1
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Ma W, Tang W, Kwok JS, Tong AH, Lo CW, Chu AT, Chung BH. A review on trends in development and translation of omics signatures in cancer. Comput Struct Biotechnol J 2024; 23:954-971. [PMID: 38385061 PMCID: PMC10879706 DOI: 10.1016/j.csbj.2024.01.024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2023] [Revised: 01/31/2024] [Accepted: 01/31/2024] [Indexed: 02/23/2024] Open
Abstract
The field of cancer genomics and transcriptomics has evolved from targeted profiling to swift sequencing of individual tumor genome and transcriptome. The steady growth in genome, epigenome, and transcriptome datasets on a genome-wide scale has significantly increased our capability in capturing signatures that represent both the intrinsic and extrinsic biological features of tumors. These biological differences can help in precise molecular subtyping of cancer, predicting tumor progression, metastatic potential, and resistance to therapeutic agents. In this review, we summarized the current development of genomic, methylomic, transcriptomic, proteomic and metabolic signatures in the field of cancer research and highlighted their potentials in clinical applications to improve diagnosis, prognosis, and treatment decision in cancer patients.
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Affiliation(s)
- Wei Ma
- Hong Kong Genome Institute, Hong Kong, China
| | - Wenshu Tang
- Hong Kong Genome Institute, Hong Kong, China
| | | | | | | | | | - Brian H.Y. Chung
- Hong Kong Genome Institute, Hong Kong, China
- Department of Pediatrics and Adolescent Medicine, School of Clinical Medicine, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong, China
| | - Hong Kong Genome Project
- Hong Kong Genome Institute, Hong Kong, China
- Department of Pediatrics and Adolescent Medicine, School of Clinical Medicine, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong, China
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2
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Li M, Xu J, Peng C, Wang Z. Deep learning-assisted flavonoid-based fluorescent sensor array for the nondestructive detection of meat freshness. Food Chem 2024; 447:138931. [PMID: 38484548 DOI: 10.1016/j.foodchem.2024.138931] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2023] [Revised: 02/27/2024] [Accepted: 03/01/2024] [Indexed: 04/10/2024]
Abstract
Gas sensors containing indicators have been widely used in meat freshness testing. However, concerns about the toxicity of indicators have prevented their commercialization. Here, we prepared three fluorescent sensors by complexing each flavonoid (fisetin, puerarin, daidzein) with a flexible film, forming a fluorescent sensor array. The fluorescent sensor array was used as a freshness indication label for packaged meat. Then, the images of the indication labels on the packaged meat under different freshness levels were collected by smartphones. A deep convolutional neural network (DCNN) model was built using the collected indicator label images and freshness labels as the dataset. Finally, the model was used to detect the freshness of meat samples, and the overall accuracy of the prediction model was as high as 97.1%. Unlike the TVB-N measurement, this method provides a nondestructive, real-time measurement of meat freshness.
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Affiliation(s)
- Min Li
- State Key Laboratory of Food Science and Resources, Jiangnan University, Wuxi 214122, PR China; School of Food Science and Technology, Jiangnan University, Wuxi 214122, PR China
| | - Jianguo Xu
- Key Laboratory of Molecular Recognition and Sensing, College of Biological, Chemical Sciences and Engineering, Jiaxing University, Jiaxing 314001, PR China
| | - Chifang Peng
- State Key Laboratory of Food Science and Resources, Jiangnan University, Wuxi 214122, PR China; School of Food Science and Technology, Jiangnan University, Wuxi 214122, PR China; School of Life Science and Health Engineering, Jiangnan University, Wuxi 214122, PR China; International Joint Laboratory On Food Safety, Jiangnan University, Wuxi 214122, PR China.
| | - Zhouping Wang
- State Key Laboratory of Food Science and Resources, Jiangnan University, Wuxi 214122, PR China; School of Food Science and Technology, Jiangnan University, Wuxi 214122, PR China; School of Life Science and Health Engineering, Jiangnan University, Wuxi 214122, PR China; International Joint Laboratory On Food Safety, Jiangnan University, Wuxi 214122, PR China
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3
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Vazaios K, Stavrakaki Ε, Vogelezang LB, Ju J, Waranecki P, Metselaar DS, Meel MH, Kemp V, van den Hoogen BG, Hoeben RC, Chiocca EA, Goins WF, Stubbs A, Li Y, Alonso MM, Calkoen FG, Hulleman E, van der Lugt J, Lamfers ML. The heterogeneous sensitivity of pediatric brain tumors to different oncolytic viruses is predicted by unique gene expression profiles. Mol Ther Oncol 2024; 32:200804. [PMID: 38694569 PMCID: PMC11060958 DOI: 10.1016/j.omton.2024.200804] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/11/2023] [Accepted: 04/11/2024] [Indexed: 05/04/2024]
Abstract
Despite decades of research, the prognosis of high-grade pediatric brain tumors (PBTs) remains dismal; however, recent cases of favorable clinical responses were documented in clinical trials using oncolytic viruses (OVs). In the current study, we employed four different species of OVs: adenovirus Delta24-RGD, herpes simplex virus rQNestin34.5v1, reovirus R124, and the non-virulent Newcastle disease virus rNDV-F0-GFP against three entities of PBTs (high-grade gliomas, atypical teratoid/rhabdoid tumors, and ependymomas) to determine their in vitro efficacy. These four OVs were screened on 14 patient-derived PBT cell cultures and the degree of oncolysis was assessed using an ATP-based assay. Subsequently, the observed viral efficacies were correlated to whole transcriptome data and Gene Ontology analysis was performed. Although no significant tumor type-specific OV efficacy was observed, the analysis revealed the intrinsic biological processes that associated with OV efficacy. The predictive power of the identified expression profiles was further validated in vitro by screening additional PBTs. In summary, our results demonstrate OV susceptibility of multiple patient-derived PBT entities and the ability to predict in vitro responses to OVs using unique expression profiles. Such profiles may hold promise for future OV preselection with effective oncolytic potency in a specific tumor, therewith potentially improving OV responses.
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Affiliation(s)
- Konstantinos Vazaios
- Princess Máxima Center for Pediatric Oncology, Heidelberglaan 25, 3584 CS Utrecht, the Netherlands
- Department of Neurosurgery, Brain Tumor Center, Erasmus Medical Center, Dr. Molewaterplein 40, 3015 GD Rotterdam, the Netherlands
- Center for Translational Immunology, University Medical Center Utrecht, Heidelberglaan 100, 3584 CX Utrecht, the Netherlands
| | - Εftychia Stavrakaki
- Department of Neurosurgery, Brain Tumor Center, Erasmus Medical Center, Dr. Molewaterplein 40, 3015 GD Rotterdam, the Netherlands
| | - Lisette B. Vogelezang
- Department of Neurosurgery, Brain Tumor Center, Erasmus Medical Center, Dr. Molewaterplein 40, 3015 GD Rotterdam, the Netherlands
| | - Jie Ju
- Department of Pathology and Clinical Bioinformatics, Erasmus Medical Center, Dr. Molewaterplein 40, 3015 GD Rotterdam, the Netherlands
| | - Piotr Waranecki
- Princess Máxima Center for Pediatric Oncology, Heidelberglaan 25, 3584 CS Utrecht, the Netherlands
| | - Dennis S. Metselaar
- Princess Máxima Center for Pediatric Oncology, Heidelberglaan 25, 3584 CS Utrecht, the Netherlands
| | - Michaël H. Meel
- Princess Máxima Center for Pediatric Oncology, Heidelberglaan 25, 3584 CS Utrecht, the Netherlands
- Department of Pediatrics, Wilhelmina Children’s Hospital, University Medical Center Utrecht, Lundlaan 6, 3584 EA Utrecht, the Netherlands
| | - Vera Kemp
- Department of Cell and Chemical Biology, Leiden University Medical Center, Einthovenweg 20, 2333 ZC Leiden, the Netherlands
| | | | - Rob C. Hoeben
- Department of Cell and Chemical Biology, Leiden University Medical Center, Einthovenweg 20, 2333 ZC Leiden, the Netherlands
| | - E. Antonio Chiocca
- Department of Neurosurgery, Brigham and Women’s Hospital, Harvard Medical School, 75 Francis Street, Boston, MA 02115, USA
| | - William F. Goins
- Department of Microbiology & Molecular Genetics, University of Pittsburgh School of Medicine, 450 Technology Dr, Pittsburgh, PA 15219, USA
| | - Andrew Stubbs
- Department of Pathology and Clinical Bioinformatics, Erasmus Medical Center, Dr. Molewaterplein 40, 3015 GD Rotterdam, the Netherlands
| | - Yunlei Li
- Department of Pathology and Clinical Bioinformatics, Erasmus Medical Center, Dr. Molewaterplein 40, 3015 GD Rotterdam, the Netherlands
| | - Marta M. Alonso
- Program in Solid Tumors, Center for Applied Medical Research (CIMA), Avda. de Pío XII, 55, 31008 Pamplona, Spain
- Department of Pediatrics, Clínica Universidad de Navarra, Av. de Pío XII, 36, 31008 Pamplona, Spain
- Health Research Institute of Navarra (IDISNA), Av. de Pío XII, 36, 31008 Pamplona, Spain
| | - Friso G. Calkoen
- Princess Máxima Center for Pediatric Oncology, Heidelberglaan 25, 3584 CS Utrecht, the Netherlands
| | - Esther Hulleman
- Princess Máxima Center for Pediatric Oncology, Heidelberglaan 25, 3584 CS Utrecht, the Netherlands
| | - Jasper van der Lugt
- Princess Máxima Center for Pediatric Oncology, Heidelberglaan 25, 3584 CS Utrecht, the Netherlands
| | - Martine L.M. Lamfers
- Department of Neurosurgery, Brain Tumor Center, Erasmus Medical Center, Dr. Molewaterplein 40, 3015 GD Rotterdam, the Netherlands
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4
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Prieto R, Barrios L, Ebrat-Mancilla E, Martín P, Tejerina E. The Significance of BRAF Mutation in the Epithelioid Glioblastoma Subtype: A Systematic Literature Review and a Case Report with a Unique Intraventricular Topography. Int J Surg Pathol 2024; 32:649-666. [PMID: 37743598 DOI: 10.1177/10668969231195026] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/26/2023]
Abstract
Epithelioid glioblastoma (E-GBM) is an exceedingly rare subtype of isocitrate dehydrogenase (IDH)-wildtype glioblastoma, first included in the WHO 2016 classification and characterized by a dominant population of epithelioid cells. Its histological and molecular defining features remain troublesome. The significance of BRAF mutations to pathological diagnosis and surgical outcome has drawn increasing attention given their promising potential for future adjuvant therapies. Herein, we describe a unique case of an E-GBM in the atrium of the left lateral ventricle and comprehensively analyze the importance of BRAF status in a cohort of 211 E-GBMs from the literature. Our patient was a 40-year-old man with occipital pain. His brain MRI revealed a large intraventricular tumor at the same location as a signal change found 10 years earlier with no additional follow-up. He underwent gross total tumor removal followed by conventional adjuvant treatment. Histopathological diagnosis was consistent with IDH-wildtype E-GBM WHO grade 4 with pleomorphic xanthoastrocytoma-like areas. BRAF p.V600 mutation was demonstrated in the tumoral genetic study. In the cohort analyzed, male patients predominated (63%), the median age was 32 years old, and the 5-year survival rate following diagnosis was 4.2%. BRAF mutations were found in 60.3% of the tumors overall, with this rate increasing to 78.3% in young adults (19-49 years, P < .001). Presence of BRAF mutations associated with tumor progression (P = .001), the event usually leading to death (P < .001). In conclusion, our study supports the importance of genetic BRAF p.V600 mutation analysis because its presence not only points to an E-GBM diagnosis but may also promote tumor progression.
