pharmacological potential. Users can manipulate filters to identify candidate proteins to establish physical contacts with a target protein, offering a powerful tool for the future design of associated therapies.
FRONTIERS IN MOLECULAR BIOSCIENCES
(2021)
Article
Multidisciplinary Sciences
Tara K. Bartolec, Xabier Vazquez-Campos, Alexander Norman, Clement Luong, Marcus Johnson, Richard J. Payne, Marc R. Wilkins, Joel P. Mackay, Jason K. K. Low
Summary: Significant advances in cryoelectron microscopy have expanded our ability to create structural models of proteins and protein complexes. Cross-linking mass spectrometry (XL-MS) is demonstrated to be a powerful tool for high-throughput experimental assessment of protein structures and interactions. The combination of XL-MS data with AlphaFold2 predictions offers opportunities to explore the structural proteome and interactome in depth.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2023)
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
Biochemistry & Molecular Biology
Aaron R. Rodriques, Aaron J. Myers, Michael E. Scharf, Uma K. Aryal, Gary W. Bennett, Ameya D. Gondhalekar
Summary: This study measured the relative abundance of the Bla g 2 protein and mRNA in different tissues and life stages of the German cockroach using immunoblotting, quantitative PCR, and LC-MS/MS-based quantitative profiling. The results showed that Bla g 2 protein was detected in all sampled tissues, including the male tergal glands, with relatively high abundance in adult males. Similarly, Bla g 2 mRNA transcript levels were also comparatively higher in male tergal glands and adult males. These findings provide new insights into the distribution and abundance of the medically significant Bla g 2 allergen in the development of the German cockroach.
ARCHIVES OF INSECT BIOCHEMISTRY AND PHYSIOLOGY
(2022)
Review
Biochemistry & Molecular Biology
Isabell Bludau
Summary: This article summarizes the advantages and limitations of mass spectrometry-based interactome screening methods, with a focus on the applicability of hypothesis-driven and discovery-driven data analysis concepts in large-scale protein-protein interaction studies. Hypothesis-driven complex- or network-centric analysis approaches are highlighted as promising strategies for comparative research.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Biochemistry & Molecular Biology
Dany Dominguez-Perez, Daniela Almeida, Josef Wissing, Andre M. Machado, Lothar Jansch, Agostinho Antunes, Luis Filipe Castro, Vitor Vasconcelos, Alexandre Campos, Isabel Cunha
Summary: This study focused on the adhesive system of the stalked goose barnacle L. anatifera, identifying a variety of proteins including cement specific adhesive proteins, proteases, protease inhibitors, and other structural proteins. Through shotgun proteomic analysis, the researchers identified and quantified peptide sequences in the adhesive gland and cement, providing insight into the composition of the adhesive proteins. The study also identified unannotated proteins with similar properties to known CPs and demonstrated the importance of Principal Components Analysis in identifying non-conserved adhesive proteins.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
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)
Review
Biochemistry & Molecular Biology
Joohyun Ryu, Stefani N. Thomas
Summary: Ovarian cancer is a deadly gynecologic malignancy with the need for new and more effective treatment strategies, while early detection and protein biomarkers play crucial roles. Targeted proteomics methods, including mass spectrometry, offer robust solutions for the development of ovarian cancer biomarkers.
Article
Medicine, Research & Experimental
Lisa Schweizer, Tina Schaller, Maximilian Zwiebel, Oezge Karayel, Johannes Bruno Mueller-Reif, Wen-Feng Zeng, Sebastian Dintner, Thierry M. Nordmann, Klaus Hirschbuehl, Bruno Maerkl, Rainer Claus, Matthias Mann
Summary: SARS-CoV-2 can cause damage to lung tissue and other organs in the human body, and this study aimed to analyze these effects comprehensively. Using a mass spectrometry proteomics workflow, the researchers identified inflammatory responses as the initial reaction in all tissues. They also found specific patterns of damage in different organs, such as diffuse alveolar damage in the lungs and organ-specific changes in the kidneys, liver, and lymphatic and vascular systems. In the brain, secondary inflammatory effects were linked to neurotransmitter receptors and myelin degradation. These findings contribute to our understanding of the mechanisms of COVID-19 and provide insights for organ-specific therapeutic interventions.
EMBO MOLECULAR MEDICINE
(2023)
Review
Oncology
Elizabeth A. Connolly, Peter S. Grimison, Lisa G. Horvath, Phillip J. Robinson, Roger R. Reddel
Summary: Sarcoma, a rare and complex disease, faces challenges in diagnosis, disease classification, lack of effective treatment options, and identification of biomarkers and drug targets. Proteomics, the study of proteins, offers insights into cancer biology. This review discusses quantitative proteomic studies in sarcoma, highlighting the potential for diagnostic, prognostic, and therapeutic biomarkers. The application of proteomic methodologies in various sarcoma subtypes is described, with a focus on histological classification and understanding disease heterogeneity. The importance of proteomic research in addressing unmet needs in sarcoma is outlined.
FRONTIERS IN ONCOLOGY
(2023)
Article
Biochemical Research Methods
Kelly A. Dingess, Pauline van Dam, Jing Zhu, Marko Mank, Karen Knipping, Albert J. R. Heck, Bernd Stahl
Summary: Immunoglobulins in human milk, especially secretory immunoglobulin A (sIgA), play a crucial role in protecting breastfed infants from pathogens. Researchers developed a sIgA ELISA method for quantitative analysis of total sIgA in human milk, which showed strong correlation with mass spectrometry-detected IgA1, suggesting it as a superior indicator compared to standard serum IgA ELISA kits.
ANALYTICAL AND BIOANALYTICAL CHEMISTRY
(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
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
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)
