Article
Oncology
Saikat Chowdhury, Matan Hofree, Kangyu Lin, Dipen Maru, Scott Kopetz, John Paul Shen
Summary: This study utilized single-cell RNA sequencing to investigate the impact of intratumor heterogeneity on the four consensus molecular subtypes (CMS) of colorectal cancer (CRC). The findings suggest that stromal and immune cell numbers strongly influence the CMS type, and tumor epithelial cell clusters derived from single-cell RNA sequencing do not align with CMS.
Article
Chemistry, Medicinal
Peng Zhao, Linghang Zhuang, Xiangzhu Wang, Song Huang, Heping Wu, Yu Zhou, Yuna Yan, Fan Zhang, Ru Shen, Jing Li, Suxing Liu, Rumin Zhang, Ping Dong, Yuchang Mao, Yuanmin Fan, Chunyong He, Jiakang Sun, Lei Zhang, Qiyue Hu, Hong Wan, Jun Feng, Chang Bai, Feng He, Weikang Tao
Summary: A molecule called SHR902275 (or molecule 33) has been discovered with significantly improved potency and solubility, which shows potential for targeting cancers with mutant RAS and wild type RAF activity. In vivo experiments have demonstrated dose dependent efficacy of molecule 33.
EUROPEAN JOURNAL OF MEDICINAL CHEMISTRY
(2022)
Review
Cell Biology
Linda Studer, Annika Blank, John-Melle Bokhorst, Iris D. Nagtegaal, Inti Zlobec, Alessandro Lugli, Andreas Fischer, Heather Dawson
Summary: Tumour budding in colorectal cancer serves as a robust and independent biomarker of aggressive tumor biology, with evidence strongly supporting its reporting in routine practice. Establishing a standardized and evidence-based scoring method is crucial for implementing tumour budding assessment, while the development of automated methods for assessment is a key focus for further research and validation to ensure accuracy and standardization.
Article
Biochemistry & Molecular Biology
Xiangjian Zhang, Xinxin Zhang, Ruokuo Han, Zhaojun Wang, Qiuhui Yang, Yiming Huang, Yuxiang Yan
Summary: The selective inhibitor BLU-554 of fibroblast growth factor receptor 4 (FGFR4) has been found to inhibit proliferation and invasion of gastric cancer cells while promoting apoptosis and cell cycle arrest.
BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS
(2022)
Article
Public, Environmental & Occupational Health
Vladimir Vonka, Ivan Hirsch
Summary: The significant progress in tumor biology and immunology in recent years has provided new opportunities for the treatment and prevention of cancer, with a focus on developing prophylactic anti-cancer vaccines. Specifically, vaccines have been successfully developed for the prevention of cervical cancer and liver cancer, indicating potential for future advancements in immunotherapy against cancer.
CENTRAL EUROPEAN JOURNAL OF PUBLIC HEALTH
(2021)
Article
Computer Science, Information Systems
Danielle Krijgsman, Marinus B. van Leeuwen, John van der Ven, Vanda Almeida, Ruud Vlutters, David Halter, Peter J. K. Kuppen, Cornelis J. H. van de Velde, Reinhold Wimberger-Friedl
Summary: In order to support therapy selection in oncology, a reliable and reproducible quantification of immune infiltrate within tumor microenvironments is needed. The automated method presented in this study allows for whole-slide image analysis of tumor-infiltrating CD8-positive lymphocytes, showing highly heterogeneous spatial density distributions in post-menopausal, estrogen receptor-positive invasive breast cancer patients receiving adjuvant tamoxifen therapy. Statistically significant correlation with clinical outcome was found for the standard deviation of the CD8 density distribution, suggesting potential clinical relevance for larger cohort studies.
IEEE JOURNAL OF BIOMEDICAL AND HEALTH INFORMATICS
(2021)
Review
Oncology
Zeger Rijs, A. Naweed Shifai, Sarah E. Bosma, Peter J. K. Kuppen, Alexander L. Vahrmeijer, Stijn Keereweer, Judith V. M. G. Bovee, Michiel A. J. van de Sande, Cornelis E. M. Sier, Pieter B. A. A. van Driel
Summary: Near-infrared imaging technology facilitates tumor identification during surgery, allowing surgeons to distinguish malignant tissue using specific biomarkers. By evaluating clinically targeted biomarkers on soft tissue sarcomas, potential candidates for near-infrared fluorescence imaging have been identified to improve surgical outcomes and enhance tumor resection accuracy. Promising biomarkers have been found in common and aggressive soft tissue sarcoma subtypes, showing potential for future clinical applications.
Article
Medicine, General & Internal
Daan Linders, Marion Deken, Maxime van der Valk, Willemieke Tummers, Shadhvi Bhairosingh, Dennis Schaap, Gesina van Lijnschoten, Elham Zonoobi, Peter Kuppen, Cornelis van de Velde, Alexander Vahrmeijer, Arantza Farina Sarasqueta, Cornelis Sier, Denise Hilling
Summary: Rectal cancer patients with a complete response after neoadjuvant therapy show low expression of CEA and EpCAM in the primary tumor bed compared to the diagnostic biopsy and adjacent mucosa, indicating their potential as suitable targets for response evaluation.