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Affiliation(s)
- Ruth Prieto
- Department of Neurosurgery, Puerta de Hierro Majadahonda University Hospital, Madrid, Spain
| | - Laura Barrios
- Statistics Department, Computing Center, C.S.I.C., Madrid, Spain
| | - Edwin Ebrat-Mancilla
- Department of Neurophysiology, Puerta de Hierro Majadahonda University Hospital, Madrid, Spain
| | - Paloma Martín
- Molecular Pathology Group, Instituto de Investigación Sanitaria Puerta de Hierro Segovia de Arana (IDIPHISA), Madrid, Spain
| | - Eva Tejerina
- Department of Pathology, Puerta de Hierro Majadahonda University Hospital, Madrid, Spain
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5
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Jensen MP, Qiang Z, Khan DZ, Stoyanov D, Baldeweg SE, Jaunmuktane Z, Brandner S, Marcus HJ. Artificial intelligence in histopathological image analysis of central nervous system tumours: A systematic review. Neuropathol Appl Neurobiol 2024; 50:e12981. [PMID: 38738494 DOI: 10.1111/nan.12981] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2024] [Revised: 04/05/2024] [Accepted: 04/10/2024] [Indexed: 05/14/2024]
Abstract
The convergence of digital pathology and artificial intelligence could assist histopathology image analysis by providing tools for rapid, automated morphological analysis. This systematic review explores the use of artificial intelligence for histopathological image analysis of digitised central nervous system (CNS) tumour slides. Comprehensive searches were conducted across EMBASE, Medline and the Cochrane Library up to June 2023 using relevant keywords. Sixty-eight suitable studies were identified and qualitatively analysed. The risk of bias was evaluated using the Prediction model Risk of Bias Assessment Tool (PROBAST) criteria. All the studies were retrospective and preclinical. Gliomas were the most frequently analysed tumour type. The majority of studies used convolutional neural networks or support vector machines, and the most common goal of the model was for tumour classification and/or grading from haematoxylin and eosin-stained slides. The majority of studies were conducted when legacy World Health Organisation (WHO) classifications were in place, which at the time relied predominantly on histological (morphological) features but have since been superseded by molecular advances. Overall, there was a high risk of bias in all studies analysed. Persistent issues included inadequate transparency in reporting the number of patients and/or images within the model development and testing cohorts, absence of external validation, and insufficient recognition of batch effects in multi-institutional datasets. Based on these findings, we outline practical recommendations for future work including a framework for clinical implementation, in particular, better informing the artificial intelligence community of the needs of the neuropathologist.
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Affiliation(s)
- Melanie P Jensen
- Pathology Department, Charing Cross Hospital, Imperial College Healthcare NHS Trust, London, UK
- Briscoe Lab, The Francis Crick Institute, London, UK
| | - Zekai Qiang
- School of Medicine and Population Health, University of Sheffield Medical School, Sheffield, UK
| | - Danyal Z Khan
- Department of Neurosurgery, National Hospital for Neurology and Neurosurgery, University College London Hospitals NHS Foundation Trust, London, UK
- Department of Computer Science, University College London, London, UK
| | - Danail Stoyanov
- Department of Computer Science, University College London, London, UK
| | - Stephanie E Baldeweg
- Department of Diabetes and Endocrinology, University College London Hospitals, London, UK
- Centre for Obesity and Metabolism, Department of Experimental and Translational Medicine, Division of Medicine, University College London, London, UK
| | - Zane Jaunmuktane
- Division of Neuropathology, National Hospital for Neurology and Neurosurgery, University College London Hospitals NHS Foundation Trust, London, UK
- Department of Neurodegenerative Disease, University College London Queen Square Institute of Neurology, London, UK
- Department of Clinical and Movement Neurosciences, University College London Queen Square Institute of Neurology, London, UK
| | - Sebastian Brandner
- Division of Neuropathology, National Hospital for Neurology and Neurosurgery, University College London Hospitals NHS Foundation Trust, London, UK
- Department of Neurodegenerative Disease, University College London Queen Square Institute of Neurology, London, UK
| | - Hani J Marcus
- Department of Neurosurgery, National Hospital for Neurology and Neurosurgery, University College London Hospitals NHS Foundation Trust, London, UK
- Department of Computer Science, University College London, London, UK
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6
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Leung ML, Abdullaev Z, Santana-Santos L, Skaugen JM, Moore S, Ji J. Microarray-Based DNA Methylation Profiling: Validation Considerations for Clinical Testing. J Mol Diagn 2024; 26:447-455. [PMID: 38378079 DOI: 10.1016/j.jmoldx.2024.02.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2023] [Revised: 02/01/2024] [Accepted: 02/08/2024] [Indexed: 02/22/2024] Open
Abstract
Microarray-based methylation profiling has emerged as a valuable tool for refining diagnoses and revealing novel tumor subtypes, particularly in central nervous system tumors. Despite the increasing adoption of this technique in clinical genomic laboratories, no technical standards have been published in establishing minimum criteria for test validation. A working group with experience and expertise in DNA-based methylation profiling tests on central nervous system tumors collaborated to develop practical discussion points and focus on important considerations for validating this test in clinical laboratory settings. The experience in validating this methodology in a clinical setting is summarized. Specifically, the advantages and challenges associated with utilizing an in-house classifier compared with a third-party classifier are highlighted. Additionally, experiences in demonstrating the assay's sensitivity and specificity, establishing minimum sample criteria, and implementing quality control metrics are described. As methylation profiling for tumor classification expands to other tumor types and continues to evolve for various other applications, the critical considerations described here are expected to serve as a guidance for future efforts in establishing professional guidelines for this assay.
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Affiliation(s)
- Marco L Leung
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Nationwide Children's Hospital, Columbus, Ohio; Departments of Pathology and Pediatrics, The Ohio State University College of Medicine, Columbus, Ohio.
| | - Zied Abdullaev
- Laboratory of Pathology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland
| | - Lucas Santana-Santos
- Department of Pathology, Feinberg School of Medicine, Northwestern University, Chicago, Illinois
| | - John M Skaugen
- Department of Pathology, University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania
| | - Stephen Moore
- Department of Molecular and Medical Genetics and Knight Diagnostic Laboratory, Oregon Health & Science University, Portland, Oregon
| | - Jianling Ji
- Department of Pathology and Laboratory Medicine, Children's Hospital Los Angeles, Los Angeles, California; Department of Pathology, Keck School of Medicine, University of Southern California, Los Angeles, California
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7
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Pekkarinen M, Nordfors K, Uusi-Mäkelä J, Kytölä V, Hartewig A, Huhtala L, Rauhala M, Urhonen H, Häyrynen S, Afyounian E, Yli-Harja O, Zhang W, Helen P, Lohi O, Haapasalo H, Haapasalo J, Nykter M, Kesseli J, Rautajoki KJ. Aberrant DNA methylation distorts developmental trajectories in atypical teratoid/rhabdoid tumors. Life Sci Alliance 2024; 7:e202302088. [PMID: 38499326 PMCID: PMC10948937 DOI: 10.26508/lsa.202302088] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2023] [Revised: 03/06/2024] [Accepted: 03/06/2024] [Indexed: 03/20/2024] Open
Abstract
Atypical teratoid/rhabdoid tumors (AT/RTs) are pediatric brain tumors known for their aggressiveness and aberrant but still unresolved epigenetic regulation. To better understand their malignancy, we investigated how AT/RT-specific DNA hypermethylation was associated with gene expression and altered transcription factor binding and how it is linked to upstream regulation. Medulloblastomas, choroid plexus tumors, pluripotent stem cells, and fetal brain were used as references. A part of the genomic regions, which were hypermethylated in AT/RTs similarly as in pluripotent stem cells and demethylated in the fetal brain, were targeted by neural transcriptional regulators. AT/RT-unique DNA hypermethylation was associated with polycomb repressive complex 2 and linked to suppressed genes with a role in neural development and tumorigenesis. Activity of the several NEUROG/NEUROD pioneer factors, which are unable to bind to methylated DNA, was compromised via the suppressed expression or DNA hypermethylation of their target sites, which was also experimentally validated for NEUROD1 in medulloblastomas and AT/RT samples. These results highlight and characterize the role of DNA hypermethylation in AT/RT malignancy and halted neural cell differentiation.
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Affiliation(s)
- Meeri Pekkarinen
- https://ror.org/033003e23 Prostate Cancer Research Center, Faculty of Medicine and Health Technology, Tampere University and Tays Cancer Center, Tampere University Hospital, Tampere, Finland
| | - Kristiina Nordfors
- https://ror.org/033003e23 Tampere Center for Child Health Research, Tays Cancer Center, Tampere University and Tampere University Hospital, Tampere, Finland
- Tays Cancer Center, Tampere University Hospital, Tampere, Finland
- Unit of Pediatric Hematology and Oncology, Tampere University Hospital, Tampere, Finland
| | - Joonas Uusi-Mäkelä
- https://ror.org/033003e23 Prostate Cancer Research Center, Faculty of Medicine and Health Technology, Tampere University and Tays Cancer Center, Tampere University Hospital, Tampere, Finland
| | - Ville Kytölä
- https://ror.org/033003e23 Prostate Cancer Research Center, Faculty of Medicine and Health Technology, Tampere University and Tays Cancer Center, Tampere University Hospital, Tampere, Finland
| | - Anja Hartewig
- https://ror.org/033003e23 Prostate Cancer Research Center, Faculty of Medicine and Health Technology, Tampere University and Tays Cancer Center, Tampere University Hospital, Tampere, Finland
| | - Laura Huhtala
- https://ror.org/033003e23 Prostate Cancer Research Center, Faculty of Medicine and Health Technology, Tampere University and Tays Cancer Center, Tampere University Hospital, Tampere, Finland
| | - Minna Rauhala
- Tays Cancer Center, Tampere University Hospital, Tampere, Finland
- https://ror.org/033003e23 Department of Neurosurgery, Tays Cancer Centre, Tampere University Hospital and Tampere University, Tampere, Finland
| | - Henna Urhonen
- https://ror.org/033003e23 Prostate Cancer Research Center, Faculty of Medicine and Health Technology, Tampere University and Tays Cancer Center, Tampere University Hospital, Tampere, Finland
| | - Sergei Häyrynen
- https://ror.org/033003e23 Prostate Cancer Research Center, Faculty of Medicine and Health Technology, Tampere University and Tays Cancer Center, Tampere University Hospital, Tampere, Finland
| | - Ebrahim Afyounian
- https://ror.org/033003e23 Prostate Cancer Research Center, Faculty of Medicine and Health Technology, Tampere University and Tays Cancer Center, Tampere University Hospital, Tampere, Finland
| | - Olli Yli-Harja
- https://ror.org/033003e23 Faculty of Medicine and Health Technology, Tampere University and Tays Cancer Center, Tampere University Hospital, Tampere, Finland
- Institute for Systems Biology, Seattle, WA, USA
| | - Wei Zhang
- Cancer Genomics and Precision Oncology, Wake Forest Baptist Comprehensive Cancer Center, Winston-Salem, NC, USA
| | - Pauli Helen
- https://ror.org/033003e23 Department of Neurosurgery, Tays Cancer Centre, Tampere University Hospital and Tampere University, Tampere, Finland
| | - Olli Lohi
- https://ror.org/033003e23 Tampere Center for Child Health Research, Tays Cancer Center, Tampere University and Tampere University Hospital, Tampere, Finland
- Tays Cancer Center, Tampere University Hospital, Tampere, Finland
- https://ror.org/033003e23 Faculty of Medicine and Health Technology, Tampere University and Tays Cancer Center, Tampere University Hospital, Tampere, Finland
| | - Hannu Haapasalo
- https://ror.org/033003e23 Faculty of Medicine and Health Technology, Tampere University and Tays Cancer Center, Tampere University Hospital, Tampere, Finland
- https://ror.org/031y6w871 Fimlab Laboratories Ltd, Tampere University Hospital, Tampere, Finland
| | - Joonas Haapasalo
- Tays Cancer Center, Tampere University Hospital, Tampere, Finland
- https://ror.org/033003e23 Department of Neurosurgery, Tays Cancer Centre, Tampere University Hospital and Tampere University, Tampere, Finland
- https://ror.org/031y6w871 Fimlab Laboratories Ltd, Tampere University Hospital, Tampere, Finland
| | - Matti Nykter
- https://ror.org/033003e23 Prostate Cancer Research Center, Faculty of Medicine and Health Technology, Tampere University and Tays Cancer Center, Tampere University Hospital, Tampere, Finland
| | - Juha Kesseli
- https://ror.org/033003e23 Prostate Cancer Research Center, Faculty of Medicine and Health Technology, Tampere University and Tays Cancer Center, Tampere University Hospital, Tampere, Finland
| | - Kirsi J Rautajoki
- https://ror.org/033003e23 Prostate Cancer Research Center, Faculty of Medicine and Health Technology, Tampere University and Tays Cancer Center, Tampere University Hospital, Tampere, Finland
- https://ror.org/033003e23 Tampere Institute for Advanced Study, Tampere University, Tampere, Finland
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8
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Padhye BD, Nawaz U, Hains PG, Reddel RR, Robinson PJ, Zhong Q, Poulos RC. Proteomic insights into paediatric cancer: Unravelling molecular signatures and therapeutic opportunities. Pediatr Blood Cancer 2024; 71:e30980. [PMID: 38556739 DOI: 10.1002/pbc.30980] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/28/2023] [Revised: 03/13/2024] [Accepted: 03/14/2024] [Indexed: 04/02/2024]
Abstract
Survival rates in some paediatric cancers have improved greatly over recent decades, in part due to the identification of diagnostic, prognostic and predictive molecular signatures, and the development of risk-directed therapies. However, other paediatric cancers have proved difficult to treat, and there is an urgent need to identify novel biomarkers that reveal therapeutic opportunities. The proteome is the total set of expressed proteins present in a cell or tissue at a point in time, and is vastly more dynamic than the genome. Proteomics holds significant promise for cancer research, as proteins are ultimately responsible for cellular phenotype and are the target of most anticancer drugs. Here, we review the discoveries, opportunities and challenges of proteomic analyses in paediatric cancer, with a focus on mass spectrometry (MS)-based approaches. Accelerating incorporation of proteomics into paediatric precision medicine has the potential to improve survival and quality of life for children with cancer.
