Article
Cell Biology
Mirella Baroni, Gabriela D. A. Guardia, Xiufen Lei, Adam Kosti, Mei Qiao, Tesha Landry, Karl Mau, Pedro A. F. Galante, Luiz O. F. Penalva
Summary: Medulloblastoma is a common malignant brain tumor in children, and its treatment often leads to neurocognitive and other sequelae. This study identified Msi1 as a major driver of medulloblastoma development, particularly in Group 4. Genomic analyses revealed that Msi1 regulates cell cycle and division. Inhibition of Msi1 with luteolin affected the growth of medulloblastoma cells, and a synergistic effect was observed when combined with vincristine, a mitosis inhibitor.
Article
Oncology
Yufeng Zhang, Haiyan Yang, Liwen Wang, Huandi Zhou, Ge Zhang, Zhiqing Xiao, Xiaoying Xue
Summary: This study revealed that high expression of TOP2A in medulloblastoma is associated with poor prognosis. Knockdown of TOP2A inhibited proliferation, migration, and invasion of MB cells, and reduced radioresistance. The Wnt/beta-catenin signaling pathway may be involved in mediating the effects of TOP2A on tumorigenicity and radioresistance in MB cells.
FRONTIERS IN ONCOLOGY
(2022)
Article
Multidisciplinary Sciences
Liana Lachinani, Mahboobeh Forouzanfar, Kianoush Dormiani, Bahram Mohammad Soltani, Kamran Dolatshahi, Sayyed Mohammadreza Hakimian, Sadat Dokanehiifard, Mohammad Hossein Nasr-Esfahani
Summary: This study identified two novel miRNAs, MSM2 and MSM3, within the intronic regions of the MSI1 gene, and demonstrated their expression in breast cancer cells. The study also found a correlation between these miRNAs and the miRNA expression in clinical samples of breast cancer.
SCIENTIFIC REPORTS
(2023)
Article
Oncology
Xinhao Han, Wei Tian, Lin Sun, Hongying Wang, Yan Li, Huixun Jia, Guohong Gao, Liudan Mai, Shuwen Yin, Qiuju Zhang, Yanlong Liu
Summary: The study aimed to explore the potential roles of eRNAs and their target ERGs in the prognosis of CC. Through multiple tiers of screening, 11 prognostic ERGs were obtained and a reliable prognostic model was constructed. This study highlighted the usefulness and specificity of eRNAs and ERGs in the clinical guidance and prognosis of early-stage CC patients.
JOURNAL OF CANCER RESEARCH AND CLINICAL ONCOLOGY
(2023)
Article
Immunology
Yingying Diao, Yan Zhao, Xinyao Li, Baoyue Li, Ran Huo, Xiaoxu Han
Summary: Thrombocytopenia is a known prognostic factor in sepsis. We developed a machine learning model based on platelet-related genes to predict poor prognosis in sepsis. The model underwent rigorous evaluation on six diverse platforms and showed impressive performance compared to traditional scoring systems.
FRONTIERS IN IMMUNOLOGY
(2023)
Article
Genetics & Heredity
Ti-Wei Miao, Fang-Ying Chen, Long-Yi Du, Wei Xiao, Juan-Juan Fu
Summary: An RBP-related signature was successfully constructed to predict prognosis in NSCLC, serving as a reference for individualized therapy. Through bioinformatics analysis and experimental validation, the signature revealed correlations between the high-risk group and immune infiltration, gene mutation frequency, chemotherapy response, and other factors.
FRONTIERS IN GENETICS
(2022)
Article
Genetics & Heredity
Maoshi Li, Zhongwei Liu, Jing Wang, Huimin Liu, Hongmei Gong, Shilian Li, Ming Jia, Qing Mao
Summary: Increasing evidence suggests that dysregulated RNA binding proteins (RBPs) play a role in the progression of several malignancies, but their clinical implications in HBV-related hepatocellular carcinoma (HCC) are not well defined. This study systematically analyzed the associations of RBPs with HBV-related HCC prognosis, identifying 54 RBPs correlated with prognosis and creating an 11-RBP model for predicting patient outcomes. The risk score derived from this model was shown to be more predictive than other clinical parameters and was validated in an external dataset, demonstrating the potential implications of RBPs in the prognostication and therapy decision for HBV-related HCC.
