Article
Microbiology
Beatrix Kocsis, Mi-Kyung Lee, Jae-Hyuk Yu, Tibor Nagy, Lajos Daroczi, Gyula Batta, Istvan Pocsi, Eva Leiter
Summary: In this study, the two bZIP type TFs AtfA and AtfB were functionally characterized to play key roles in stress response pathways in filamentous fungi, with significant effects on oxidative stress sensitivity and heavy metal stress tolerance.
FRONTIERS IN MICROBIOLOGY
(2022)
Article
Microbiology
Sung-Hun Son, Mi-Kyung Lee, Ye-Eun Son, Hee-Soo Park
Summary: HbxB in Aspergillus nidulans functions as a key transcription factor regulating trehalose biosynthesis, stress tolerance, beta-glucan degradation, and sterigmatocystin production in conidia. Its deletion affects gene expression associated with these processes, leading to increased sensitivity to UV stress and alterations in beta-glucan levels and sterigmatocystin production.
Article
Cell Biology
Xiaoyu Li, Yanxia Zhao, Heungyun Moon, Jieyin Lim, Hee-Soo Park, Zhiqiang Liu, Jae-Hyuk Yu
Summary: VadH is a crucial transcription factor in Aspergillus nidulans, involved in regulating asexual/sexual development, osmotic stress response, and mycotoxin sterigmatocystin production.
Article
Biochemistry & Molecular Biology
Bernadett Bakany, Wen-Bing Yin, Beatrix Dienes, Tibor Nagy, Eva Leiter, Tamas Emri, Nancy P. Keller, Istvan Pocsi
Summary: NapA plays a crucial role in oxidative stress response by regulating intracellular reactive species production and catalase activities, while RsmA slightly negatively regulates catalase activities. The highest concentration of sterigmatocystin was measured in the double deletion mutant, but elevated production was also found in the strain with overexpressed genes.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Microbiology
Barnabas Cs. Gila, Karoly Antal, Zsuzsanna Birko, Judit Sz. Keseru, Istvan Pocsi, Tamas Emri
Summary: Understanding the coordinated regulation of CAZyme genes in fungi has practical importance. Transcriptional changes in Aspergillus nidulans under different carbon source conditions revealed upregulation of many CAZyme genes, especially on arabinogalactan.
Article
Biotechnology & Applied Microbiology
Barnabas Csaba Gila, Heungyun Moon, Karoly Antal, Marton Hajdu, Reka Kovacs, Andrea P. Jonas, Tunde Pusztahelyi, Jae-Hyuk Yu, Istvan Pocsi, Tamas Emri
Summary: Glutathione (GSH) plays a crucial role in redox regulation in fungi, affecting oxidative stress defense, protein secretion, secondary metabolite production, and sexual and asexual differentiations. Even slight changes in GSH levels can significantly disturb fungal homeostasis, highlighting the importance of understanding GSH metabolism for biotechnological applications.
APPLIED AND ENVIRONMENTAL MICROBIOLOGY
(2021)
Article
Biochemistry & Molecular Biology
Louis A. Chevalier, Mario Pinar, Remi Le Borgne, Catherine Durieu, Miguel Penalva, Arezki Boudaoud, Nicolas Minc
Summary: Hyphal tip growth in filamentous fungi is driven by the expansion of a protective cell wall (CW) secreted from apical vesicles. We found that tip growth is associated with balanced rates of CW secretion and expansion, and affecting this balance leads to immediate changes in CW thickness, mechanics, and shape. These findings provide unprecedented insights into the dynamics of CW secretion and expansion, and their role in stabilizing fungal tip growth and promoting morphogenetic plasticity.
Article
Biology
Li Liu, Christoph Sasse, Benedict Dirnberger, Oliver Valerius, Eniko Fekete-Szuecs, Rebekka Harting, Daniela E. Nordzieke, Stefanie Poeggeler, Petr Karlovsky, Jennifer Gerke, Gerhard H. Braus
Summary: The study shows that fungal Hulle cells play a crucial role in regulating development and secondary metabolism of Aspergillus nidulans, accumulating metabolites with antifeedant activity to protect reproductive structures from animal predators.
Article
Oncology
Erik van Dijk, Erik van Werkhoven, Rebecca Asher, Jennifer K. Mooi, David Espinoza, Hendrik F. van Essen, Harm van Tinteren, Nicole C. T. van Grieken, Cornelis J. A. Punt, Niall C. Tebbutt, Bauke Ylstra
Summary: The VEGF-A monoclonal antibody bevacizumab is recommended as first-line treatment for metastatic colorectal cancer patients. A retrospective study showed improved survival outcomes in patients with chromosome 18q11.2-q12.1 loss who received bevacizumab treatment. The analysis of the AGITG-MAX trial also provided supportive evidence for chromosome 18q11.2-q12.1 as a predictive marker for bevacizumab in mCRC patients.