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Affiliation(s)
- Bhavna D Padhye
- Cancer Centre for Children, The Children's Hospital at Westmead, Westmead, New South Wales, Australia
- Kids Research, Children's Cancer Research Unit, The Children's Hospital at Westmead, Westmead, New South Wales, Australia
| | - Urwah Nawaz
- ProCan, Children's Medical Research Institute, Faculty of Medicine and Health, The University of Sydney, Westmead, New South Wales, Australia
| | - Peter G Hains
- ProCan, Children's Medical Research Institute, Faculty of Medicine and Health, The University of Sydney, Westmead, New South Wales, Australia
| | - Roger R Reddel
- ProCan, Children's Medical Research Institute, Faculty of Medicine and Health, The University of Sydney, Westmead, New South Wales, Australia
| | - Phillip J Robinson
- ProCan, Children's Medical Research Institute, Faculty of Medicine and Health, The University of Sydney, Westmead, New South Wales, Australia
| | - Qing Zhong
- ProCan, Children's Medical Research Institute, Faculty of Medicine and Health, The University of Sydney, Westmead, New South Wales, Australia
| | - Rebecca C Poulos
- ProCan, Children's Medical Research Institute, Faculty of Medicine and Health, The University of Sydney, Westmead, New South Wales, Australia
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9
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Edsjö A, Russnes HG, Lehtiö J, Tamborero D, Hovig E, Stenzinger A, Rosenquist R. High-throughput molecular assays for inclusion in personalised oncology trials - State-of-the-art and beyond. J Intern Med 2024; 295:785-803. [PMID: 38698538 DOI: 10.1111/joim.13785] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 05/05/2024]
Abstract
In the last decades, the development of high-throughput molecular assays has revolutionised cancer diagnostics, paving the way for the concept of personalised cancer medicine. This progress has been driven by the introduction of such technologies through biomarker-driven oncology trials. In this review, strengths and limitations of various state-of-the-art sequencing technologies, including gene panel sequencing (DNA and RNA), whole-exome/whole-genome sequencing and whole-transcriptome sequencing, are explored, focusing on their ability to identify clinically relevant biomarkers with diagnostic, prognostic and/or predictive impact. This includes the need to assess complex biomarkers, for example microsatellite instability, tumour mutation burden and homologous recombination deficiency, to identify patients suitable for specific therapies, including immunotherapy. Furthermore, the crucial role of biomarker analysis and multidisciplinary molecular tumour boards in selecting patients for trial inclusion is discussed in relation to various trial concepts, including drug repurposing. Recognising that today's exploratory techniques will evolve into tomorrow's routine diagnostics and clinical study inclusion assays, the importance of emerging technologies for multimodal diagnostics, such as proteomics and in vivo drug sensitivity testing, is also discussed. In addition, key regulatory aspects and the importance of patient engagement in all phases of a clinical trial are described. Finally, we propose a set of recommendations for consideration when planning a new precision cancer medicine trial.
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Affiliation(s)
- Anders Edsjö
- Department of Clinical Genetics, Pathology and Molecular Diagnostics, Office for Medical Services, Region Skåne, Lund, Sweden
- Division of Pathology, Department of Clinical Sciences, Lund University, Lund, Sweden
| | - Hege G Russnes
- Department of Pathology, Oslo University Hospital, Oslo, Norway
- Department of Cancer Genetics, Institute for Cancer Research, Oslo University Hospital, Oslo, Norway
- Institute for Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway
| | - Janne Lehtiö
- Department of Oncology and Pathology, Karolinska Institutet, Science for Life Laboratory, Stockholm, Sweden
- Cancer genomics and proteomics, Karolinska University Hospital, Solna, Sweden
| | - David Tamborero
- Department of Oncology and Pathology, Karolinska Institutet, Science for Life Laboratory, Stockholm, Sweden
| | - Eivind Hovig
- Center for Bioinformatics, Department of Informatics, University of Oslo, Oslo, Norway
- Department of Tumor Biology, Institute for Cancer Research, Oslo University Hospital, Oslo, Norway
| | - Albrecht Stenzinger
- Institute of Pathology, Division of Molecular Pathology, University Hospital Heidelberg, Heidelberg, Germany
| | - Richard Rosenquist
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden
- Clinical Genetics and Genomics, Karolinska University Hospital, Solna, Sweden
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10
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Ono T, Suzuki H, Nanjo H, Shimizu H. Clinical Course after Carmustine Wafer Implantation for Newly Diagnosed Adult-type Diffuse Gliomas; A controlled propensity matched analysis of a single center cohort. J Neurooncol 2024:10.1007/s11060-024-04679-2. [PMID: 38780714 DOI: 10.1007/s11060-024-04679-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2024] [Accepted: 04/10/2024] [Indexed: 05/25/2024]
Abstract
PURPOSE It remains unclear whether combining carmustine wafer (CW) implantation with the standard treatment for adult-type diffuse gliomas is safe and has a prognostic impact. This study aimed to investigate the prognostic value and safety of CW implantation. METHODS Adult patients with IDH-wild-type and -mutant gliomas, grades 3-4 treated with surgical resection, radiotherapy, and temozolomide chemotherapy between 2013 and 2023 were surveyed. CWs were implanted except in cases of intraoperative wide ventricle opening or marked preoperative brain swelling. For survival analyses, a case-matched dataset based on propensity score matching (PSM), including multiple factors (patient background, diagnosis, and extent of resection) was generated. Progression-free survival (PFS), overall survival (OS), and frequency of complications of CW implantation (brain edema, infection, and cerebrospinal fluid leakage) were compared between the CW and non-use groups. RESULTS In total, 127 patients (75 in the CW use group and 52 in the non-use group) were enrolled. Regardless of stratification, no significant differences in PFS and OS were observed between the CW use and non-use groups. The frequency of postoperative brain edema was significantly higher in the CW use group than in the non-use group. An adjusted dataset containing 41 patients in the CW use and nonuse groups was generated. Even after PSM, CW implantation had no prognostic effect. CONCLUSIONS CW implantation with standard treatment demonstrated little beneficial effect for the present strategy of CW use.
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Affiliation(s)
- Takahiro Ono
- Department of Neurosurgery, Akita University Graduate School of Medicine, 1-1-1 Hondo, Akita, Akita, 010-8543, Japan.
| | - Hayato Suzuki
- Department of Neurosurgery, Akita University Graduate School of Medicine, 1-1-1 Hondo, Akita, Akita, 010-8543, Japan
| | - Hiroshi Nanjo
- Department of Surgical Pathology, Akita University Hospital, 44-2 Hasunuma Hiroomote, Akita, Akita, 010-8543, Japan
| | - Hiroaki Shimizu
- Department of Neurosurgery, Akita University Graduate School of Medicine, 1-1-1 Hondo, Akita, Akita, 010-8543, Japan
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11
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Vizcaino MA, Giannini C, Lalich D, Nael A, Jenkins RB, Tran Q, Orr BA, Abdullaev Z, Aldape K, Vaubel RA. Ganglioglioma with anaplastic/high-grade transformation: Histopathologic, molecular, and epigenetic characterization of 3 cases. J Neuropathol Exp Neurol 2024; 83:416-424. [PMID: 38699943 DOI: 10.1093/jnen/nlae038] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/05/2024] Open
Abstract
Ganglioglioma (GG) with anaplasia (anaplastic ganglioglioma) is a rare and controversial diagnosis. When present, anaplasia involves the glial component of the tumor, either at presentation or at recurrence. To date, most published cases lack molecular characterization. We describe the histologic and molecular features of 3 patients presenting with BRAF p. V600E-mutant GG (CNS WHO grade 1) with high-grade glial transformation at recurrence. The tumors occurred in pediatric patients (age 9-16 years) with time to recurrence from 20 months to 7 years. At presentation, each tumor was low-grade, with a BRAFV600E-positive ganglion cell component and a glial component resembling pleomorphic xanthoastrocytoma (PXA) or fibrillary astrocytoma. At recurrence, tumors resembled anaplastic PXA or high-grade astrocytomas without neuronal differentiation. CDKN2A homozygous deletion (HD) was absent in all primary tumors. At recurrence, 2 cases acquired CDKN2A HD; the third case showed loss of p16 and MTAP immunoexpression, but no CDKN2A/B HD or mutation was identified. By DNA methylation profiling, all primary and recurrent tumors either grouped or definitely matched to different methylation classes. Our findings indicate that malignant progression of the glial component can occur in GG and suggest that CDKN2A/B inactivation plays a significant role in this process.