FRONTIERS IN GENETICS
(2021)
Article
Cell Biology
Chang Gu, Xin Shi, Wenli Qiu, Zhenyu Huang, Yan Yu, Feng Shen, Yumei Chen, Xufeng Pan
Summary: This study explored the prognostic role and mutational characteristics of m6A-related genes in LUSC, identifying three potential independent prognostic m6A-related genes (WTAP, YTHDC1, and YTHDF1) for OS in LUSC patients. The study used LUSC gene expression data and mutational data from The Cancer Genome Atlas database, identifying differentially expressed genes and exploring gene mutations in LUSC patients, investigating the correlations among m6A-related genes, and developing a nomogram model. The study also found significant co-occurrence frequencies among certain m6A-related genes and identified prognostic factors for OS in LUSC patients through multivariate Cox analysis.
FRONTIERS IN CELL AND DEVELOPMENTAL BIOLOGY
(2021)
Article
Critical Care Medicine
Zefang Sun, Tao Zhang, Caihong Ning, Dingcheng Shen, Wenwu Pei, Rui Zhou, Shuai Zhu, Gengwen Huang
Summary: This study investigated the association between Helicobacter pylori infection and gastric cancer using gene expression profiling and single-cell RNA sequencing. The results showed a significant correlation between H. pylori infection and gastric cancer development. Furthermore, the study found that H. pylori infection could induce gastric cancer cells to enhance their invasion and metastasis abilities by expressing specific genes.
Article
Oncology
Dongfeng Sun, Zhibo Gai, Jie Wu, Qingfa Chen
Summary: This study reveals angiogenesis-related genes (ARGs) and their associated networks in lung adenocarcinoma (LUAD), identifying POSTN as a significant ARG that is highly expressed in LUAD patients and associated with prognosis. Functional enrichment analysis and immunohistochemistry suggest that POSTN may modulate the activation of the tubulointerstitial system, epithelial cells, and immune cells, ultimately altering the immune microenvironment and affecting patient survival.
FRONTIERS IN ONCOLOGY
(2022)
Article
Medicine, Research & Experimental
Jianjun Hou, Shaobing Yang, Ying Guo, Ning Yan, Shaobin Jia
Summary: The RNA-binding capacity of FUS in atherosclerosis and its impact on gene expression and alternative splicing were investigated. Knockdown of FUS significantly affected gene expression in human umbilical vein endothelial cells (HUVECs) and extensively regulated alternative splicing events. Functional analysis revealed its involvement in cell cycle and cell population proliferation pathways.
EXPERIMENTAL BIOLOGY AND MEDICINE
(2023)
Article
Cell Biology
Deng Li, Shiwei Liu, Jie Xu, Lei Chen, Chaoliang Xu, Feiteng Chen, Zijie Xu, Yu Zhang, Shujie Xia, Yi Shao, Yi Wang
Summary: Through bioinformatic analyses, it was found that CHAC1 has the potential to predict malignancy and prognosis in KIRC. Various analyses confirmed that up-regulated CHAC1 is an independent risk factor for poor prognosis in KIRC, and a model was constructed to predict patient survival rates. CHAC1 was also found to be associated with immune pathway markers and checkpoint genes.
JOURNAL OF CELLULAR AND MOLECULAR MEDICINE
(2021)
Article
Genetics & Heredity
Eva Niggl, Arjan Bouman, Lauren C. Briere, Remco M. Hoogenboezem, Ilse Wallaard, Joohyun Park, Jakob Admard, Martina Wilke, Emilio D. R. O. Harris-Mostert, Minetta Elgersma, Jennifer Bain, Meena Balasubramanian, Siddharth Banka, Paul J. Benke, Miriam Bertrand, Alyssa E. Blesson, Jill Clayton-Smith, Jamie M. Ellingford, Madelyn A. Gillentine, Dana H. Goodloe, Tobias B. Haack, Mahim Jain, Ian Krantz, Sharon M. Luu, Molly McPheron, Candace L. Muss, Sarah E. Raible, Nathaniel H. Robin, Michael Spiller, Susan Starling, David A. Sweetser, Isabelle Thiffault, Francesco Vetrini, Dennis Witt, Emily Woods, Ype Genomics England Res Consortium, Annelot C. M. van Undiagnosed Dis Network, Ype Elgersma, Annelot C. M. van Esbroeck
Summary: Described 13 individuals with global developmental delay and intellectual disability caused by heterozygous HNRNPC germline variants. These variants lead to decreased HNRNPC levels and affect alternative splicing of multiple genes associated with intellectual disability. This study strongly supports the inclusion of HNRNPC to the family of HNRNP-related neurodevelopmental disorders.
