Article
Chemistry, Multidisciplinary
Daniel Englert, Regina Matveeva, Murat Sunbul, Richard Wombacher, Andres Jaschke
Summary: This study describes the development of a proximity-induced bio-orthogonal inverse electron-demand Diels-Alder reaction for covalent RNA labeling, utilizing the high-affinity interaction between a dienophile-modified RhoBAST aptamer and its tetramethyl rhodamine methyltetrazine substrate.
CHEMICAL COMMUNICATIONS
(2021)
Article
Chemistry, Multidisciplinary
Connor W. W. Barth, Syed Zaki Husain Rizvi, Anas M. M. Masillati, Samrat Chakraborty, Lei G. G. Wang, Antonio R. R. Montano, Dani A. A. Szafran, William S. S. Greer, Nynke S. S. van den Berg, Jonathan Sorger, Deepa A. A. Rao, Adam W. G. Alani, Summer L. L. Gibbs
Summary: Patients undergoing gynecological procedures often suffer from long-term side effects caused by nerve damage. A near-infrared fluorescent contrast agent, LGW08-35, has been developed for real-time visualization of important nerves during nerve-sparing gynecologic surgeries, which can help eliminate incontinence and sexual dysfunction in patients.
Article
Biotechnology & Applied Microbiology
Yanting Su, Yuanyuan Guo, Jieyu Guo, Ting Zeng, Ting Wang, Wu Liu
Summary: The TurboID technique successfully identified a large number of proteins that interact with FOXO1 in cells, laying the foundation for further study of FOXO1 function and its regulatory network.
Article
Biochemistry & Molecular Biology
Olanrewaju Ayodeji Durojaye
Summary: Specialized biological processes in cells are closely related to the function of proteins and their interactions, which require detailed identification of proteins to understand the underlying mechanisms. Mass spectrometry methods have been utilized for proteomic characterization, but limitations in purification methods and contamination still exist.
CELL AND BIOSCIENCE
(2021)
Article
Orthopedics
Simon B. M. MacLean, Teriana Maheno, Alex Boyle, Amanda Ragg, Gregory Bain, Ian Galley
Summary: This study used MRI to define the location of the axillary nerve in vivo from defined bony surgical landmarks. The proximity of the axillary nerve to certain anatomic points changes as it passes from anterior to posterior, while its distance from the anterolateral edge of the acromion remains relatively constant. Both distances may be influenced by humeral head size, which is important for shoulder surgeons to consider during arthroscopic or open surgery.
JOURNAL OF SHOULDER AND ELBOW SURGERY
(2021)
Review
Nanoscience & Nanotechnology
Yue Gao, Chengyan Chu, Anna Jablonska, Jeff W. M. Bulte, Piotr Walczak, Miroslaw Janowski
Summary: Extracellular vesicles (EVs) have garnered attention as potential therapeutic agents, especially in the field of central nervous system diseases. Successful clinical studies require more information on the biodistribution and tracking of EVs in vivo. Advanced imaging techniques play a crucial role in facilitating the clinical translation of EV-based therapeutics.
WILEY INTERDISCIPLINARY REVIEWS-NANOMEDICINE AND NANOBIOTECHNOLOGY
(2021)
Review
Oncology
Imke Boekestijn, Matthias N. van Oosterom, Paolo Dell'Oglio, Floris H. P. van Velden, Martin Pool, Tobias Maurer, Daphne D. D. Rietbergen, Tessa Buckle, Fijs W. B. van Leeuwen
Summary: Molecular imaging technologies are increasingly important in the diagnosis, monitoring, and treatment of cancer. The relevance and accessibility of surgical targets, as well as the selection of the correct combination of imaging agents for visualizing disease sites with high affinity and specificity are crucial. Developments within engineering/imaging physics continue to drive image-guided surgery, enhancing sensitivity and spatial resolution to ensure cancer sites are not overlooked during surgery.
Article
Chemistry, Multidisciplinary
Ying Wen, Zhiqing Long, Fangjun Huo, Caixia Yin
Summary: In this study, a metabolic probe MB-C was developed to label tumors based on metabolic differences, allowing for precise visualization.
SCIENCE CHINA-CHEMISTRY
(2022)
Article
Multidisciplinary Sciences
Ahmad Zada, Imran Khan, Min Zhang, Yuting Cheng, Xueyun Hu
Summary: The novel version of BioID, called AirID, has been proven to be more effective in identifying protein-protein interactions (PPIs) in plants compared to other PL enzymes. This method can be applied to study various plant proteins.