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Affiliation(s)
- M Adelita Vizcaino
- Department of Laboratory Medicine and Pathology, Mayo Clinic Rochester, Minnesota, USA
| | - Caterina Giannini
- Department of Laboratory Medicine and Pathology, Mayo Clinic Rochester, Minnesota, USA
- Department of Biomedical and Neuromotor Sciences, University of Bologna, Bologna, Italy
| | - Daniel Lalich
- Department of Pathology, Robert J. Dole VA Medical Center and Wesley Healthcare Center, Wichita, Kansas, USA
| | - Ali Nael
- Department of Pathology, Children's Hospital of Orange County and University of California Irvine, Orange County, California, USA
| | - Robert B Jenkins
- Department of Laboratory Medicine and Pathology, Mayo Clinic Rochester, Minnesota, USA
| | - Quynh Tran
- Department of Pathology, St Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Brent A Orr
- Department of Pathology, St Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Zied Abdullaev
- Laboratory of Pathology, National Cancer Institute/Center for Cancer Research, Bethesda, Maryland, USA
| | - Kenneth Aldape
- Laboratory of Pathology, National Cancer Institute/Center for Cancer Research, Bethesda, Maryland, USA
| | - Rachael A Vaubel
- Department of Laboratory Medicine and Pathology, Mayo Clinic Rochester, Minnesota, USA
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12
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Simon M, Kuschel LP, von Hoff K, Yuan D, Hernáiz Driever P, Hain EG, Koch A, Capper D, Schulz M, Thomale UW, Euskirchen P. Rapid DNA methylation-based classification of pediatric brain tumors from ultrasonic aspirate specimens. J Neurooncol 2024:10.1007/s11060-024-04702-6. [PMID: 38769169 DOI: 10.1007/s11060-024-04702-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2023] [Accepted: 04/30/2024] [Indexed: 05/22/2024]
Abstract
BACKGROUND Although cavitating ultrasonic aspirators are commonly used in neurosurgical procedures, the suitability of ultrasonic aspirator-derived tumor material for diagnostic procedures is still controversial. Here, we explore the feasibility of using ultrasonic aspirator-resected tumor tissue to classify otherwise discarded sample material by fast DNA methylation-based analysis using low pass nanopore whole genome sequencing. METHODS Ultrasonic aspirator-derived specimens from pediatric patients undergoing brain tumor resection were subjected to low-pass nanopore whole genome sequencing. DNA methylation-based classification using a neural network classifier and copy number variation analysis were performed. Tumor purity was estimated from copy number profiles. Results were compared to microarray (EPIC)-based routine neuropathological histomorphological and molecular evaluation. RESULTS 19 samples with confirmed neuropathological diagnosis were evaluated. All samples were successfully sequenced and passed quality control for further analysis. DNA and sequencing characteristics from ultrasonic aspirator-derived specimens were comparable to routinely processed tumor tissue. Classification of both methods was concordant regarding methylation class in 17/19 (89%) cases. Application of a platform-specific threshold for nanopore-based classification ensured a specificity of 100%, whereas sensitivity was 79%. Copy number variation profiles were generated for all cases and matched EPIC results in 18/19 (95%) samples, even allowing the identification of diagnostically or therapeutically relevant genomic alterations. CONCLUSION Methylation-based classification of pediatric CNS tumors based on ultrasonic aspirator-reduced and otherwise discarded tissue is feasible using time- and cost-efficient nanopore sequencing.
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Affiliation(s)
- Michèle Simon
- Department of Pediatric Oncology and Hematology, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt Universität zu Berlin, Augustenburger Platz 1, 13353, Berlin, Germany
| | - Luis P Kuschel
- Department of Neurology, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt Universität zu Berlin, Charitéplatz 1, 10117, Berlin, Germany
| | - Katja von Hoff
- Department of Paediatric and Adolescent Medicine, Aarhus University Hospital, Aarhus, Denmark
| | - Dongsheng Yuan
- Department of Neurology, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt Universität zu Berlin, Charitéplatz 1, 10117, Berlin, Germany
| | - Pablo Hernáiz Driever
- Department of Pediatric Oncology and Hematology, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt Universität zu Berlin, Augustenburger Platz 1, 13353, Berlin, Germany
| | - Elisabeth G Hain
- Department of Neuropathology, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt Universität zu Berlin, Charitéplatz 1, 10117, Berlin, Germany
| | - Arend Koch
- Department of Neuropathology, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt Universität zu Berlin, Charitéplatz 1, 10117, Berlin, Germany
| | - David Capper
- Department of Neuropathology, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt Universität zu Berlin, Charitéplatz 1, 10117, Berlin, Germany
- German Cancer Consortium (DKTK), partner site Berlin, a partnership between DKFZ and Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - Matthias Schulz
- Department of Pediatric Neurosurgery, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt Universität zu Berlin, Augustenburger Platz 1, 13353, Berlin, Germany
| | - Ulrich-Wilhelm Thomale
- Department of Pediatric Neurosurgery, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt Universität zu Berlin, Augustenburger Platz 1, 13353, Berlin, Germany
| | - Philipp Euskirchen
- Department of Neurology, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt Universität zu Berlin, Charitéplatz 1, 10117, Berlin, Germany.
- Department of Neuropathology, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt Universität zu Berlin, Charitéplatz 1, 10117, Berlin, Germany.
- German Cancer Consortium (DKTK), partner site Berlin, a partnership between DKFZ and Charité - Universitätsmedizin Berlin, Berlin, Germany.
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13
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Lin FY, Stuckert A, Tat C, White M, Ruggieri L, Zhang H, Mehta B, Lapteva N, Mei Z, Major A, Thakkar S, Shum T, Parikh K, Wu MF, Lindsay HB, Scherer L, Shekar M, Baxter P, Wang T, Grilley B, Moeller K, Hicks J, Roy A, Anastas J, Malbari F, Aldave G, Chintagumpala M, Blaney S, Parsons DW, Brenner MK, Heslop HE, Rooney CM, Omer B. Phase I Trial of GD2.CART Cells Augmented With Constitutive Interleukin-7 Receptor for Treatment of High-Grade Pediatric CNS Tumors. J Clin Oncol 2024:JCO2302019. [PMID: 38771986 DOI: 10.1200/jco.23.02019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2023] [Revised: 12/26/2023] [Accepted: 02/12/2024] [Indexed: 05/23/2024] Open
Abstract
PURPOSE T cells modified with chimeric antigen receptors (CARTs) have demonstrated efficacy for hematologic malignancies; however, benefit for patients with CNS tumors has been limited. To enhance T cell activity against GD2+ CNS malignancies, we modified GD2-directed CART cells (GD2.CARTs) with a constitutively active interleukin (IL)-7 receptor (C7R-GD2.CARTs). METHODS Patients age 1-21 years with H3K27-altered diffuse midline glioma (DMG) or other recurrent GD2-expressing CNS tumors were eligible for this phase I trial (ClinicalTrials.gov identifier: NCT04099797). All subjects received standard-of-care adjuvant radiation therapy or chemotherapy before study enrollment. The first treatment cohort received GD2.CARTs alone (1 × 107 cells/m2), and subsequent cohorts received C7R-GD2.CARTs at two dose levels (1 × 107 cells/m2; 3 × 107 cells/m2). Standard lymphodepletion with cyclophosphamide and fludarabine was included at all dose levels. RESULTS Eleven patients (age 4-18 years) received therapy without dose-limiting toxicity. The GD2.CART cohort did not experience toxicity, but had disease progression after brief improvement of residual neurologic deficits (≤3 weeks). The C7R-GD2.CART cohort developed grade 1 tumor inflammation-associated neurotoxicity in seven of eight (88%) cases, controllable with anakinra. Cytokine release syndrome was observed in six of eight (75%, grade 1 in all but one patient) and associated with increased circulating IL-6 and IP-10 (P < .05). Patients receiving C7R-GD2.CARTs experienced temporary improvement from baseline neurologic deficits (range, 2 to >12 months), and seven of eight (88%) remained eligible for additional treatment cycles (range 2-4 cycles). Partial responses by iRANO criteria were observed in two of seven (29%) patients with DMG treated by C7R-GD2.CARTs. CONCLUSION Intravenous GD2.CARTs with and without C7R were well tolerated. Patients treated with C7R-GD2.CARTs exhibited transient improvement of neurologic deficits and increased circulating cytokines/chemokines. Treatment with C7R-GD2.CARTs represents a novel approach warranting further investigation for children with these incurable CNS cancers.