AMERICAN JOURNAL OF HUMAN GENETICS
(2023)
Article
Oncology
Fu Zhao, Zhi-Wei Zhang, Jing Zhang, Shun Zhang, Heng Zhang, Chi Zhao, Yang Chen, Lin Luo, Wei-Min Tong, Chunde Li, Yamei Niu, Pinan Liu
Summary: The study revealed that decreased global 5hmC levels in medulloblastoma patients were associated with poor prognosis, as well as cell proliferation and TET protein expression.
FRONTIERS IN ONCOLOGY
(2021)
Article
Clinical Neurology
Mingming Li, Min Yao, Kangmei Shao, Xueyang Shen, Zhaoming Ge, Yongnan Li
Summary: This study found that the serum levels of cold-inducible RNA-binding protein (CIRP) are elevated in patients with acute ischemic stroke (AIS) and are associated with the severity and prognosis of the disease. The serum CIRP levels were significantly correlated with the severity of cerebral infarction and poor prognosis. Therefore, serum CIRP levels can serve as an important biomarker for assessing brain injury in AIS patients.
FRONTIERS IN NEUROLOGY
(2023)
Article
Pathology
Nassim Bouteldja, David Laurin Hoelscher, Barbara Mara Klinkhammer, Roman David Buelow, Johannes Lotz, Nick Weiss, Christoph Daniel, Kerstin Amann, Peter Boor
Summary: This research proposes a novel concept of stain augmentation to develop stain-independent CNNs for digital pathology. It outperforms state-of-the-art techniques and enables segmentation on immunohistochemical stainings without additional annotations, achieving performance comparable to the annotated stain. Examples of application in inflammation and fibrosis quantification are presented, indicating the effectiveness of stain augmentation in deep-learning segmentation algorithms.
AMERICAN JOURNAL OF PATHOLOGY
(2023)
Article
Oncology
Florian Selt, Romain Sigaud, Gintvile Valinciute, Philipp Sievers, Julia Zaman, Clara Alco, Simone Schmid, Heike Peterziel, Jessica W. Tsai, Romain Guiho, Juan Pedro Martinez-Barbera, Stefan Pusch, Jing Deng, Yifan Zhai, Cornelis M. van Tilburg, Martin U. Schuhman, Ahmed E. L. Damaty, Pratiti Bandopadhayay, Christel Herold-Mende, Andreas von Deimling, Stefan M. Pfister, Joan Montero, David Capper, Ina Oehme, Felix Sahm, David T. W. Jones, Olaf Witt, Till Milde
Summary: Our study demonstrates that BCL-XL is critical for the survival of senescent PA tumor cells and provides evidence for the use of clinically available BCL-XL-dependent senolytic agents.
Editorial Material
Oncology
Young Suk Kwon, Michael Dohopolski, Howard Morgan, Aurelie Garant, David Sher, Asal Rahimi, Nina N. Sanford, Dat T. Vo, Kevin Albuquerque, Kiran Kumar, Robert Timmerman, Steve B. Jiang
PRACTICAL RADIATION ONCOLOGY
(2023)
Article
Clinical Neurology
Maximilian Deng, Felix Hinz, Semi Harrabi, Dominik Sturm, Martin Sill, Andrey Korshunov, Tanja Eichkorn, Juliane Hoerner-Rieber, Klaus Herfarth, Christine Jungk, Andreas Unterberg, Stefan Pfister, Wolfgang Wick, Andreas von Deimling, David Jones, Juergen Debus, Felix Sahm, Laila Koenig
Summary: Molecular brain tumor classification using DNA methylation profiling has revealed that the methylation-class of pleomorphic xanthoastrocytoma (mcPXA) comprised a substantial portion of divergent initial diagnoses. This study aimed to characterize the survival outcome in patients with mcPXAs and determine the benefit of postoperative radiotherapy. The results demonstrated that adult patients with mcPXAs display a worse progression-free survival compared to the reported WHO grade 2 PXAs.
