Is this you? As a journalist, you can create a free Muck Rack account to customize your profile, list your contact preferences, and upload a portfolio of your best work.
Claim your profile
Articles by Jan Koster
Statescope: an integrative deconvolution framework for discovering cell states in tumors
Abstract Accurate deconvolution of cell states from bulk tumor RNA-seq is hindered by heterogeneous malignant cells specifically in cancer applications. We present Statescope, a Bayesian framework that incorporates DNA-derived malignant cell purity to overcome this heterogeneity and explicitly models inter-sample variation to accurately identify cell states.
The immune landscape of pediatric Brain and Solid Tumors: A systematic review and integration of immunohistochemistry and single-cell RNA sequencing data
Abstract Background: Immunotherapies achieved remarkable success in adult cancers, yet their efficacy in pediatric brain and solid tumors remains limited. Insights into the unique immune landscape of pediatric tumors are crucial to improve immunotherapies for pediatric patients. Methods: We performed a systematic search for studies reporting immunohistochemistry (IHC), single-cell- or single-nucleus RNA-sequencing (sc/snSeq) data on the immune landscape of pediatric tumors.
The pan-cancer proteome atlas, a mass spectrometry-based landscape for discovering tumor biology, biomarkers, and therapeutic targets
|
1Amsterdam UMC, location Vrije Universiteit Amsterdam, Department of Medical Oncology, OncoProteomics Laboratory, De Boelelaan 1117, Amsterdam, the Netherlands 2Cancer Center Amsterdam, Imaging and Biomarkers, Amsterdam, the Netherlands 3School of Medicine, Westlake University, Hangzhou, Zhejiang, China 4Westlake Center for Intelligent Proteomics, Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, Zhejiang, China 5Amsterdam UMC location Vrije Universiteit Amsterdam, Department of...
By Jaco C. Knol, Mengge Lyu, Franziska Böttger, Madalena Nunes Monteiro, Thang V. Pham, Frank Rolfs, Andrea Vallés-Martí, Tim Schelfhorst, Irene V. Bijnsdorp, Shuaiyao Wang, Fangfei Zhang, Bart Westerman, Barbara Sitek, Janne Lehtiö, Jan Koster, Jan IJzermans, Maarten F. Bijlsma, Jan Paul Medema, Alex A. Henneman, Sander R. Piersma, Ruud H Brakenhoff, Jacqueline Cloos, Valentina Cordo', Daphne de Jong, Geert Kazemier, Danijela Koppers-Lalic, Mariette Labots, John Martens, Jules P.P. Meijerink, Madiha Mumtaz, Chantal Scheepbouwer, Robby E. Kibbelaar, David P. Noske, Renske D.M. Steenbergen, Winan van Houdt, Elisa Giovannetti, Jos Jonkers, tong liu, Meisi Yan, Xiaolu Zhan, Tiannan Guo, Connie R. Jimenez
|
Cell Press
Verified
Isolation of a Square Pyramidal Bis(amidophenolate)‐supported As(III)‐Cation: Coordination‐Induced Electromerism at As
Supporting Information As a service to our authors and readers, this journal provides supporting information supplied by the authors. Such materials are peer reviewed and may be re-organized for online delivery, but are not copy-edited or typeset. Technical support issues arising from supporting information (other than missing files) should be addressed to the authors.
Reporting Bone Cytopathology-A Proposal Based on a Single Tertiary Centre Experience
1 Introduction Bone tumours, whether benign or malignant, pose diagnostic and therapeutic challenges due to their varied presentation. Accurate and timely diagnosis is crucial for effective management. Imaging studies are particularly useful in differentiating between benign and malignant bone neoplasms, narrowing the diagnostic possibilities.
Identification of pancreatic cancer-specific protease substrates for protease-dependent targeted delivery - Oncogenesis
Abstract Pancreatic ductal adenocarcinoma (PDAC) presents significant challenges due to the inadequacy of existing chemotherapeutics, which often result in toxicity-dependent dose limitations and premature cessation of therapy. Targeted delivery of therapeutic molecules offers a promising solution. Given that PDAC is marked by a desmoplastic reaction with extensive aberrant protease activity, protease-dependent targeted delivery could minimize off-target toxicities and is of increasing interest.