INTERNATIONAL JOURNAL OF CANCER
(2022)
Article
Oncology
Jessica Rodrigues Placa, Arjan Diepstra, Tjitske Los, Matias Mendeville, Annika Seitz, Pieternella J. Lugtenburg, Josee Zijlstra, King Lam, Wilson Araujo da Silva Jr, Bauke Ylstra, Daphne de Jong, Anke van den Berg, Marcel Nijland
Summary: This study reproduced four gene expression signatures in DLBCL patients and validated three of them. In addition to the cell of origin, other signatures related to immune response and MYC activity were identified. These signatures capture different aspects of DLBCL biology and can co-occur in the same patient.
Editorial Material
Oncology
Matias Mendeville, Jurriaan Janssen, Yongsoo Kim, Erik van Dijk, Daphne de Jong, Bauke Ylstra
Article
Multidisciplinary Sciences
Kristiaan J. Lenos, Sander Bach, Leandro Ferreira Moreno, Sanne ten Hoorn, Nina R. Sluiter, Sanne Bootsma, Felipe A. Vieira Braga, Lisanne E. Nijman, Tom van den Bosch, Daniel M. Miedema, Erik van Dijk, Bauke Ylstra, Ruth Kulicke, Fred P. Davis, Nicolas Stransky, Gromoslaw A. Smolen, Robert R. J. Coebergh van den Braak, Jan N. M. IJzermans, John W. M. Martens, Sally Hallam, Andrew D. Beggs, Geert J. P. L. Kops, Nico Lansu, Vivian P. Bastiaenen, Charlotte E. L. Klaver, Maria C. Lecca, Khalid El Makrini, Clara C. Elbers, Mark P. G. Dings, Carel J. M. van Noesel, Onno Kranenburg, Jan Paul Medema, Jan Koster, Lianne Koens, Cornelis J. A. Punt, Pieter J. Tanis, Ignace H. de Hingh, Maarten F. Bijlsma, Jurriaan B. Tuynman, Louis Vermeulen
Summary: A significant proportion of colorectal cancer patients develop peritoneal metastases, which are associated with poor disease outcome. This study characterizes peritoneal metastases from 52 patients and identifies a distinct molecular subtype. The researchers also discover the key role of the structural protein Moesin in peritoneal dissemination and confirm that polyclonal metastatic seeding underlies these lesions.
NATURE COMMUNICATIONS
(2022)
Article
Oncology
Jos B. Poell, Leon J. Wils, Arjen Brink, Ralf Dietrich, Christine Krieg, Eunike Velleuer, Ilkay Evren, Elisabeth R. Brouns, Jan G. de Visscher, Elisabeth Bloemena, Bauke Ylstra, Ruud H. Brakenhoff
Summary: This study developed a noninvasive genetic assay to detect genetically altered fields in the oral cavity. The assay demonstrated high accuracy and predicted the development of oral squamous cell carcinoma in high-risk individuals. This method can be used for cancer screening in high-risk populations and to map the extent of lesions beyond what is visible.
INTERNATIONAL JOURNAL OF CANCER
(2023)
Article
Hematology
Jakoba J. Eertink, Gerben J. C. Zwezerijnen, Sanne E. Wiegers, Simone Pieplenbosch, Martine E. D. Chamuleau, Pieternella J. Lugtenburg, Daphne de Jong, Bauke Ylstra, Matias Mendeville, Ulrich Duehrsen, Christine Hanoun, Andreas Huettmann, Julia Richter, Wolfram Klapper, Yvonne W. S. Jauw, Otto S. Hoekstra, Henrica C. W. de Vet, Ronald Boellaard, Josee M. Zijlstra
Summary: This study investigated whether combining clinical, molecular genotype, and radiomics features can improve the outcome prediction of patients with aggressive B-cell lymphoma. The results showed that adding radiomics features improved the model performance and positive predictive values, aiding in the identification of poor prognosis patients.
Article
Oncology
Sanne ten Hoorn, Linda Mol, Dirkje W. Sommeijer, Lisanne Nijman, Tom van den Bosch, Tim R. de Back, Bauke Ylstra, Erik van Dijk, Carel J. M. van Noesel, Roy J. Reinten, Iris D. Nagtegaal, Miriam Koopman, Cornelis J. A. Punt, Louis Vermeulen
Summary: We evaluated the potential efficacy of adding anti-EGFR therapy to anti-VEGF therapy in a subgroup of patients with metastatic colorectal cancer. The retrospective study (CAIRO2 trial, n = 736) showed no benefit of anti-EGFR addition within the subgroup, but an overall survival increase of 6.5 months compared to the original trial.
CLINICAL COLORECTAL CANCER
(2023)
Article
Oncology
G. Tjitske Los-de Vries, Phylicia Stathi, Ryanne Rutkens, Nathalie J. Hijmering, Jeroen A. C. W. Luijks, Patricia J. T. A. Groenen, Daphne de Jong, Bauke Ylstra, Margaretha G. M. Roemer
Summary: Primary and relapsed LBCL-IP have a common set of genetic alterations that support survival and proliferation, providing insight into the disease progression.