NEURO-ONCOLOGY PRACTICE
(2023)
Article
Oncology
Venu Thatikonda, S. M. Ashiqul Islam, Robert J. Autry, Barbara C. Jones, Susanne N. Groebner, Gregor Warsow, Barbara Hutter, Daniel Huebschmann, Stefan Froehling, Marcel Kool, Mirjam Blattner-Johnson, David T. W. Jones, Ludmil B. Alexandrov, Stefan M. Pfister, Natalie Jaeger
Summary: Jager and colleagues analyzed the mutational patterns in pediatric cancers and found marked differences compared to adult cancers, providing insights into molecular mechanisms. They identified a small number of mutational signatures specific to pediatric cancers and discovered a previously unreported indel signature in pediatric leukemias. This study provides a systematic overview of mutational signatures in pediatric cancers, which is highly relevant for understanding tumor biology and developing biomarkers for treatment response.
Letter
Critical Care Medicine
Daniel Gagiannis, Carsten Hackenbroch, Wilhelm Bloch, Fabian Zech, Frank Kirchhoff, Sonja Djudjaj, Saskia von Stillfried, Roman Buelow, Peter Boor, Konrad Steinestel
AMERICAN JOURNAL OF RESPIRATORY AND CRITICAL CARE MEDICINE
(2023)
Article
Biochemistry & Molecular Biology
Han Wang, Antonia Margarethe Stehr, Jeeshan Singh, Leticija Zlatar, Arndt Hartmann, Katja Evert, Elisabeth Naschberger, Saskia von Stillfried, Peter Boor, Luis E. E. Munoz, Jasmin Knopf, Michael Stuerzl, Martin Herrmann
Summary: During inflammatory responses, neutrophils utilize various defense mechanisms, such as phagocytosis, degranulation, recruitment of immune cells, secretion of anti-microbials, and release of neutrophil extracellular traps (NETs). Detection of NETs in tissue sections can be challenging due to the high fluorescence signals emitted from condensed nuclear DNA. However, using anti-DNA-IgM antibodies can effectively detect the extended DNA patches of NETs, providing a new perspective for studying neutrophil-associated immune reactions in diseases.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Letter
Oncology
Christian P. Kratz, Dmitrii Smirnov, Robert Autry, Natalie Jaeger, Sebastian M. Waszak, Anika Grosshennig, Riccardo Berutti, Mareike Wendorff, Pierre Hainaut, Stefan M. Pfister, Holger Prokisch, Tim Ripperger, David Malkin
JNCI-JOURNAL OF THE NATIONAL CANCER INSTITUTE
(2023)
Article
Biochemistry & Molecular Biology
Dominik Sturm, David Capper, Felipe Andreiuolo, Marco Gessi, Christian Koelsche, Annekathrin Reinhardt, Philipp Sievers, Annika K. Wefers, Azadeh Ebrahimi, Abigail K. Suwala, Gerrit H. Gielen, Martin Sill, Daniel Schrimpf, Damian Stichel, Volker Hovestadt, Bjarne Daenekas, Agata Rode, Stefan Hamelmann, Christopher Previti, Natalie Jaeger, Ivo Buchhalter, Mirjam Blattner-Johnson, Barbara C. Jones, Monika Warmuth-Metz, Brigitte Bison, Kerstin Grund, Christian Sutter, Steffen Hirsch, Nicola Dikow, Martin Hasselblatt, Ulrich Schueller, Nicolas U. Gerber, Christine L. White, Molly K. Buntine, Kathryn Kinross, Elizabeth M. Algar, Jordan R. Hansford, Nicholas G. Gottardo, Pablo Hernaiz Driever, Astrid Gnekow, Olaf Witt, Hermann L. Mueller, Gabriele Calaminus, Gudrun Fleischhack, Uwe Kordes, Martin Mynarek, Stefan Rutkowski, Michael C. Fruehwald, Christof M. Kramm, Andreas von Deimling, Torsten Pietsch, Felix Sahm, Stefan M. Pfister, David. T. W. Jones
Summary: This study prospectively integrated DNA methylation profiling and targeted gene panel sequencing to evaluate their utility in routine neuropathology for newly diagnosed pediatric patients with CNS tumors. The integration of multi-omics improved diagnostic accuracy by refining DNA methylation classification, detecting relevant genetic alterations, and identifying cancer predisposition syndromes. Discrepancies between neuropathological classification and DNA methylation classification were particularly relevant for high-grade gliomas, and patients with lower-grade molecular profiles had improved survival.