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Affiliation(s)
- Frank Y Lin
- Texas Children's Cancer Center, Baylor College of Medicine, Houston, TX
- Dan L Duncan Comprehensive Cancer Center, Houston, TX
| | - Austin Stuckert
- Texas Children's Cancer Center, Baylor College of Medicine, Houston, TX
| | - Candise Tat
- Texas Children's Cancer Center, Baylor College of Medicine, Houston, TX
| | - Mark White
- Texas Children's Cancer Center, Baylor College of Medicine, Houston, TX
| | - Lucia Ruggieri
- Department of Neurosurgery, Baylor College of Medicine, Houston, TX
| | - Huimin Zhang
- Center for Cell and Gene Therapy, Baylor College of Medicine, Texas Children's Hospital and Houston Methodist Hospital, Houston, TX
| | - Birju Mehta
- Center for Cell and Gene Therapy, Baylor College of Medicine, Texas Children's Hospital and Houston Methodist Hospital, Houston, TX
| | - Natalia Lapteva
- Center for Cell and Gene Therapy, Baylor College of Medicine, Texas Children's Hospital and Houston Methodist Hospital, Houston, TX
| | - Zhuyong Mei
- Center for Cell and Gene Therapy, Baylor College of Medicine, Texas Children's Hospital and Houston Methodist Hospital, Houston, TX
| | - Angela Major
- Department of Pathology, Baylor College of Medicine, Houston, TX
| | - Sachin Thakkar
- Texas Children's Cancer Center, Baylor College of Medicine, Houston, TX
- Center for Cell and Gene Therapy, Baylor College of Medicine, Texas Children's Hospital and Houston Methodist Hospital, Houston, TX
| | - Thomas Shum
- Center for Cell and Gene Therapy, Baylor College of Medicine, Texas Children's Hospital and Houston Methodist Hospital, Houston, TX
- Department of Radiology, Brigham and Women's Hospital, Boston, MA
| | - Kathan Parikh
- Center for Cell and Gene Therapy, Baylor College of Medicine, Texas Children's Hospital and Houston Methodist Hospital, Houston, TX
| | - Meng-Fen Wu
- Center for Cell and Gene Therapy, Baylor College of Medicine, Texas Children's Hospital and Houston Methodist Hospital, Houston, TX
- Department of Medicine, Baylor College of Medicine, Houston, TX
| | - Holly B Lindsay
- Department of Pediatrics Heme-Onc and Bone Marrow Transplantation, Children's Hospital Colorado Center for Cancer and Blood Disorders, University of Colorado Anschutz Medical Campus, Denver, CO
| | - Lauren Scherer
- Texas Children's Cancer Center, Baylor College of Medicine, Houston, TX
| | - Meghan Shekar
- Texas Children's Cancer Center, Baylor College of Medicine, Houston, TX
| | - Patricia Baxter
- Texas Children's Cancer Center, Baylor College of Medicine, Houston, TX
- Dan L Duncan Comprehensive Cancer Center, Houston, TX
| | - Tao Wang
- Dan L Duncan Comprehensive Cancer Center, Houston, TX
- Center for Cell and Gene Therapy, Baylor College of Medicine, Texas Children's Hospital and Houston Methodist Hospital, Houston, TX
- Department of Medicine, Baylor College of Medicine, Houston, TX
| | - Bambi Grilley
- Texas Children's Cancer Center, Baylor College of Medicine, Houston, TX
- Center for Cell and Gene Therapy, Baylor College of Medicine, Texas Children's Hospital and Houston Methodist Hospital, Houston, TX
| | - Karen Moeller
- Department of Radiology, Baylor College of Medicine, Houston, TX
| | - John Hicks
- Department of Pathology, Baylor College of Medicine, Houston, TX
| | - Angshumoy Roy
- Dan L Duncan Comprehensive Cancer Center, Houston, TX
- Department of Pathology, Baylor College of Medicine, Houston, TX
| | - Jamie Anastas
- Department of Neurosurgery, Baylor College of Medicine, Houston, TX
| | - Fatema Malbari
- Department of Neurology, Baylor College of Medicine, Houston, TX
| | - Guillermo Aldave
- Department of Neurosurgery, Baylor College of Medicine, Houston, TX
| | - Murali Chintagumpala
- Texas Children's Cancer Center, Baylor College of Medicine, Houston, TX
- Dan L Duncan Comprehensive Cancer Center, Houston, TX
| | - Susan Blaney
- Texas Children's Cancer Center, Baylor College of Medicine, Houston, TX
- Dan L Duncan Comprehensive Cancer Center, Houston, TX
| | - D Williams Parsons
- Texas Children's Cancer Center, Baylor College of Medicine, Houston, TX
- Dan L Duncan Comprehensive Cancer Center, Houston, TX
| | - Malcolm K Brenner
- Texas Children's Cancer Center, Baylor College of Medicine, Houston, TX
- Dan L Duncan Comprehensive Cancer Center, Houston, TX
- Center for Cell and Gene Therapy, Baylor College of Medicine, Texas Children's Hospital and Houston Methodist Hospital, Houston, TX
- Department of Medicine, Baylor College of Medicine, Houston, TX
| | - Helen E Heslop
- Texas Children's Cancer Center, Baylor College of Medicine, Houston, TX
- Dan L Duncan Comprehensive Cancer Center, Houston, TX
- Center for Cell and Gene Therapy, Baylor College of Medicine, Texas Children's Hospital and Houston Methodist Hospital, Houston, TX
- Department of Medicine, Baylor College of Medicine, Houston, TX
| | - Cliona M Rooney
- Texas Children's Cancer Center, Baylor College of Medicine, Houston, TX
- Dan L Duncan Comprehensive Cancer Center, Houston, TX
- Center for Cell and Gene Therapy, Baylor College of Medicine, Texas Children's Hospital and Houston Methodist Hospital, Houston, TX
| | - Bilal Omer
- Texas Children's Cancer Center, Baylor College of Medicine, Houston, TX
- Dan L Duncan Comprehensive Cancer Center, Houston, TX
- Center for Cell and Gene Therapy, Baylor College of Medicine, Texas Children's Hospital and Houston Methodist Hospital, Houston, TX
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14
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Han PC, Baker TG. Glial and glioneuronal tumors: Navigating the complexity of evolving concepts and new classification. J Neurol Sci 2024; 461:123058. [PMID: 38781807 DOI: 10.1016/j.jns.2024.123058] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2024] [Revised: 04/25/2024] [Accepted: 05/18/2024] [Indexed: 05/25/2024]
Abstract
The World Health Organization (WHO) published the 5th edition classification of tumors of central nervous system in 2021, commonly abbreviated as WHO CNS5, which became the new standard for brain tumor diagnosis and therapy. This edition dramatically impacted tumor diagnostics. In short it introduced new tumors, changed the names of previously recognized tumors, and modified the working definition of previously known tumors. The new system appears complex due to the integration of morphological and multiple molecular criteria. The most radical changes occurred in the field of glial and glioneuronal tumors, which constitutes the lengthy first chapter of this new edition. Herein we present an illustrative outline of the evolving concepts of glial and glioneuronal tumors. We also attempt to explain the rationales behind this substantial change in tumor classification and the challenges to update and integrate it into clinical practice. We aim to present a concise and precise roadmap to aid navigation through the intricate conceptual framework of glial and glioneuronal tumors in the context of WHO CNS5.
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Affiliation(s)
- Peng Cheng Han
- Department of Pathology, Anatomy and Laboratory Medicine, Department of Neuroscience, West Virginia University, Morgantown, WV 26505, United States of America.
| | - Tiffany G Baker
- Department of Pathology and Laboratory Medicine, Medical University of South Carolina, Charleston, SC 29425, United States of America
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15
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Hoang DT, Shulman ED, Turakulov R, Abdullaev Z, Singh O, Campagnolo EM, Lalchungnunga H, Stone EA, Nasrallah MP, Ruppin E, Aldape K. Prediction of DNA methylation-based tumor types from histopathology in central nervous system tumors with deep learning. Nat Med 2024:10.1038/s41591-024-02995-8. [PMID: 38760587 DOI: 10.1038/s41591-024-02995-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2023] [Accepted: 04/11/2024] [Indexed: 05/19/2024]
Abstract
Precision in the diagnosis of diverse central nervous system (CNS) tumor types is crucial for optimal treatment. DNA methylation profiles, which capture the methylation status of thousands of individual CpG sites, are state-of-the-art data-driven means to enhance diagnostic accuracy but are also time consuming and not widely available. Here, to address these limitations, we developed Deep lEarning from histoPathoLOgy and methYlation (DEPLOY), a deep learning model that classifies CNS tumors to ten major categories from histopathology. DEPLOY integrates three distinct components: the first classifies CNS tumors directly from slide images ('direct model'), the second initially generates predictions for DNA methylation beta values, which are subsequently used for tumor classification ('indirect model'), and the third classifies tumor types directly from routinely available patient demographics. First, we find that DEPLOY accurately predicts beta values from histopathology images. Second, using a ten-class model trained on an internal dataset of 1,796 patients, we predict the tumor categories in three independent external test datasets including 2,156 patients, achieving an overall accuracy of 95% and balanced accuracy of 91% on samples that are predicted with high confidence. These results showcase the potential future use of DEPLOY to assist pathologists in diagnosing CNS tumors within a clinically relevant short time frame.
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Affiliation(s)
- Danh-Tai Hoang
- Biological Data Science Institute, College of Science, Australian National University, Canberra, Australian Capital Territory, Australia
| | - Eldad D Shulman
- Cancer Data Science Laboratory, Center for Cancer Research, National Cancer Institute, Bethesda, MD, USA
| | - Rust Turakulov
- Laboratory of Pathology, Center for Cancer Research, National Cancer Institute, Bethesda, MD, USA
| | - Zied Abdullaev
- Laboratory of Pathology, Center for Cancer Research, National Cancer Institute, Bethesda, MD, USA
| | - Omkar Singh
- Laboratory of Pathology, Center for Cancer Research, National Cancer Institute, Bethesda, MD, USA
| | - Emma M Campagnolo
- Cancer Data Science Laboratory, Center for Cancer Research, National Cancer Institute, Bethesda, MD, USA
| | - H Lalchungnunga
- Laboratory of Pathology, Center for Cancer Research, National Cancer Institute, Bethesda, MD, USA
| | - Eric A Stone
- Biological Data Science Institute, College of Science, Australian National University, Canberra, Australian Capital Territory, Australia
| | - MacLean P Nasrallah
- Division of Neuropathology, Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Eytan Ruppin
- Cancer Data Science Laboratory, Center for Cancer Research, National Cancer Institute, Bethesda, MD, USA.
| | - Kenneth Aldape
- Laboratory of Pathology, Center for Cancer Research, National Cancer Institute, Bethesda, MD, USA.
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16
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Drexler R, Khatri R, Sauvigny T, Mohme M, Maire CL, Ryba A, Zghaibeh Y, Dührsen L, Salviano-Silva A, Lamszus K, Westphal M, Gempt J, Wefers AK, Neumann JE, Bode H, Hausmann F, Huber TB, Bonn S, Jütten K, Delev D, Weber KJ, Harter PN, Onken J, Vajkoczy P, Capper D, Wiestler B, Weller M, Snijder B, Buck A, Weiss T, Göller PC, Sahm F, Menstel JA, Zimmer DN, Keough MB, Ni L, Monje M, Silverbush D, Hovestadt V, Suvà ML, Krishna S, Hervey-Jumper SL, Schüller U, Heiland DH, Hänzelmann S, Ricklefs FL. A prognostic neural epigenetic signature in high-grade glioma. Nat Med 2024:10.1038/s41591-024-02969-w. [PMID: 38760585 DOI: 10.1038/s41591-024-02969-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2023] [Accepted: 04/03/2024] [Indexed: 05/19/2024]
Abstract
Neural-tumor interactions drive glioma growth as evidenced in preclinical models, but clinical validation is limited. We present an epigenetically defined neural signature of glioblastoma that independently predicts patients' survival. We use reference signatures of neural cells to deconvolve tumor DNA and classify samples into low- or high-neural tumors. High-neural glioblastomas exhibit hypomethylated CpG sites and upregulation of genes associated with synaptic integration. Single-cell transcriptomic analysis reveals a high abundance of malignant stemcell-like cells in high-neural glioblastoma, primarily of the neural lineage. These cells are further classified as neural-progenitor-cell-like, astrocyte-like and oligodendrocyte-progenitor-like, alongside oligodendrocytes and excitatory neurons. In line with these findings, high-neural glioblastoma cells engender neuron-to-glioma synapse formation in vitro and in vivo and show an unfavorable survival after xenografting. In patients, a high-neural signature is associated with decreased overall and progression-free survival. High-neural tumors also exhibit increased functional connectivity in magnetencephalography and resting-state magnet resonance imaging and can be detected via DNA analytes and brain-derived neurotrophic factor in patients' plasma. The prognostic importance of the neural signature was further validated in patients diagnosed with diffuse midline glioma. Our study presents an epigenetically defined malignant neural signature in high-grade gliomas that is prognostically relevant. High-neural gliomas likely require a maximized surgical resection approach for improved outcomes.