JOVE-JOURNAL OF VISUALIZED EXPERIMENTS
(2022)
Review
Radiology, Nuclear Medicine & Medical Imaging
Judith A. Stibbe, Petra Hoogland, Friso B. Achterberg, Derek R. Holman, Raoul S. Sojwal, Jacobus Burggraaf, Alexander L. Vahrmeijer, Wouter B. Nagengast, Stephan Rogalla
Summary: Flexible high-definition white-light endoscopy is the current gold standard for screening gastrointestinal cancer, but miss rates are high, especially in high-risk populations. Fluorescence molecular endoscopy allows real-time visualization of (pre)malignant lesions based on specific molecular features, improving detection and clinical decision-making.
MOLECULAR IMAGING AND BIOLOGY
(2023)
Article
Biochemical Research Methods
Yixin Fu, Husun Qian, Xi Zhou, You Wu, Lin Song, Kena Chen, Dan Bai, Yujun Yang, Junjie Li, Guoming Xie
Summary: This study presents a proximity ligation assay mediated rolling circle amplification (PLA-RCA) strategy for amplified imaging of glycosylated PD-L1 in situ. The feasibility of the strategy has been validated by visualizing PD-L1 glycosylation in different cancer cells and monitoring the variation of PD-L1 glycosylation during drug treatment. This work offers a useful alternative to track protein-specific glycosylation and potentially advances the investigation of the dynamic glycan state associated with the disease process.
ANALYTICAL AND BIOANALYTICAL CHEMISTRY
(2021)
Article
Medicine, Research & Experimental
Fuqiang Shao, Yu Long, Hao Ji, Dawei Jiang, Ping Lei, Xiaoli Lan
Summary: CAR-T therapy shows promising results in hematological cancers, but faces challenges in solid tumors, requiring more precise monitoring and assessment methods like radionuclide-based molecular imaging.
Article
Chemistry, Analytical
Yaxue Dai, Yongjia Tang, Wenjing Huang, Yue Zhao, Xin Gao, Yueqing Gu
Summary: This study designed novel EpCAM-targeting peptides YQ-S for precise detection of breast cancer. YQ-S2 showed greater binding affinity and ideal biosafety profile, and was chosen to represent YQ-S. By linking with a near-infrared fluorescent dye, the EpCAM-targeting probe YQ-S2-MPA was developed for real-time imaging and fluorescence-guided resection of breast cancer tumors. In vivo experiments showed higher tumor uptake of YQ-S2-MPA compared to SNF-MPA, and successful detection of metastatic lesions. YQ-S2-MPA also performed excellently in surgical navigation studies in preclinical models.
Review
Chemistry, Physical
Rui-Qin Yang, Kang-Liang Lou, Pei-Yuan Wang, Yi-Yang Gao, Yong-Qu Zhang, Min Chen, Wen-He Huang, Guo-Jun Zhang
Summary: NIR-II fluorescence imaging has shown unique advantages in guiding tumor resection surgery, with improved penetration depths and signal-to-noise ratios. Its application in cancer surgery has demonstrated significant prospects for improving surgical outcomes.
Article
Biochemical Research Methods
Yunfeng Long, Zhunjie Li, Long Wang, Xin Ao, Zhengrong Zhang, Qingjie Chen, Dan Zhu, Xinghui Liu, Ruolan Liu, Banghang Chen, He Zhu, Yanting Su
Summary: This study presents a novel approach to enrich and identify complex O-glycosylation using a highly efficient proximity labeling method. The authors demonstrate the presence of abundant O-glycosylation in nucleocytoplasmic proteins, indicating a new pathway of O-glycosylation synthesis in cells.
BIOTECHNOLOGY JOURNAL
(2023)
Article
Multidisciplinary Sciences
Kathrin Klaesener, Julia Jellusova, Geoffroy Andrieux, Ulrich Salzer, Chiara Boehler, Sebastian N. Steiner, Jonas B. Albinus, Marco Cavallari, Beatrix Suess, Reinhard E. Voll, Melanie Boerries, Bernd Wollscheid, Michael Reth
Summary: CD20 regulates the nanoscale organization of receptors on resting B lymphocytes, and its disruption leads to B cell activation and internalization of membrane proteins.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2021)
Article
Biochemical Research Methods
Andrea Fossati, Chen Li, Federico Uliana, Fabian Wendt, Fabian Frommelt, Peter Sykacek, Moritz Heusel, Mahmoud Hallal, Isabell Bludau, Tumay Capraz, Peng Xue, Jiangning Song, Bernd Wollscheid, Anthony W. Purcell, Matthias Gstaiger, Ruedi Aebersold
Summary: The study introduces a toolkit called PCprophet that predicts protein complexes and characterizes their changes using SEC-SWATH-MS data. PCprophet demonstrates improved performance compared to other methods and introduces a Bayesian approach to analyze changes in protein-protein interactions.