Hypoxia Abrogates Tumor-Suppressive Activities of C/EBPδ in Pancreatic Cancer
All articles published by MDPI are made immediately available worldwide under an open access license. No special permission is required to reuse all or part of the article published by MDPI, including figures and tables. For articles published under an open access Creative Common CC BY license, any part of the article may be reused without permission provided that the original article is clearly cited. For more information, please refer to https://www.mdpi.com/openaccess.
Gemcitabine therapeutically disrupts essential SIRT1-mediated p53 repression in atypical teratoid/rhabdoid tumors
Keywords atypical teratoid/rhabdoid tumor sirtuin 1 patient-derived models therapy development pediatric oncology gemcitabine ATRT neuro oncology p53 Introduction Atypical teratoid/rhabdoid tumors (ATRTs) are highly malignant embryonal tumors of the central nervous system (CNS), often found in infants and young children.
Structural Variants in the SMC1A Gene Associated With Near‐Haploidy in Undifferentiated Pleomorphic Sarcomas
Supporting Information Filename Description gcc23255-sup-0001-TableS1.xlsxExcel 2007 spreadsheet , 247.9 KB Table S1. gcc23255-sup-0002-TableS2.xlsxExcel 2007 spreadsheet , 288 KB Table S2. References 1, , , et al., “Genome Doubling Shapes the Evolution and Prognosis of Advanced Cancers,” Nature Genetics 50 (2018): 1189–1195. 2, , , et al., “Signatures of Copy Number Alterations in Human Cancer,” Nature 606 (2022): 984–991.
The transcriptional co-repressor Runx1t1 is essential for MYCN-driven neuroblastoma tumorigenesis - Nature Communications
|
Abstract MYCN oncogene amplification is frequently observed in aggressive childhood neuroblastoma. Using an unbiased large-scale mutagenesis screen in neuroblastoma-prone transgenic mice, we identify a single germline point mutation in the transcriptional corepressor Runx1t1, which abolishes MYCN-driven tumorigenesis. This loss-of-function mutation disrupts a highly conserved zinc finger domain within Runx1t1.
By Emanuele Valli, Giorgio Milazzo, Chelsea Mayoh, Andrew Gifford, Jamie Fletcher, Laura Gamble, Daniel Carter Verified, Helen Forgham, Amanda Russell, Antoine de Weck, Piergiuseppe De Rosa, Joel P. Mackay, Glenn Marshall, Federico M. Giorgi, Jan Koster, Giovanni Perini, Michelle Haber, Nisitha Jayatilleke, Frances K. Kusuma, Martina Santulli
|
Nature
Verified
The pluripotency factor NANOG contributes to mesenchymal plasticity and is predictive for outcome in esophageal adenocarcinoma - Communications Medicine
Abstract Despite the advent of neoadjuvant chemoradiotherapy (CRT), overall survival rates of esophageal adenocarcinoma (EAC) remain low. A readily induced mesenchymal transition of EAC cells contributes to resistance to CRT. In this study, we aimed to chart the heterogeneity in cell state transition after CRT and to identify its underpinnings. A panel of 12 esophageal cultures were treated with CRT and ranked by their relative epithelial-mesenchymal plasticity.
Germline specific genes increase DNA double-strand break repair and radioresistance in lung adenocarcinoma cells - Cell Death & Disease
Abstract In principle, germline cells possess the capability to transmit a nearly unaltered set of genetic material to infinite future generations, whereas somatic cells are limited by strict growth constraints necessary to assure an organism’s physical structure and eventual mortality. As the potential to replicate indefinitely is a key feature of cancer, we hypothesized that the activation of a “germline program” in somatic cells can contribute to oncogenesis.
Development of a CMS Classifier for Clinical CRC Samples
Thank you for your interest in spreading the word about bioRxiv. NOTE: Your email address is requested solely to identify you as the sender of this article. Your Email * Your Name * Send To * Enter multiple addresses on separate lines or separate them with commas. Message Subject (Your Name) has forwarded a page to you from bioRxiv Message Body (Your Name) thought you would like to see this page from the bioRxiv website.
Vaccination provides superior in vivo recall capacity of SARS-CoV-2 specific memory CD8 T cells
Kavazović et al. compare SARS-CoV-2-specific memory CD8 T cells from people after infection, vaccination or both. Infection induces a more clonally diverse memory pool than vaccination, but these cells produce less TNF after in vivo recall. Subsequent vaccination negates differences, stressing the importance of boosting irrespective of antigenic history.