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Affiliation(s)
- Richard Drexler
- Department of Neurosurgery, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- Department of Neurology, Stanford University, Stanford, CA, USA
| | - Robin Khatri
- Institute of Medical Systems Biology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- Center for Biomedical AI, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Thomas Sauvigny
- Department of Neurosurgery, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Malte Mohme
- Department of Neurosurgery, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Cecile L Maire
- Department of Neurosurgery, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Alice Ryba
- Department of Neurosurgery, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Yahya Zghaibeh
- Department of Neurosurgery, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Lasse Dührsen
- Department of Neurosurgery, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Amanda Salviano-Silva
- Department of Neurosurgery, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Katrin Lamszus
- Department of Neurosurgery, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Manfred Westphal
- Department of Neurosurgery, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Jens Gempt
- Department of Neurosurgery, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Annika K Wefers
- Institute of Neuropathology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- Mildred Scheel Cancer Career Center HaTriCS4, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Julia E Neumann
- Institute of Neuropathology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- Center for Molecular Neurobiology Hamburg (ZMNH), University Hospital Hamburg Eppendorf, Hamburg, Germany
| | - Helena Bode
- Research Institute Children's Cancer Center Hamburg, Hamburg, Germany
| | - Fabian Hausmann
- Institute of Medical Systems Biology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- Center for Biomedical AI, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Tobias B Huber
- III. Department of Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- Hamburg Center for Kidney Health (HCKH), University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Stefan Bonn
- Institute of Medical Systems Biology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- Center for Biomedical AI, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Kerstin Jütten
- Department of Neurosurgery, University Hospital Aachen, Aachen, Germany
| | - Daniel Delev
- Department of Neurosurgery, University Hospital Aachen, Aachen, Germany
- Department of Neurosurgery, University Clinic Erlangen, Friedrich-Alexander Universität Erlangen-Nürnberg, Erlangen, Germany
| | - Katharina J Weber
- Neurological Institute (Edinger Institute), University Hospital Frankfurt, Frankfurt am Main, Germany
- German Cancer Consortium (DKTK), Heidelberg, Germany and German Cancer Research Center (DKFZ), Heidelberg, Germany
- Frankfurt Cancer Institute (FCI), Frankfurt am Main, Germany
- University Cancer Center (UCT) Frankfurt, Frankfurt am Main, Germany
| | - Patrick N Harter
- Neurological Institute (Edinger Institute), University Hospital Frankfurt, Frankfurt am Main, Germany
- Institute of Neuropathology, Faculty of Medicine, LMU Munich, Munich, Germany
| | - Julia Onken
- Department of Neurosurgery, Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - Peter Vajkoczy
- Department of Neurosurgery, Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - David Capper
- Department of Neuropathology, Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
| | - Benedikt Wiestler
- Department of Neuroradiology, Klinikum rechts der Isar, School of Medicine, Technical University Munich, Munich, Germany
| | - Michael Weller
- Department of Neurology, Clinical Neuroscience Center, University Hospital Zurich, Zurich, Switzerland
- Department of Neurology, University of Zürich, Zurich, Switzerland
| | - Berend Snijder
- Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland
| | - Alicia Buck
- Department of Neurology, Clinical Neuroscience Center, University Hospital Zurich, Zurich, Switzerland
- Department of Neurology, University of Zürich, Zurich, Switzerland
| | - Tobias Weiss
- Department of Neurology, Clinical Neuroscience Center, University Hospital Zurich, Zurich, Switzerland
- Department of Neurology, University of Zürich, Zurich, Switzerland
| | - Pauline C Göller
- Hopp Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany
- Department of Neuropathology, University Hospital Heidelberg, Heidelberg, Germany
| | - Felix Sahm
- Hopp Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany
- Department of Neuropathology, University Hospital Heidelberg, Heidelberg, Germany
| | - Joelle Aline Menstel
- Department of Neurosurgery, Medical Center University of Freiburg, Freiburg, Germany
| | - David Niklas Zimmer
- Department of Neurosurgery, Medical Center University of Freiburg, Freiburg, Germany
| | | | - Lijun Ni
- Department of Neurology, Stanford University, Stanford, CA, USA
| | - Michelle Monje
- Department of Neurology, Stanford University, Stanford, CA, USA
| | - Dana Silverbush
- Department of Cancer Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Abramson Family Cancer Research Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Volker Hovestadt
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Mario L Suvà
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Department of Pathology and Center for Cancer Research, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Saritha Krishna
- Department of Neurological Surgery, University of California, San Francisco, CA, USA
| | - Shawn L Hervey-Jumper
- Department of Neurological Surgery, University of California, San Francisco, CA, USA
| | - Ulrich Schüller
- Institute of Neuropathology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- Research Institute Children's Cancer Center Hamburg, Hamburg, Germany
- Department of Pediatric Hematology and Oncology, Research Institute Children's Cancer Center Hamburg, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Dieter H Heiland
- Department of Neurosurgery, University Clinic Erlangen, Friedrich-Alexander Universität Erlangen-Nürnberg, Erlangen, Germany
- Department of Neurosurgery, Medical Center University of Freiburg, Freiburg, Germany
- Translational Neurosurgery, Friedrich-Alexander Universität Erlangen-Nürnberg, Erlangen, Germany
- Department of Neurological Surgery, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
- German Cancer Consortium (DKTK), Partner Site Freiburg, Freiburg, Germany
| | - Sonja Hänzelmann
- Institute of Medical Systems Biology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- Center for Biomedical AI, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- III. Department of Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- Hamburg Center for Kidney Health (HCKH), University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Franz L Ricklefs
- Department of Neurosurgery, University Medical Center Hamburg-Eppendorf, Hamburg, Germany.
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17
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Schreck KC, Strowd RE, Nabors LB, Ellingson BM, Chang M, Tan SK, Abdullaev Z, Turakulov R, Aldape K, Danda N, Desideri S, Fisher J, Iacoboni M, Surakus T, Rudek MA, Bettegowda C, Grossman SA, Ye X. Response Rate and Molecular Correlates to Encorafenib and Binimetinib in BRAF-V600E Mutant High-Grade Glioma. Clin Cancer Res 2024; 30:2048-2056. [PMID: 38446982 PMCID: PMC11096001 DOI: 10.1158/1078-0432.ccr-23-3241] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2023] [Revised: 01/25/2024] [Accepted: 03/04/2024] [Indexed: 03/08/2024]
Abstract
PURPOSE Although fewer than 5% of high-grade gliomas (HGG) are BRAF-V600E mutated, these tumors are notable as BRAF-targeted therapy shows efficacy for some populations. The purpose of this study was to evaluate response to the combination of encorafenib with binimetinib in adults with recurrent BRAF-V600-mutated HGG. PATIENTS AND METHODS In this phase 2, open-label, Adult Brain Tumor Consortium (ABTC) trial (NCT03973918), encorafenib and binimetinib were administered at their FDA-approved doses continuously in 28-day cycles. Eligible patients were required to have HGG or glioblastoma with a BRAF-V600E alteration that was recurrent following at least one line of therapy, including radiotherapy. RESULTS Five patients enrolled between January 2020 and administrative termination in November 2021 (due to closure of the ABTC). Enrolled patients received treatment for 2 to 40 months; currently one patient remains on treatment. Centrally determined radiographic response rate was 60%, with one complete response and two partial responses. Methylation profiling revealed that all tumors cluster most closely with anaplastic pleomorphic xanthoastrocytoma (PXA). Transcriptional profile for MAPK-response signature was similar across all tumors at baseline and did not correlate with response in this small population. Circulating tumor DNA measured in plasma samples before treatment, during response, and upon progression showed feasibility of detection for the BRAF-V600E alteration. No new safety signal was detected. CONCLUSIONS Encorafenib and binimetinib exhibit positive tumor responses in patients with recurrent BRAF-V600E mutant HGG in this small series, warranting therapeutic consideration. Although toxicity remains a concern for BRAF-targeted therapies, no new safety signal was observed in these patients.
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Affiliation(s)
- Karisa C Schreck
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, Maryland
- Sidney Kimmel Comprehensive Cancer Center, Baltimore, Maryland
| | - Roy E Strowd
- Department of Neurology, Wake Forest University School of Medicine, Winston Salem, North Carolina
| | - Louis B Nabors
- Department of Neurology, Heersink School of Medicine, University of Alabama at Birmingham, Alabama
| | - Benjamin M Ellingson
- Department of Radiological Sciences, UCLA Brain Tumor Imaging Laboratory, University of California Los Angeles, Los Angeles, California
| | - Michael Chang
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Sze K Tan
- Department of Neurosurgery, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Zied Abdullaev
- Laboratory of Pathology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland
| | - Rust Turakulov
- Victorian Comprehensive Cancer Center, Melbourne, Victoria, Australia
| | - Kenneth Aldape
- Laboratory of Pathology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland
| | - Neeraja Danda
- Sidney Kimmel Comprehensive Cancer Center, Baltimore, Maryland
| | - Serena Desideri
- Sidney Kimmel Comprehensive Cancer Center, Baltimore, Maryland
| | - Joy Fisher
- Sidney Kimmel Comprehensive Cancer Center, Baltimore, Maryland
| | | | - Trisha Surakus
- Sidney Kimmel Comprehensive Cancer Center, Baltimore, Maryland
| | | | - Chetan Bettegowda
- Department of Neurosurgery, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | | | - Xiaobu Ye
- Sidney Kimmel Comprehensive Cancer Center, Baltimore, Maryland
- Department of Neurosurgery, Johns Hopkins University School of Medicine, Baltimore, Maryland
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18
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Calin VL, Mihailescu M, Petrescu GE, Lisievici MG, Tarba N, Calin D, Ungureanu VG, Pasov D, Brehar FM, Gorgan RM, Moisescu MG, Savopol T. Grading of glioma tumors using digital holographic microscopy. Heliyon 2024; 10:e29897. [PMID: 38694030 PMCID: PMC11061684 DOI: 10.1016/j.heliyon.2024.e29897] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2024] [Revised: 03/14/2024] [Accepted: 04/17/2024] [Indexed: 05/03/2024] Open
Abstract
Gliomas are the most common type of cerebral tumors; they occur with increasing incidence in the last decade and have a high rate of mortality. For efficient treatment, fast accurate diagnostic and grading of tumors are imperative. Presently, the grading of tumors is established by histopathological evaluation, which is a time-consuming procedure and relies on the pathologists' experience. Here we propose a supervised machine learning procedure for tumor grading which uses quantitative phase images of unstained tissue samples acquired by digital holographic microscopy. The algorithm is using an extensive set of statistical and texture parameters computed from these images. The procedure has been able to classify six classes of images (normal tissue and five glioma subtypes) and to distinguish between gliomas types from grades II to IV (with the highest sensitivity and specificity for grade II astrocytoma and grade III oligodendroglioma and very good scores in recognizing grade III anaplastic astrocytoma and grade IV glioblastoma). The procedure bolsters clinical diagnostic accuracy, offering a swift and reliable means of tumor characterization and grading, ultimately the enhancing treatment decision-making process.