Article
Gastroenterology & Hepatology
Maarten te Groen, Lauranne A. A. P. Derikx, Lisa van Lierop, Bauke Ylstra, Frank Hoentjen, Iris D. Nagtegaal, Femke Simmer
Summary: The presence of previous colorectal neoplasia is the most significant indicator for the development of pouch neoplasia in inflammatory bowel disease. However, the underlying mechanism remains unknown. Our study found evidence of clonality between colorectal and pouch neoplasia in 30% of patients, suggesting that most pouch neoplasia develops independently from prior colorectal lesions.
INFLAMMATORY BOWEL DISEASES
(2023)
Article
Oncology
Anna Lena van Gulik, Ellen Sluydts, Liesbet Vervoort, Mark Kockx, Pim Kortman, Bauke Ylstra, Stephen P. Finn, Lukas Bubendorf, Idris Bahce, Daoud Sie, Teodora Radonic, Birgit Lissenberg-Witte, Erik Thunnissen
Summary: This study investigates the impact of cell size and ploidy on FISH results. The results show that in liver cell nuclei, the number of FISH signals increases with nuclear size and section thickness. In non-small cell lung cancer cases, tumor cells with higher ploidy levels and nuclear size have an increased chance of single signals. In addition, no rearrangements were found in lung cancer samples with borderline ALK FISH results, proving a false positive result.
TRANSLATIONAL LUNG CANCER RESEARCH
(2023)
Letter
Hematology
Wendy B. C. Stevens, G. Tjitske Los-de Vries, Carole Langois-Jacques, Andrew J. Clear, Phylicia Stathi, Birgitta Sander, Andreas Rosenwald, Maria Calaminici, Eva Hoster, Wolfgang Hiddemann, Philippe Gaulard, Gilles Salles, Wolfram Klapper, Luc Xerri, Catherine Burton, Reuben M. Tooze, Alexandra G. Smith, Christian Buske, David W. Scott, Yasodha Natkunam, Ranjana Advani, Laurie H. Sehn, John Raemaekers, John Gribben, Sandra Lockmer, Eva Kimby, Marie Jose Kersten, Delphine Maucort-Boulch, Bauke Ylstra, Erik van Dijk, Daphne de Jong
Article
Hematology
Patricia Johansson, Stefan Alig, Julia Richter, Christine Hanoun, Jan Rekowski, Jan Duerig, Bauke Ylstra, Daphne de Jong, Wolfram Klapper, Ash A. Alizadeh, Ulrich Duehrsen, Andreas Huettmann
Summary: In DLBCL, a positive interim PET scan predicts treatment failure, and combining it with the presence of an IgM gammopathy can improve prediction. The combination of interim PET and IgM gammopathy can dichotomize the population into high-risk and low-risk groups with significantly different outcomes. Only the interim PET result and IgM gammopathy status were significantly associated with outcome, making them important factors in risk-adapted treatment strategies.
ANNALS OF HEMATOLOGY
(2023)
Editorial Material
Hematology
Bauke Ylstra, Daphne de Jong
Summary: In this study, the authors demonstrate the usefulness of a dark zone signature (DZsig) for diagnosing aggressive B-cell lymphoma with DLBCL morphology, and highlight its strong prognostic value.
Article
Pathology
Tanya T. D. Soeratram, Hedde D. Biesma, Jacqueline M. P. Egthuijsen, Elma Meershoek-Klein Kranenbarg, Henk H. Hartgrink, Cornelis J. H. van de Velde, Aart Mookhoek, Erik van Dijk, Yongsoo Kim, Bauke Ylstra, Hanneke W. M. van Laarhoven, Nicole C. T. van Grieken
Summary: Tumor-infiltrating lymphocytes are important for the survival of gastric cancer patients, and T-cell densities in different regions of the tumor can serve as prognostic markers. CD8OIM and FOXP3TC are identified as key factors for survival, and the combination of their densities can stratify patients into distinct subgroups with different prognosis. These immune subgroups are independent predictors for cancer-specific survival in resectable gastric cancer.
Article
Multidisciplinary Sciences
Margaretha G. M. Roemer, Tim van de Brug, Erik Bosch, Daniella Berry, Nathalie Hijmering, Phylicia Stathi, Karin Weijers, Jeannette Doorduijn, Jacoline Bromberg, Mark van de Wiel, Bauke Ylstra, Daphne de Jong, Yongsoo Kim
Summary: In order to understand the clinical relevance of the tumor microenvironment (TME), it is important to study the interactions between malignant and non-malignant cells in clinical samples. Researchers have developed a computational framework to comprehensively analyze the spatial context of the TME, including close and long-distance interactions between different cell types. This framework was applied to imaging data from 88 primary central nervous system lymphomas, revealing significant prognostic subgroups mainly determined by the spatial context. The results highlight the importance of spatial context in predicting patient survival, particularly in relation to macrophage infiltration near specific cell types.