Review
Biochemistry & Molecular Biology
Ricky B. van de Water, Danielle Krijgsman, Ruben D. Houvast, Alexander L. Vahrmeijer, Peter J. K. Kuppen
Summary: Tumor HLA-G expression is associated with poor clinical outcomes in breast, esophageal, gastric, and hepatocellular carcinoma patients, but not in ovarian and oral carcinoma patients. Discrepancies in cervical, colorectal, lung, and pancreatic carcinoma patients make it inconclusive. Standardized methodologies are recommended to clarify the relationship between tumor HLA-G expression and clinical outcomes.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Review
Oncology
Martijn A. van Dam, Floris A. Vuijk, Judith A. Stibbe, Ruben D. Houvast, Saskia A. C. Luelmo, Stijn Crobach, Shirin Shahbazi Feshtali, Lioe-Fee de Geus-Oei, Bert A. Bonsing, Cornelis F. M. Sier, Peter J. K. Kuppen, Rutger-Jan Swijnenburg, Albert D. Windhorst, Jacobus Burggraaf, Alexander L. Vahrmeijer, J. Sven D. Mieog
Summary: Pancreatic cancer patients have a poor prognosis with a low survival rate, emphasizing the need for better imaging tools to support surgical resection. Tumor-targeted PET/CT before surgery and real-time fluorescence-guidance during surgery could potentially improve patient outcomes, but further research is needed to determine their actual value in clinical practice.
Article
Oncology
Ruben D. Houvast, Kira Thijse, Jesse Groen, JiaXin Chua, Mireille Vankemmelbeke, Lindy G. Durrant, J. Sven D. Mieog, Bert A. Bonsing, Alexander L. Vahrmeijer, Peter J. K. Kuppen, A. Stijn L. P. Crobach, Cornelis F. M. Sier
Summary: The study found that several specific sugar molecules and mucins are significantly higher on pancreatic cancer cells compared to surrounding tissues, making them potential targets for visualization of lymph node metastases and improving pancreatic cancer treatment. Targeted molecular imaging may overcome current challenges in preoperative and intraoperative delineation of pancreatic ductal adenocarcinoma (PDAC).
Review
Biology
Lisanne K. A. Neijenhuis, Lysanne D. A. N. de Myunck, Okker D. Bijlstra, Peter J. K. Kuppen, Denise E. Hilling, Frank J. Borm, Danielle Cohen, J. Sven D. Mieog, Willem H. Steup, Jerry Braun, Jacobus Burggraaf, Alexander L. Vahrmeijer, Merlijn Hutteman
Summary: Lung cancer, particularly non-small cell lung cancer (NSCLC), is prevalent worldwide. Near-infrared (NIR) fluorescence imaging has been tested as an intraoperative technique to localize pulmonary nodules, allowing tumor identification, detection of additional lesions, and prevention of positive resection margins.
Article
Biochemistry & Molecular Biology
Simone van de Weerd, Marloes A. Smit, Jessica Roelands, Wilma E. Mesker, Davide Bedognetti, Peter J. K. Kuppen, Hein Putter, Rob A. E. M. Tollenaar, Jeanine M. L. Roodhart, Wouter Hendrickx, Jan Paul Medema, J. Han J. M. van Krieken
Summary: This study evaluated the association between four distinct histopathological features and two gene expression-based classifiers. The presence of tumor infiltrating lymphocytes and a mucinous phenotype were strongly correlated with certain subtypes. Higher budding counts were seen in specific subtypes. However, identifying molecular subtypes solely based on histopathology proved to be infeasible.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Medicine, General & Internal
Simone Benhamou, Evelyne Fournier, Giacomo Puppa, Thomas McKee, Frederic Ris, Laura Rubbia-Brandt, Valeria Viassolo, Thomas Zilli, Inti Zlobec, Pierre Olivier Chappuis, Elisabetta Rapiti
Summary: This study established a large cohort of colorectal cancer (CRC) patients and their relatives to investigate the impact of family history and tumor biomarkers on patient outcomes. The cohort includes 5499 patients and provides detailed clinical and molecular data. Future plans involve further research and correlation analysis with the latest follow-up data.
Article
Pathology
Magdalena Skoworonska, Annika Blank, Irene Centeno, Caroline Hammer, Aurel Perren, Inti Zlobec, Tilman T. Rau
Summary: The standardized preanalytical code (SPREC) is a precise format for aggregating warm ischemia (WIT), cold ischemia (CIT), and fixation times (FIT). Through empirical research, the Tissue Bank Bern has developed a fully informative SPREC code and identified its dual role as a sample characteristic and a traceable process parameter. The study also reveals specific differences in WIT, CIT, and FIT values in various organs, as well as the potential to optimize the SPREC fixation and adapt its categories based on real-life data.