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Affiliation(s)
- Violeta L. Calin
- Biophysics and Cellular Biotechnology Dept., Faculty of Medicine, University of Medicine and Pharmacy Carol Davila, 8 Eroii Sanitari Blvd., 050474, Bucharest, Romania
- Excellence Center for Research in Biophysics and Cellular Biotechnology, Faculty of Medicine, University of Medicine and Pharmacy Carol Davila, 8 Eroii Sanitari Blvd., 050474, Bucharest, Romania
| | - Mona Mihailescu
- Digital Holography Imaging and Processing Laboratory, Physics Department, Faculty of Applied Sciences, National University for Science and Technology Politehnica Bucharest, 313 Splaiul Independentei, 060042, Bucharest, Romania
- Centre for Fundamental Sciences Applied in Engineering, National University for Science and Technology Politehnica Bucharest, 313 Splaiul Independentei, 060042, Bucharest, Romania
| | - George E.D. Petrescu
- Department of Neurosurgery, “Bagdasar-Arseni” Clinical Emergency Hospital, 12 Berceni st., 041915, Bucharest, Romania
- Department of Neurosurgery, Faculty of Medicine, University of Medicine and Pharmacy Carol Davila, 8 Eroii Sanitari Blvd., 050474, Bucharest, Romania
| | - Mihai Gheorghe Lisievici
- Department of Pathology, “Bagdasar Arseni” Clinical Emergency Hospital, 12 Berceni st., 041915, Bucharest, Romania
| | - Nicolae Tarba
- Doctoral School of Automatic Control and Computers, National University for Science and Technology Politehnica Bucharest, 313 Splaiul Independentei, 060042, Bucharest, Romania
| | - Daniel Calin
- Biophysics and Cellular Biotechnology Dept., Faculty of Medicine, University of Medicine and Pharmacy Carol Davila, 8 Eroii Sanitari Blvd., 050474, Bucharest, Romania
| | - Victor Gabriel Ungureanu
- Biophysics and Cellular Biotechnology Dept., Faculty of Medicine, University of Medicine and Pharmacy Carol Davila, 8 Eroii Sanitari Blvd., 050474, Bucharest, Romania
| | - Diana Pasov
- Department of Pathology, “Bagdasar Arseni” Clinical Emergency Hospital, 12 Berceni st., 041915, Bucharest, Romania
| | - Felix M. Brehar
- Department of Neurosurgery, “Bagdasar-Arseni” Clinical Emergency Hospital, 12 Berceni st., 041915, Bucharest, Romania
- Department of Neurosurgery, Faculty of Medicine, University of Medicine and Pharmacy Carol Davila, 8 Eroii Sanitari Blvd., 050474, Bucharest, Romania
| | - Radu M. Gorgan
- Department of Neurosurgery, “Bagdasar-Arseni” Clinical Emergency Hospital, 12 Berceni st., 041915, Bucharest, Romania
- Department of Neurosurgery, Faculty of Medicine, University of Medicine and Pharmacy Carol Davila, 8 Eroii Sanitari Blvd., 050474, Bucharest, Romania
| | - Mihaela G. Moisescu
- Biophysics and Cellular Biotechnology Dept., Faculty of Medicine, University of Medicine and Pharmacy Carol Davila, 8 Eroii Sanitari Blvd., 050474, Bucharest, Romania
- Excellence Center for Research in Biophysics and Cellular Biotechnology, Faculty of Medicine, University of Medicine and Pharmacy Carol Davila, 8 Eroii Sanitari Blvd., 050474, Bucharest, Romania
| | - Tudor Savopol
- Biophysics and Cellular Biotechnology Dept., Faculty of Medicine, University of Medicine and Pharmacy Carol Davila, 8 Eroii Sanitari Blvd., 050474, Bucharest, Romania
- Excellence Center for Research in Biophysics and Cellular Biotechnology, Faculty of Medicine, University of Medicine and Pharmacy Carol Davila, 8 Eroii Sanitari Blvd., 050474, Bucharest, Romania
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19
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Kumaria A, Leggate AJ, Dow GR, Ingale HA, Robertson IJA, Byrne PO, Basu S, Macarthur DC, Smith SJ. A common tumour in a rare location: a single centre case series of cerebellar glioblastoma. Br J Neurosurg 2024:1-6. [PMID: 38741545 DOI: 10.1080/02688697.2024.2348598] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2023] [Accepted: 04/23/2024] [Indexed: 05/16/2024]
Abstract
Although glioblastoma is the commonest primary brain tumour in adults, its location in the cerebellum is extremely rare. We present thirteen cases (3 female, 10 male; median age at presentation 56 [age range 21-77]) of surgically managed, histologically confirmed, primary cerebellar glioblastoma (cGB) over a 17 year period (2005-2022). Pre-operative radiological diagnosis was challenging given cGB rarity, although MRI demonstrated ring enhancement in all cases. Surgical management included posterior fossa craniectomy and debulking in 11 cases and burr hole biopsy in two. CSF diversion was necessary in four cases. No evidence of IDH or ATRX gene mutations was found when tested. Survival ranged from 1 to 22 months after diagnosis (mean 10.9 months). We also seek to understand why glioblastoma is rare in this location and discuss potential reasons for this. We hypothesise that increasing anatomical distance from germinal regions and decreased local endogenous neural stem cell activity (which has been associated with glioblastoma) may explain why glioblastoma is rare in the cerebellum. We hereby seek to add to the limited literature on cGB as this is the largest UK cGB series to date.
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Affiliation(s)
- Ashwin Kumaria
- Department of Neurosurgery, Queen's Medical Centre, Nottingham, UK
| | - Alex J Leggate
- Department of Neurosurgery, Queen's Medical Centre, Nottingham, UK
| | - Graham R Dow
- Department of Neurosurgery, Queen's Medical Centre, Nottingham, UK
| | - Harshal A Ingale
- Department of Neurosurgery, Queen's Medical Centre, Nottingham, UK
| | | | - Paul O Byrne
- Department of Neurosurgery, Queen's Medical Centre, Nottingham, UK
| | - Surajit Basu
- Department of Neurosurgery, Queen's Medical Centre, Nottingham, UK
| | | | - Stuart J Smith
- Department of Neurosurgery, Queen's Medical Centre, Nottingham, UK
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20
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Xia J, Li Z, Ding Y, Shah LA, Zhao H, Ye D, Zhang J. Construction and Application of Nanozyme Sensor Arrays. Anal Chem 2024. [PMID: 38740384 DOI: 10.1021/acs.analchem.4c00670] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/16/2024]
Abstract
Compared with traditional "lock-key mode" biosensors, a sensor array consists of a series of sensing elements based on intermolecular interactions (typically hydrogen bonds, van der Waals forces, and electrostatic interactions). At the same time, sensor arrays also have the advantages of fast response, high sensitivity, low energy consumption, low cost, rich output signals, and imageability, which have attracted widespread attention from researchers. Nanozymes are nanomaterials which own enzyme-like properties. Because of the adjustable activity, high stability, and cost effectiveness of nanozymes, they are potential candidates for construction of sensor arrays to output different signals from analytes through the chemoresponse of colorants, which solves the shortcomings of traditional sensors that they cannot support multiple detection and lack universality. Recently, a sensor array based on nanozymes as nonspecific recognition receptors has attracted much more attention from researchers and has been applied to precise recognition of proteins, bacteria, and heavy metals. In this perspective, attention is given to nanozymes and the regulation of their enzyme-like activity. Particularly, the building principles and methods for sensor arrays based on nanozymes are analyzed, and the applications are summarized. Finally, the approaches to overcome the challenges and perspectives are also presented and analyzed for facilitating further research and development of nanozyme sensor arrays. This perspective should be helpful for gaining insight into research ideas within the field of nanozyme sensor arrays.
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Affiliation(s)
- Jianing Xia
- Department of Chemistry & Institute for Sustainable Energy, College of Sciences, Shanghai University, Shanghai 200444, PR China
| | - Zhen Li
- Department of Chemistry & Institute for Sustainable Energy, College of Sciences, Shanghai University, Shanghai 200444, PR China
| | - Yaping Ding
- Department of Chemistry & Institute for Sustainable Energy, College of Sciences, Shanghai University, Shanghai 200444, PR China
| | - Luqman Ali Shah
- Department of Chemistry & Institute for Sustainable Energy, College of Sciences, Shanghai University, Shanghai 200444, PR China
| | - Hongbin Zhao
- Department of Chemistry & Institute for Sustainable Energy, College of Sciences, Shanghai University, Shanghai 200444, PR China
| | - Daixin Ye
- Department of Chemistry & Institute for Sustainable Energy, College of Sciences, Shanghai University, Shanghai 200444, PR China
| | - Jiujun Zhang
- Department of Chemistry & Institute for Sustainable Energy, College of Sciences, Shanghai University, Shanghai 200444, PR China
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21
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Schüller U, Gocke A, Godbole S, Delbridge C, Thomas C, Neumann JE. Anaplastic histology and distinct molecular features in a small series of spinal cord ependymomas. Acta Neuropathol 2024; 147:83. [PMID: 38735021 PMCID: PMC11089008 DOI: 10.1007/s00401-024-02740-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2024] [Revised: 05/07/2024] [Accepted: 05/07/2024] [Indexed: 05/13/2024]
Affiliation(s)
- Ulrich Schüller
- Department of Pediatric Hematology and Oncology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- Research Institute Children's Cancer Center Hamburg, Hamburg, Germany
- Institute of Neuropathology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Antonia Gocke
- Center for Molecular Neurobiology Hamburg (ZMNH), University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- Section of Mass Spectrometric Proteomics, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Shweta Godbole
- Center for Molecular Neurobiology Hamburg (ZMNH), University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Claire Delbridge
- Institute of Pathology, Department of Neuropathology, TUM School of Medicine and Health, Technical University Munich, Munich, Germany
| | - Christian Thomas
- Institute of Neuropathology, University Hospital Münster, Münster, Germany
| | - Julia E Neumann
- Institute of Neuropathology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany.
- Center for Molecular Neurobiology Hamburg (ZMNH), University Medical Center Hamburg-Eppendorf, Hamburg, Germany.
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22
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Xu H, Chen X, Sun Y, Hu X, Zhang X, Wang Y, Tang Q, Zhu Q, Song K, Chen H, Sheng X, Yao Y, Zhuang D, Chen L, Mao Y, Qin Z. Comprehensive molecular characterization of long-term glioblastoma survivors. Cancer Lett 2024:216938. [PMID: 38734160 DOI: 10.1016/j.canlet.2024.216938] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2024] [Revised: 05/01/2024] [Accepted: 05/02/2024] [Indexed: 05/13/2024]
Abstract
Fewer than 5% glioblastoma (GBM) patients survive over five years and are termed long-term survivors (LTS), yet their molecular background is unclear. The present cohort included 72 isocitrate dehydrogenase (IDH)-wildtype GBM patients, consisting of 35 LTS and 37 short-term survivors (STS), and we employed whole exome sequencing, RNA-seq and DNA methylation array to delineate this largest LTS cohort to date. Although LTS and STS demonstrated analogous clinical characters and classical GBM biomarkers, CASC5 (P = 0.002) and SPEN (P = 0.013) mutations were enriched in LTS, whereas gene-to-gene fusions were concentrated in STS (P = 0.007). Importantly, LTS exhibited higher tumor mutation burden (P < 0.001) and copy number (CN) increase (P = 0.013), but lower mutant-allele tumor heterogeneity score (P < 0.001) and CN decrease (P = 0.026). Additionally, LTS demonstrated hypermethylated genome (P < 0.001) relative to STS. Differentially expressed and methylated genes both enriched in olfactory transduction. Further, analysis of the tumor microenvironment revealed higher infiltration of M1 macrophages (P = 0.043), B cells (P = 0.016), class-switched memory B cells (P = 0.002), central memory CD4+ T cells (P = 0.031) and CD4+ Th1 cells (P = 0.005) in LTS. We also separately analyzed a subset of patients who were methylation class-defined GBM, contributing 70.8% of the entire cohort, and obtained similar results relative to prior analyses. Finally, we demonstrated that LTS and STS could be distinguished using a subset of molecular features. Taken together, the present study delineated unique molecular attributes of LTS GBM.