Article
Multidisciplinary Sciences
Federico Uliana, Matej Vizovisek, Laura Acquasaliente, Rodolfo Ciuffa, Andrea Fossati, Fabian Frommelt, Sandra Goetze, Bernd Wollscheid, Matthias Gstaiger, Vincenzo De Filippis, Ulrich Auf Dem Keller, Ruedi Aebersold
Summary: A new method for profiling protease activity is introduced, which is faster, cheaper, less demanding, easy to multiplex, and produces accurate protease fingerprints. By analyzing protease-specific peptides from cell lysates in a 96-well format, mechanistic insights into blood proteases and the prediction of protease substrates are enabled.
NATURE COMMUNICATIONS
(2021)
Review
Biochemistry & Molecular Biology
Jelena Cuklina, Chloe H. Lee, Evan G. Williams, Tatjana Sajic, Ben C. Collins, Maria Rodriguez Martinez, Varun S. Sharma, Fabian Wendt, Sandra Goetze, Gregory R. Keele, Bernd Wollscheid, Ruedi Aebersold, Patrick G. A. Pedrioli
Summary: This study discusses proteomic experiments involving hundreds of samples, and how to assess, normalize, and correct batch effects in proteomic data. The research reviews methodologies from various fields and offers solutions specific to challenges in proteomics, ultimately providing a set of techniques for controlling the quality of batch effect adjustment.
MOLECULAR SYSTEMS BIOLOGY
(2021)
Article
Biochemical Research Methods
Sandra Goetze, Kathrin Frey, Lucia Rohrer, Silvija Radosavljevic, Jan Kruetzfeldt, Ulf Landmesser, Marco Bueter, Patrick G. A. Pedrioli, Arnold von Eckardstein, Bernd Wollscheid
Summary: Advancements in mass spectrometry-based proteotype analysis have enabled a comprehensive study of High-density lipoprotein (HDL), revealing diverse protein and peptide forms in HDL. Data-independent acquisition (DIA) strategies have facilitated the establishment of spectral libraries with hundreds of protein groups and peptidoforms, aiding in the analysis of HDL proteotype differences across various physiological states and identifying post-translational modifications that may affect HDL functionality. The analysis demonstrates that protein and peptide quantities are currently more indicative of different HDL proteotypes than peptidoforms alone, highlighting the potential of DIA-based HDL proteotyping for examining larger clinical cohorts.
JOURNAL OF PROTEOME RESEARCH
(2021)
Article
Infectious Diseases
Heather L. Glasgow, Kurtis Cruz, Sean C. Murphy
Summary: Broad-range PCR targeting both ribosomal RNA and DNA significantly enhances the ability to detect and identify fungal pathogens in clinical samples, especially with RT-PCR showing a substantial increase in sensitivity.
Article
Biochemical Research Methods
Sandra Goetze, Peter Schueffler, Alcibiade Athanasiou, Anika Koetemann, Cedric Poyet, Christian Daniel Fankhauser, Peter J. Wild, Ralph Schiess, Bernd Wollscheid
Summary: Using Mass Spectrometry-GUidED Immunoassay DEvelopment (MS-GUIDE), we screened 48 literature-derived biomarker candidates to evaluate their potential utility in risk stratification scoring of prostate cancer patients. Machine learning analysis prequalified fibronectin and vitronectin as candidate biomarkers. Clinical-grade ELISAs were developed for these candidates and tested in a larger patient cohort.
CLINICAL PROTEOMICS
(2022)
Article
Microbiology
Susanna Bidgood, Jerzy Samolej, Karel Novy, Abigail Collopy, David Albrecht, Melanie Krause, Jemima Burden, Bernd Wollscheid, Jason Mercer
Summary: This study investigates the composition of poxviruses and the role of poxvirus redox proteins in host cells. Using mass spectrometry, a large number of candidate cellular and viral proteins, including redox proteins, were identified. The results show that poxvirus infection has an antioxidative effect on host cells and deletion of redox proteins is insufficient to modulate host cell redox reactions, suggesting the existence of functional redundancy.