Article
Oncology
Emily C. Hardin, Simone Schmid, Alexander Sommerkamp, Carina Bodden, Anna-Elisa Heipertz, Philipp Sievers, Andrea Wittmann, Till Milde, Stefan M. Pfister, Andreas von Deimling, Svea Horn, Nina A. Herz, Michele Simon, Ashwyn A. Perera, Amedeo Azizi, Ofelia Cruz, Sarah Curry, An Van Damme, Miklos Garami, Darren Hargrave, Antonis Kattamis, Barbara Faganel Kotnik, Paeivi Laehteenmaeki, Katrin Scheinemann, Antoinette Y. N. Schouten-van Meeteren, Astrid Sehested, Elisabetta Viscardi, Ole Mikal Wormdal, Michal Zapotocky, David S. Ziegler, Arend Koch, Pablo Hernaiz Driever, Olaf Witt, David Capper, Felix Sahm, David T. W. Jones, Cornelis M. van Tilburg
Summary: The addition of RNA-Seq to current diagnostic methods improves diagnostic accuracy, making precision oncology treatments more accessible for pediatric low-grade glioma (pLGG) patients. The study suggests including RNA-Seq as part of routine diagnostics, especially when no common pLGG alteration is identified.
Article
Oncology
Maryam Mashayekhi, Rafe McBeth, Dan Nguyen, Allen Yen, Zipalkumar Trivedi, Dominic Moon, Vlad Avkshtol, Dat Vo, David Sher, Steve Jiang, Mu-Han Lin
CLINICAL AND TRANSLATIONAL RADIATION ONCOLOGY
(2023)
Article
Oncology
David J. Sher, Dominic H. Moon, Dat Vo, Jing Wang, Liyuan Chen, Michael Dohopolski, Randall Hughes, Baran D. Sumer, Chul Ahn, Vladimir Avkshtol
Summary: This prospective phase II study indicates that elective neck irradiation is no longer mandatory for head and neck squamous cell carcinoma treatment, and radiation therapy can effectively reduce tumor recurrence and improve patients' quality of life.
CLINICAL CANCER RESEARCH
(2023)
Article
Computer Science, Interdisciplinary Applications
Isaac Shiri, Behrooz Razeghi, Alireza Vafaei Sadr, Mehdi Amini, Yazdan Salimi, Sohrab Ferdowsi, Peter Boor, Deniz Guenduez, Slava Voloshynovskiy, Habib Zaidi
Summary: A federated learning (FL) framework was developed for multi-institutional PET/CT image segmentation. The FL algorithms showed comparable performance to centralized learning methods and outperformed the single center-based baseline. The results have promising implications for HN tumor segmentation from PET/CT images.
COMPUTER METHODS AND PROGRAMS IN BIOMEDICINE
(2023)
Article
Oncology
Konstantin Okonechnikov, Piyush Joshi, Mari Sepp, Kevin Leiss, Ioannis Sarropoulos, Florent Murat, Martin Sill, Pengbo Beck, Kenneth Chun-Ho Chan, Andrey Korshunov, Felix Sah, Maximilian Y. Deng, Dominik Sturm, John DeSisto, Andrew M. Donson, Nicholas K. Foreman, Adam L. Green, Giles Robinson, Brent A. Orr, Qingsong Gao, Emily Darrow, Jennifer L. Hadley, Paul A. Northcott, Johannes Gojo, Daisuke Kawauchi, Volker Hovestadt, Mariella G. Filbin, Andreas von Deimling, Marc Zuckermann, Kristian W. Pajtler, Marcel Kool, David T. W. Jones, Natalie Jaeger, Lena M. Kutscher, Henrik Kaessmann, Stefan M. Pfister
Summary: This study successfully identified the cellular origins of the three most common pediatric brain tumors and identified potential therapeutic targets based on the tumor-specific genes expressed in these cellular origins.
Article
Biochemical Research Methods
Elias Ulrich, Stefan M. Pfister, Natalie Jaeger
Summary: As non-coding driver mutations become more important in cancer research, a comprehensive and user-friendly software solution for regulatory variant analysis and data visualization is highly relevant. A tool called Revana has been introduced, which can aggregate and visually represent regulatory variants from cancer genomes in a gene-centric manner. It requires whole-genome and RNA sequencing data of a tumor sample cohort and creates interactive HTML reports summarizing the most important regulatory events.