JOURNAL OF PATHOLOGY CLINICAL RESEARCH
(2023)
Article
Biochemistry & Molecular Biology
Jessica Roelands, Peter J. K. Kuppen, Eiman I. Ahmed, Raghvendra Mall, Tariq Masoodi, Parul Singh, Gianni Monaco, Christophe Raynaud, Noel F. C. C. de Miranda, Luigi Ferraro, Tatiana C. Carneiro-Lobo, Najeeb Syed, Arun Rawat, Amany Awad, Julie Decock, William Mifsud, Lance D. Miller, Shimaa Sherif, Mahmoud G. Mohamed, Darawan Rinchai, Marc Van den Eynde, Rosalyn W. Sayaman, Elad Ziv, Francois Bertucci, Mahir Abdulla Petkar, Stephan Lorenz, Lisa Sara Mathew, Kun Wang, Selvasankar Murugesan, Damien Chaussabel, Alexander L. Vahrmeijer, Ena Wang, Anna Ceccarelli, Khalid A. Fakhro, Gabriele Zoppoli, Alberto Ballestrero, Rob A. E. M. Tollenaar, Francesco M. Marincola, Jerome Galon, Souhaila Al Khodor, Michele Ceccarelli, Wouter Hendrickx, Davide Bedognetti
Summary: The lack of multi-omics cancer datasets with extensive follow-up information hinders the identification of accurate biomarkers of clinical outcome. In this cohort study, comprehensive genomic analyses were performed on fresh-frozen samples from 348 patients with primary colon cancer. The study revealed a gene expression signature called Immunologic Constant of Rejection that outperformed conventional prognostic molecular biomarkers. Additionally, a favorable outcome was associated with a microbiome signature driven by Ruminococcus bromii.
Article
Biochemistry & Molecular Biology
Zeger Rijs, Esther Belt, Gijsbert M. M. Kalisvaart, Cornelis F. M. Sier, Peter J. K. Kuppen, Arjen H. G. Cleven, Alexander L. L. Vahrmeijer, Michiel A. J. van de Sande, Pieter B. A. A. van Driel
Summary: This study aims to evaluate the expression of eight promising biomarkers for FGS in MFS tissue samples and adjacent healthy tissue. The results show that TEM-1 is the most suitable biomarker for FGS in MFS and should be further investigated to optimize MFS treatment.
Article
Biochemistry & Molecular Biology
Oxana (Sachenkova) Lundstrom, Max Adriaan Verbiest, Feifei Xia, Helyaneh Ziaei Jam, Inti Zlobec, Maria Anisimova, Melissa Gymrek
Summary: Short tandem repeats (STRs), consisting of repeated one to six nucleotide motifs, have been shown to influence various traits in humans. However, the study of STRs has been limited due to technical challenges. Recent advancements in genome-wide analysis tools have enabled large-scale analysis of STR variations in populations.
JOURNAL OF MOLECULAR BIOLOGY
(2023)
Article
Pathology
Ana Leni Frei, Raphael Oberson, Elias Baumann, Aurel Perren, Rainer Grobholz, Alessandro Lugli, Heather Dawson, Christian Abbet, Ibai Lertxundi, Stefan Reinhard, Aart Mookhoek, Johann Feichtinger, Rossella Sarro, Gallus Gadient, Corina Dommann-Scherrer, Jessica Barizzi, Sabina Berezowska, Katharina Glatz, Susanne Dertinger, Yara Banz, Rene Schoenegg, Laura Rubbia-Brandt, Achim Fleischmann, Guenter Saile, Pierre Mainil-Varlet, Ruggero Biral, Luca Giudici, Alex Soltermann, Audrey Baur Chaubert, Sylvia Stadlmann, Joachim Diebold, Kristof Egervaril, Charles Beniere, Francesca Saro, Andrew Janowczyk, Inti Zlobec
Summary: Estimating tumor cell fraction (TCF) is a common clinical task with high variability among pathologists. This study evaluated the impact of using a tumor cell fraction computer-aided diagnostic (TCFCAD) tool to support pathologists' evaluation. The results showed that with the assistance of TCFCAD, interobserver variability decreased and estimates were closer to the ground truth. Pathologists also reported increased confidence in their assessments when aided by the TCFCAD tool.
Article
Hematology
Rayna J. S. Anijs, El Houari Laghmani, Betul Unlu, Szymon M. Kielbasa, Hailiang Mei, Suzanne C. Cannegieter, Frederikus A. Klok, Peter J. K. Kuppen, Henri H. Versteeg, Jeroen T. Buijs
Summary: This study aimed to identify novel tumor-expressed miRNAs associated with VTE in colorectal cancer. Through sequencing analysis, 19 differentially regulated tumor-expressed miRNAs were identified, which may provide insights into the biological mechanism and serve as potential predictive biomarkers.
RESEARCH AND PRACTICE IN THROMBOSIS AND HAEMOSTASIS
(2022)