Article
Biochemistry & Molecular Biology
Kathrin Frey, Sandra Goetze, Lucia Rohrer, Arnold von Eckardstein, Bernd Wollscheid
Summary: This study used chemoproteomic technologies to analyze the interaction between high-density lipoprotein (HDL) and cell surface receptors, identifying numerous potential HDL receptors, including the known scavenger receptor B1 (SCRB1) and other co-regulated receptors. Additionally, the study found that vascular endothelial growth factor A (VEGF-A) can remodel the cell surface composition, affecting the binding and uptake of HDL. Furthermore, the study identified another HDL receptor, receptor tyrosine-protein kinase Mer (MERTK), and demonstrated its contribution to HDL binding and its spatial proximity to SCRB1 on endothelial cells.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Immunology
Diego R. Hijano, Zhengming Gu, Jessica Brazelton, Haiqing Zhu, Sri Suganda, Heather L. Glasgow, Himani Darji, Li Tang, Thomas P. Fabrizio, Kim J. Allison, E. Kaitlynn Allen, Jeremie H. Estepp, Aditya H. Gaur, Joshua Wolf, Paul G. Thomas, Richard J. Webby, Randall T. Hayden
Summary: This study validates a quantitative SARS-CoV-2 digital PCR assay and correlates viral RNA load with symptoms and disease severity. The standardized method of measuring viral load in SARS-CoV-2 infection provided by this study is significant.
OPEN FORUM INFECTIOUS DISEASES
(2022)
Correction
Hematology
Beat Bornhauser, Gunnar Cario, Anna Rinaldi, Thomas Risch, Virginia Rodriguez Martinez, Moritz Schuette, Hans-Joerg Warnatz, Nastassja Scheidegger, Paulina Mirkowska, Martina Temperli, Claudia Moller, Angela Schumich, Michael Dworzak, Andishe Attarbaschi, Monika Brueggemann, Mathias Ritgen, Ester Mejstrikova, Andreas Hofmann, Barbara Buldini, Pamela Scarparo, Giuseppe Basso, Oscar Maglia, Giuseppe Gaipa, Tessa Lara Skroblyn, Quy A. Ngo, Geertruij te Kronnie, Elena Vendramini, Renate Panzer-Gruemayer, Malwine Jeanette Barz, Blerim Marovca, Mathias Hauri-Hohl, Felix Niggli, Cornelia Eckert, Martin Schrappe, Martin Stanulla, Martin Zimmermann, Bernd Wollscheid, Marie-Laure Yaspo, Jean-Pierre Bourquin
Meeting Abstract
Endocrinology & Metabolism
Patrick Forny, Ximena Bonilla, David Lamparter, Wenguang Shao, Tanja Plessl, Caroline Frei, Anna Bingisser, Sandra Goetze, Audrey Van Drogen, Keith Harshman, Patrick Pedrioli, Florian Traversi, Ioannis Xenarios, Ruedi Aebersold, Nicola Zamboni, Gunnar Ratsch, Emmanouil Dermitzakis, Bernd Wollscheid, D. Sean Froese, Matthias R. Baumgartner
MOLECULAR GENETICS AND METABOLISM
(2022)
Meeting Abstract
Medicine, General & Internal
P. Schuerch, L. Malinovska, M. Hofstetter, M. Hleihil, M. Losa, M. H. Wildschut, V. Lysenko, A. Lakkaraju, C. A. Maat, D. Benke, A. Aguzzi, B. Wollscheid, P. Picotti, A. P. Theocharides
SWISS MEDICAL WEEKLY
(2021)
Meeting Abstract
Medicine, General & Internal
R. Wegmann, M. Julien, S. Chevrier, T. Wildschut, T. Thavayogarajah, O. Vilinovski, F. Singer, J. Kuipers, C. Beisel, M. Levesque, B. Wollscheid, B. Bodenmiller, N. Beerenwinkel, M. Manz, B. Snijder, A. Theocharides
SWISS MEDICAL WEEKLY
(2021)
Article
Medicine, Research & Experimental
Bettina Sobottka, Marta Nowak, Anja Laura Frei, Martina Haberecker, Samuel Merki, Mitchell P. Levesque, Reinhard Dummer, Holger Moch, Viktor Hendrik Koelzer
Summary: CD8+ tumor-infiltrating T cells play a crucial role in predicting responses to immune checkpoint inhibitors in immune-oncology. A computational diagnostic algorithm was established to quantitatively measure the spatial densities of these cells in tumor compartments, leading to the successful classification into immune diagnostic categories. This approach allows for efficient immune phenotyping of metastatic lesions, even in the absence of material from the invasive margin, providing valuable insights for immunotherapy strategies in metastatic melanoma.
LABORATORY INVESTIGATION
(2021)