A5084043525- Advanced Proteomics Techniques and Applications
- Mass Spectrometry Techniques and Applications
- Metabolomics and Mass Spectrometry Studies
- Pancreatic and Hepatic Oncology Research
- Extracellular vesicles in disease
- Colorectal Cancer Treatments and Studies
- FOXO transcription factor regulation
- Lung Cancer Treatments and Mutations
- Cancer, Lipids, and Metabolism
- Molecular Biology Techniques and Applications
- Cancer Genomics and Diagnostics
- RNA modifications and cancer
- MicroRNA in disease regulation
- Ferroptosis and cancer prognosis
- Cancer Cells and Metastasis
- Peptidase Inhibition and Analysis
- Genetic factors in colorectal cancer
- Chemical Reactions and Isotopes
- Cancer Research and Treatments
- Redox biology and oxidative stress
- Cell Adhesion Molecules Research
- Renal cell carcinoma treatment
- Cancer, Hypoxia, and Metabolism
- Machine Learning in Bioinformatics
- Tuberculosis Research and Epidemiology
Amsterdam UMC Location Vrije Universiteit Amsterdam
2016-2025
Cancer Center Amsterdam
2011-2025
Vrije Universiteit Amsterdam
2006-2024
Amsterdam University Medical Centers
2018-2024
University Medical Center
2009-2024
University Hospital and Clinics
2011-2024
The University of Texas MD Anderson Cancer Center
2024
University of Amsterdam
2016-2023
Dutch Cancer Society
2023
Alzheimer’s Disease Neuroimaging Initiative
2023
Exosomes are small endosome-derived extracellular vesicles implicated in cell–cell communication and secreted by living cells when multivesicular bodies (MVBs) fuse with the plasma membrane (PM). Current techniques to study exosome physiology based on isolation procedures after secretion, precluding direct dynamic insight into mechanics of biogenesis regulation their release. In this study, we propose real-time visualization MVB–PM fusion overcome these limitations. We designed...
The cell envelope of mycobacteria, a group Gram positive bacteria, is composed plasma membrane and Gram-negative-like outer containing mycolic acids. In addition, the surface mycobacteria coated with an ill-characterized layer extractable, non-covalently linked glycans, lipids proteins, collectively known as capsule, whose occurrence matter debate. By using plunge freezing cryo-electron microscopy technique, we were able to show that pathogenic produce thick only present when cells grown...
Abstract Urine is commonly used for clinical diagnosis and biomedical research. The discovery of extracellular vesicles (EV) in urine opened a new fast‐growing scientific field. In the last decade urinary (uEVs) were shown to mirror molecular processes as well physiological pathological conditions kidney, urothelial prostate tissue. Therefore, several methods isolate characterize uEVs have been developed. However, methodological aspects EV separation analysis, including normalization...
Summary ESX‐5 is one of the five type VII secretion systems found in mycobacteria. These are also known as ESAT‐6‐like systems. Here, we have determined secretome by a proteomic approach two different strains Mycobacterium marinum . Comparison profile wild‐type and their mutants showed that number PE_PGRS PPE‐MPTR proteins dependent on for transport. The PE PPE protein families unique to mycobacteria, highly expanded several pathogenic species, such tuberculosis M. , certain family members...
The postsynaptic density contains multiple protein complexes that together relay the presynaptic neurotransmitter input to activation of neuron. In present study we took two independent proteome approaches for characterization complement density, namely 1) two-dimensional gel electrophoresis separation proteins in conjunction with mass spectrometry identify tryptic peptides spots and 2) isolation trypsin-digested sample was labeled isotope-coded affinity tag, followed by liquid...
Abstract Motivation: Spectral count data generated from label-free tandem mass spectrometry-based proteomic experiments can be used to quantify protein's abundances reliably. Comparing spectral different sample groups such as control and disease is an essential step in statistical analysis for the determination of altered protein level biomarker discovery. The Fisher's exact test, G-test, t-test local-pooled-error technique (LPE) are commonly differential data. However, our initial two...
The imaging capabilities of time-of-flight secondary ion mass spectrometry (ToF−SIMS) and MALDI-MS sample preparation methods were combined. We used this method, named matrix-enhanced (ME) SIMS, for direct molecular nervous tissue at micrometer spatial resolution. Cryosections the cerebral ganglia freshwater snail Lymnaea stagnalis placed on indium−tin−oxide (ITO)-coated conductive glass slides covered with a thin layer 2,5-dihydroxybenzoic acid by electrospray deposition. High-resolution...