SOX11 regulates SWI/SNF complex components as member of the adrenergic neuroblastoma core regulatory circuitry - Nature Communications
|
Samples and cell lines Copy number analysis was performed on primary untreated NB tumors, representative of all genomic subtypes including 263 and 223 samples11,12 of the NRC cohort (GSE8504717), 556 samples of the NB high-risk cohort (GSE10312310), and one unpublished in-house sample. In addition, copy number data of 33 NB cell lines11 and the cell line COG-N-373 (Fig. 1a) were used.
By Bieke Decaesteker, Siebe Loontiens, Fanny De Vloed, Juliette Roels, Jo Van Dorpe, Christophe Van Neste, Matthias Fischer Verified, Pieter Van Vlierberghe, Johannes H. Schulte, Sara Ek, Rogier Versteeg, Jan Koster, Mark Zimmerman, Katleen De Preter, Amber Louwagie, Sarah-Lee Bekaert, Suzanne Vanhauwaert
|
Nature
Verified
Molecular characterization of colorectal cancer related peritoneal metastatic disease - Nature Communications
Abstract A significant proportion of colorectal cancer (CRC) patients develop peritoneal metastases (PM) in the course of their disease. PMs are associated with a poor quality of life, significant morbidity and dismal disease outcome. To improve care for this patient group, a better understanding of the molecular characteristics of CRC-PM is required. Here we present a comprehensive molecular characterization of a cohort of 52 patients.
Urinary 3-Methoxytyramine Is a Biomarker for MYC Activity in Patients With Neuroblastoma
Neuroblastoma is the most common extracranial pediatric solid tumor, accounting for approximately 15% of pediatric cancer‒related deaths.1 Patients with neuroblastoma are typically allocated into specific risk groups on the basis of a variety of factors such as the disease stage, the patient's age at diagnosis, and amplification of the MYCN gene (MNA).2,3 These risk groups were originally developed to optimize the match between expected disease severity—defined as event-free survival (EFS)...
Comparative cytological and histological assessment of 828 primary soft tissue and bone lesions, and proposal for a system for reporting soft tissue cytopathology
Abstract Introduction The aim of the study was to evaluate the diagnostic utility of fine needle aspiration (FNA) cytology and core needle biopsies (CNBs) in a series of primary soft tissue and bone lesions and to test a possible system for reporting results of FNA cytology of soft tissue lesion.
Author Correction: c-Kit-positive ILC2s exhibit an ILC3-like signature that may contribute to IL-17-mediated pathologies
Correction to: Nature Immunology https://doi.org/10.1038/s41590-019-0423-0, published online 1 July 2019. In the version of this article initially published, the cell conversion was stated incorrectly (‘ILC2s to ILC1-like cells’) in the first sentence of the second paragraph in the second Results subsection; the correct description is ‘ILC1s to ILC2-like cells’. Also, the far left plot in Fig. 1d was missing the vertical axis label; this should be ‘IL-13−APC’. Finally, in the legend to Fig.
c-Kit-positive ILC2s exhibit an ILC3-like signature that may contribute to IL-17-mediated pathologies
Abstract Here we identify a group 2 innate lymphoid cell (ILC2) subpopulation that can convert into interleukin-17 (IL-17)-producing NKp44− ILC3-like cells. c-Kit and CCR6 define this ILC2 subpopulation that exhibits ILC3 features, including RORγt, enabling the conversion into IL-17-producing cells in response to IL-1β and IL-23.
A library of Neo Open Reading Frame peptides (NOPs) as a sustainable resource of common neoantigens in up to 50% of cancer patients
Abstract Somatic mutations in cancer can result in neoantigens against which patients can be vaccinated. The quest for tumor specific neoantigens has yielded no targets that are common to all tumors, yet foreign to healthy cells. Single base pair substitutions (SNVs) at best can alter 1 amino acid which can result in a neoantigen; with the exception of rare site-specific oncogenic driver mutations (such as RAS) such mutations are private.