Mycobacteria possess different type VII secretion (T7S) systems to secrete proteins across their unusual cell envelope. One of these systems, ESX-5, is only present in slow-growing mycobacteria and responsible for the multiple substrates. However, role ESX-5 substrates growth and/or virulence largely unknown. In this study, we show that esx-5 essential both Mycobacterium marinum bovis. Remarkably, essentiality can be rescued by increasing permeability outer membrane, either altering its...
Summary Pathogenic mycobacteria require type VII secretion ( T7S ) systems to transport virulence factors across their complex cell envelope. These bacteria have up five of these systems, termed ESX ‐1 ‐5. Here, we show that ‐5 M ycobacterium tuberculosis mediates the EsxN , PPE and PE_PGRS proteins, indicating is a major pathway in this important pathogen. Using system marinum bovis BCG as model, purified analysed membrane under native conditions. blue native‐ PAGE immunoprecipitation...
Background Cancer cells are able to change the protein expression and behavior of non‐cancerous surrounding cells. Exosomes, secreted by prostate cancer (PCa) cells, may have a functional role in metastasis present promising source for biomarkers. The aim study was identify which proteins exosomes can influence determine whether we use urine exosomal high‐risk PCa patients. Method Exosomes were isolated ultracentrifugation. Migration invasion studied transwell (invasion) assay. Proteomics...
Complex interactions between DNA herpesviruses and host factors determine the establishment of a life-long asymptomatic latent infection. The lymphotropic Epstein-Barr virus (EBV) seems to avoid recognition by innate sensors despite massive transcription immunostimulatory small RNAs (EBV-EBERs). Here we demonstrate that in latently infected B cells, EBER1 transcripts interact with lupus antigen (La) ribonucleoprotein, avoiding cytoplasmic RNA sensors. However, coculture experiments observed...
In order to successfully enter the latent stage, Mycobacterium tuberculosis must adapt conditions such as nutrient limitation and hypoxia. vitro models that mimic infection are valuable tools for describing changes in metabolism occur when bacterium exists a non-growing form. We used two complementary proteomic approaches, label-free LC-MS/MS analysis two-dimensional difference gel electrophoresis, determine proteome profile of extracellular proteins from M. cultured under starvation....
Estrogen receptor alpha (ERα) is involved in numerous physiological and pathological processes, including breast cancer. Breast cancer therapy therefore currently directed at inhibiting the transcriptional potency of ERα, either by blocking estrogen production through aromatase inhibitors or antiestrogens that compete for hormone binding. Due to resistance, new treatment modalities are needed as ERα dimerization essential its activity, interference with offers a opportunity exploit drug...
The cancer cell secretome has emerged as an attractive subproteome for discovery of candidate blood-based biomarkers. To choose the best performing workflow, we assessed performance three first-dimension separation strategies prior to nanoLC-MS/MS analysis: (1) 1D gel electrophoresis (1DGE), (2) peptide SCX chromatography, and (3) tC2 protein reversed phase chromatography. 1DGE using 4-12% gradient gels outperformed methods with respect number identified proteins (1092 vs 979 580,...
Patients with liver metastases from colon carcinoma show highly variable responses to chemotherapy and tumor recurrence is frequently observed. Therapy-resistant cancer stem cells have been implicated in drug resistance recurrence. However, the factors determining therapy are poorly understood. The aim of this study was gain insight into these mechanisms by comparing proteomes patient-derived cell cultures their differentiated isogenic offspring. We established colonosphere derived resection...
ABSTRACT Outer membrane vesicles (OMVs) are spherical nanoparticles that naturally shed from Gram-negative bacteria. They rich in immunostimulatory proteins and lipopolysaccharide but do not replicate, which increases their safety profile renders them attractive vaccine vectors. By packaging foreign polypeptides OMVs, specific immune responses can be raised toward heterologous antigens the context of an intrinsic adjuvant. Antigens exposed at vesicle surface have been suggested to elicit...
Method12 April 2019Open Access Transparent process INKA, an integrative data analysis pipeline for phosphoproteomic inference of active kinases Robin Beekhof orcid.org/0000-0002-9500-528X Medical Oncology, Cancer Center Amsterdam, Amsterdam UMC, Vrije Universiteit The Netherlands OncoProteomics Laboratory, Search more papers by this author Carolien van Alphen Alex A Henneman orcid.org/0000-0002-3746-4410 Jaco C Knol Thang V Pham Frank Rolfs Mariette Labots Evan Henneberry Tessa YS Le Large...