RAS-MAPK Pathway-Driven Tumor Progression Is Associated with Loss of CIC and Other Genomic Aberrations in Neuroblastoma
RAS–MAPK Pathway-Driven Tumor Progression Is Associated with Loss of CIC and Other Genomic Aberrations in Neuroblastoma Thomas F. Eleveld, Linda Schild, Jan Koster, Danny A. Zwijnenburg, Lindy K. Alles, Marli E. Ebus, Richard Volckmann, Godelieve A. Tijtgat, Peter van Sluis, Rogier Versteeg and Jan J. Molenaar Cancer Res November 1 2018 (78) (21) 6297-6307; DOI: 10.1158/0008-5472.CAN-18-1045
Interferon-induced epithelial response to rhinovirus-16 in asthma relates to inflammation and FEV1
Publication HistoryPublished online: October 05, 2018Accepted: September 4, 2018; Received in revised form: August 2, 2018; Received: April 5, 2018;
RAS-MAPK pathway-driven tumor progression is associated with loss of CIC and other genomic aberrations in neuroblastoma
RAS-MAPK pathway-driven tumor progression is associated with loss of CIC and other genomic aberrations in neuroblastoma Thomas F Eleveld, Linda Schild, Jan Koster, Danny A Zwijnenburg, Lindy K Alles, Marli E Ebus, Richard Volckmann, Godelieve A.M. Tytgat, Peter van Sluis, Rogier Versteeg and Jan J. Molenaar Cancer Res August 16 2018 DOI: 10.1158/0008-5472.CAN-18-1045
Tumorigenic and Antiproliferative Properties of the TALE-Transcription Factors MEIS2D and MEIS2A in Neuroblastoma
Molecular Cell Biology Tumorigenic and Antiproliferative Properties of the TALE-Transcription Factors MEIS2D and MEIS2A in Neuroblastoma Anja Groß, Catrine Schulz, Jasmine Kolb, Jan Koster, Sibylle Wehner, Sebastian Czaplinski, Abdulghani Khilan, Hermann Rohrer, Patrick N. Harter, Thomas Klingebiel, Julian D. Langer, Dirk Geerts and Dorothea Schulte
Tumorigenic and anti-proliferative properties of the TALE-transcription factors MEIS2D and MEIS2A in neuroblastoma
Tumorigenic and anti-proliferative properties of the TALE-transcription factors MEIS2D and MEIS2A in neuroblastoma Anja S Groß, Catrine Schulz, Jasmine Kolb, Jan Koster, Sibylle Wehner, Sebastian Czaplinski, Abdulghani Khilan, Hermann Rohrer, Patrick N Harter, Thomas Klingebiel, Julian D Langer, Dirk Geerts and Dorothea Schulte Cancer Res January 30 2018 DOI: 10.1158/0008-5472.CAN-17-1860
Uncommon Work Perks That Maintain Employee Motivation
Outdoor clothing and equipment retailer Patagonia provides its employees with exercise-related stress relievers. For instance, staff members can join an on-site yoga class offered every morning, where they can clear their heads and stretch their limbs to start the day off right. The California-based company also provides bikes and a volleyball court.
The CMO’s Perspective on Digital Disruption
The digital era is fundamentally changing the way companies operate and market to their customers. Significant change is increasingly necessary as previously entrenched industry barriers collapse, and tech-savvy customers demand more from the companies they deal with. Today’s businesses face tremendous challenges to differentiate, adapt, and meet the ever-changing buying behaviors of digitally empowered customers.
Big Data & IoT Change The Rules For Retailers And Consumers
Technology today is transforming industries across the board. Smart devices, wearable devices, and Big Data are reshaping retail. Companies need to infuse digital solutions into everything from product creation to customer interaction. In ten years, retail is likely to be different, just as retail was much different a decade ago. While the physical storefront will likely remain a cornerstone, the landscape is changing fast. Consumers can buy goods anywhere and at any time.
Internet Of Things: Where Is All The Data Going?
The Internet of Things (IoT) is no longer happening in a galaxy far, far away. It’s happening right here, right now. It may be in your pocket, on your wrist, in your clothes – heck, it might even be helping you drive your car. In fact, IoT is moving so fast, we’re actually on the third wave, according to a panel of experts who weighed in on the topic during a recent episode of Internet of Things with Game-Changers, presented by SAP.
Show More
loading
Actions
Is this you?
As a journalist, you can create a free Muck Rack account to customize your profile, list your contact preferences, and upload a portfolio of your best work.Get in touch with Jan
Contact Jan, search articles and posts on X, monitor coverage, and track replies from one place.
Learn more about Muck Rack