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Affiliation(s)
- Hao Xu
- Department of Neurosurgery, Huashan Hospital, Fudan University, Shanghai, China; National Center for Neurological Disorders, Shanghai, China; Shanghai Key Laboratory of Brain Function Restoration and Neural Regeneration, Shanghai, China
| | - Xinyu Chen
- Department of Breast and Urological Medical Oncology, Fudan University Shanghai Cancer Center, Shanghai Medical College, Fudan University, Shanghai, China
| | - Ying Sun
- GenomiCare Biotechnology (Shanghai) Co. Ltd., Shanghai, China; Department of Data Science, Shanghai CreateCured Biotechnology Co. Ltd., Shanghai, China
| | - Xiaomu Hu
- Department of Pathology, Huashan Hospital, Fudan University, Shanghai, China
| | - Xuan Zhang
- GenomiCare Biotechnology (Shanghai) Co. Ltd., Shanghai, China
| | - Ye Wang
- Department of Neurosurgery, Huashan Hospital, Fudan University, Shanghai, China; National Center for Neurological Disorders, Shanghai, China; Shanghai Key Laboratory of Brain Function Restoration and Neural Regeneration, Shanghai, China
| | - Qisheng Tang
- Department of Neurosurgery, Huashan Hospital, Fudan University, Shanghai, China; National Center for Neurological Disorders, Shanghai, China; Shanghai Key Laboratory of Brain Function Restoration and Neural Regeneration, Shanghai, China
| | - Qiongji Zhu
- Department of Neurosurgery, Huashan Hospital, Fudan University, Shanghai, China; National Center for Neurological Disorders, Shanghai, China; Shanghai Key Laboratory of Brain Function Restoration and Neural Regeneration, Shanghai, China
| | - Kun Song
- Department of Neurosurgery, Huashan Hospital, Fudan University, Shanghai, China; National Center for Neurological Disorders, Shanghai, China; Shanghai Key Laboratory of Brain Function Restoration and Neural Regeneration, Shanghai, China
| | - Hong Chen
- Department of Pathology, Huashan Hospital, Fudan University, Shanghai, China
| | - Xiaofang Sheng
- Department of Radiation Oncology, Huashan hospital, Fudan University, Shanghai, China
| | - Yu Yao
- Department of Neurosurgery, Huashan Hospital, Fudan University, Shanghai, China; National Center for Neurological Disorders, Shanghai, China; Shanghai Key Laboratory of Brain Function Restoration and Neural Regeneration, Shanghai, China
| | - Dongxiao Zhuang
- Department of Neurosurgery, Huashan Hospital, Fudan University, Shanghai, China; National Center for Neurological Disorders, Shanghai, China; Shanghai Key Laboratory of Brain Function Restoration and Neural Regeneration, Shanghai, China
| | - Lingchao Chen
- Department of Neurosurgery, Huashan Hospital, Fudan University, Shanghai, China; National Center for Neurological Disorders, Shanghai, China; Shanghai Key Laboratory of Brain Function Restoration and Neural Regeneration, Shanghai, China.
| | - Ying Mao
- Department of Neurosurgery, Huashan Hospital, Fudan University, Shanghai, China; National Center for Neurological Disorders, Shanghai, China; Shanghai Key Laboratory of Brain Function Restoration and Neural Regeneration, Shanghai, China.
| | - Zhiyong Qin
- Department of Neurosurgery, Huashan Hospital, Fudan University, Shanghai, China; National Center for Neurological Disorders, Shanghai, China; Shanghai Key Laboratory of Brain Function Restoration and Neural Regeneration, Shanghai, China.
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23
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Xie T, Danieli-Mackay A, Buccarelli M, Barbieri M, Papadionysiou I, D'Alessandris QG, Robens C, Übelmesser N, Vinchure OS, Lauretti L, Fotia G, Schwarz RF, Wang X, Ricci-Vitiani L, Gopalakrishnan J, Pallini R, Papantonis A. Pervasive structural heterogeneity rewires glioblastoma chromosomes to sustain patient-specific transcriptional programs. Nat Commun 2024; 15:3905. [PMID: 38724522 PMCID: PMC11082206 DOI: 10.1038/s41467-024-48053-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2023] [Accepted: 04/18/2024] [Indexed: 05/12/2024] Open
Abstract
Glioblastoma multiforme (GBM) encompasses brain malignancies marked by phenotypic and transcriptional heterogeneity thought to render these tumors aggressive, resistant to therapy, and inevitably recurrent. However, little is known about how the spatial organization of GBM genomes underlies this heterogeneity and its effects. Here, we compile a cohort of 28 patient-derived glioblastoma stem cell-like lines (GSCs) known to reflect the properties of their tumor-of-origin; six of these were primary-relapse tumor pairs from the same patient. We generate and analyze 5 kbp-resolution chromosome conformation capture (Hi-C) data from all GSCs to systematically map thousands of standalone and complex structural variants (SVs) and the multitude of neoloops arising as a result. By combining Hi-C, histone modification, and gene expression data with chromatin folding simulations, we explain how the pervasive, uneven, and idiosyncratic occurrence of neoloops sustains tumor-specific transcriptional programs via the formation of new enhancer-promoter contacts. We also show how even moderately recurrent neoloops can relate to patient-specific vulnerabilities. Together, our data provide a resource for dissecting GBM biology and heterogeneity, as well as for informing therapeutic approaches.
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Affiliation(s)
- Ting Xie
- Institute of Pathology, University Medical Center Göttingen, Göttingen, Germany
| | - Adi Danieli-Mackay
- Institute of Pathology, University Medical Center Göttingen, Göttingen, Germany
| | - Mariachiara Buccarelli
- Department of Oncology and Molecular Medicine, Istituto Superiore di Sanità, Rome, Italy
| | - Mariano Barbieri
- Institute of Pathology, University Medical Center Göttingen, Göttingen, Germany
| | | | - Q Giorgio D'Alessandris
- Department of Neuroscience, Catholic University School of Medicine, Rome, Italy
- Department of Neuroscience, Fondazione Policlinico Universitario A. Gemelli IRCCS, Roma, Italy
| | - Claudia Robens
- Institute for Computational Cancer Biology (ICCB), Center for Integrated Oncology (CIO), Cancer Research Center Cologne Essen (CCCE), University of Cologne, Cologne, Germany
| | - Nadine Übelmesser
- Institute of Pathology, University Medical Center Göttingen, Göttingen, Germany
| | - Omkar Suhas Vinchure
- Institute of Human Genetics, University Hospital and Heinrich-Heine-University Düsseldorf, Düsseldorf, Germany
| | - Liverana Lauretti
- Department of Neuroscience, Catholic University School of Medicine, Rome, Italy
| | - Giorgio Fotia
- Centre for Advanced Studies, Research and Development in Sardinia (CRS4), Pula, Italy
| | - Roland F Schwarz
- Institute for Computational Cancer Biology (ICCB), Center for Integrated Oncology (CIO), Cancer Research Center Cologne Essen (CCCE), University of Cologne, Cologne, Germany
- Berlin Institute for the Foundations of Learning and Data (BIFOLD), Berlin, Germany
| | - Xiaotao Wang
- Institute of Reproduction and Development, Fudan University, Shanghai, China
- Research Units of Embryo Original Diseases, Chinese Academy of Medical Sciences, Shanghai, China
| | - Lucia Ricci-Vitiani
- Department of Oncology and Molecular Medicine, Istituto Superiore di Sanità, Rome, Italy
| | - Jay Gopalakrishnan
- Institute of Human Genetics, University Hospital and Heinrich-Heine-University Düsseldorf, Düsseldorf, Germany
- Institute of Human Genetics, Jena University Hospital and Friedrich Schiller University of Jena, Jena, Germany
| | - Roberto Pallini
- Department of Neuroscience, Catholic University School of Medicine, Rome, Italy.
| | - Argyris Papantonis
- Institute of Pathology, University Medical Center Göttingen, Göttingen, Germany.
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24
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Ehret F, Perez E, Teichmann D, Meier S, Geiler C, Cosmas Z, Franke H, Roohani S, Wasilewksi D, Onken J, Vajkoczy P, Schweizer L, Kaul D, Capper D. Clinical implications of DNA methylation-based integrated classification of histologically defined grade 2 meningiomas. Acta Neuropathol Commun 2024; 12:74. [PMID: 38720399 PMCID: PMC11080225 DOI: 10.1186/s40478-024-01739-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2023] [Accepted: 02/08/2024] [Indexed: 05/12/2024] Open
Abstract
The combination of DNA methylation analysis with histopathological and genetic features allows for a more accurate risk stratification and classification of meningiomas. Nevertheless, the implications of this classification for patients with grade 2 meningiomas, a particularly heterogeneous tumor entity, are only partially understood. We correlate the outcomes of histopathologically confirmed grade 2 meningioma with an integrated molecular-morphologic risk stratification and determine its clinical implications. Grade 2 meningioma patients treated at our institution were re-classified using an integrated risk stratification involving DNA methylation array-based data, copy number assessment and TERT promoter mutation analyses. Grade 2 meningioma cases according to the WHO 2021 criteria treated between 2007 and 2021 (n = 100) were retrospectively analyzed. The median clinical and radiographic follow-up periods were 59.8 and 54.4 months. A total of 38 recurrences and 17 deaths were observed. The local control rates of the entire cohort after 2-, 4-, and 6-years were 84.3%, 68.5%, and 50.8%, with a median local control time of 77.2 months. The distribution of the integrated risk groups were as follows: 31 low, 54 intermediate, and 15 high risk cases. In the multivariable Cox regression analysis, integrated risk groups were significantly associated with the risk of local recurrence (hazard ratio (HR) intermediate: 9.91, HR high-risk: 7.29, p < 0.01). Gross total resections decreased the risk of local tumor progression (HR gross total resection: 0.19, p < 0.01). The comparison of 1p status and integrated risk groups (low vs. intermediate/high) revealed nearly identical local control rates within their respective subgroups. In summary, only around 50% of WHO 2021 grade 2 meningiomas have an intermediate risk profile. Integrated molecular risk stratification is crucial to guide the management of patients with grade 2 tumors and should be routinely applied to avoid over- and undertreatment, especially concerning the use of adjuvant radiotherapy.
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Affiliation(s)
- Felix Ehret
- Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Department of Radiation Oncology, Berlin, Germany.
- Charité - Universitätsmedizin Berlin, Berlin, Germany; German Cancer Consortium (DKTK), partner site Berlin, and German Cancer Research Center (DKFZ), Heidelberg, Germany.
| | - Eilís Perez
- Charité - Universitätsmedizin Berlin, Berlin, Germany; German Cancer Consortium (DKTK), partner site Berlin, and German Cancer Research Center (DKFZ), Heidelberg, Germany
- Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Department of Neuropathology, Berlin, Germany
- Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin School of Integrative Oncology (BSIO), Berlin, Germany
| | - Daniel Teichmann
- Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Department of Neuropathology, Berlin, Germany
| | - Sandra Meier
- Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Department of Neuropathology, Berlin, Germany
| | - Carola Geiler
- Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Department of Neuropathology, Berlin, Germany
| | - Zeus Cosmas
- Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Department of Neuropathology, Berlin, Germany
| | - Helene Franke
- Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Department of Radiation Oncology, Berlin, Germany
| | - Siyer Roohani
- Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Department of Radiation Oncology, Berlin, Germany
- Charité - Universitätsmedizin Berlin, Berlin, Germany; German Cancer Consortium (DKTK), partner site Berlin, and German Cancer Research Center (DKFZ), Heidelberg, Germany
- Berlin Institute of Health at Charité - Universitätsmedizin Berlin, BIH Biomedical Innovation Academy, BIH Charité Junior Clinician Scientist Program, Berlin, Germany
| | - David Wasilewksi
- Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Department of Neurosurgery, Berlin, Germany
| | - Julia Onken
- Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Department of Neurosurgery, Berlin, Germany
| | - Peter Vajkoczy
- Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Department of Neurosurgery, Berlin, Germany
| | - Leonille Schweizer
- Institute of Neurology (Edinger Institute), University Hospital Frankfurt, Goethe University Frankfurt, Frankfurt Am Main, Germany
| | - David Kaul
- Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Department of Radiation Oncology, Berlin, Germany
- Charité - Universitätsmedizin Berlin, Berlin, Germany; German Cancer Consortium (DKTK), partner site Berlin, and German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - David Capper
- Charité - Universitätsmedizin Berlin, Berlin, Germany; German Cancer Consortium (DKTK), partner site Berlin, and German Cancer Research Center (DKFZ), Heidelberg, Germany
- Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Department of Neuropathology, Berlin, Germany
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25
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Dottermusch M, Biabani A, Lempertz T, Schumann Y, Navolic J, Godbole S, Obrecht D, Frank S, Dorostkar MM, Voß H, Schlüter H, Rutkowski S, Schüller U, Neumann JE. Integrated proteomics spotlight the proteasome as a therapeutic vulnerability in embryonal tumors with multilayered rosettes. Neuro Oncol 2024; 26:935-949. [PMID: 38158710 PMCID: PMC11066909 DOI: 10.1093/neuonc/noad265] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2023] [Indexed: 01/03/2024] Open
Abstract
BACKGROUND Embryonal tumors with multilayered rosettes (ETMR) are rare malignant embryonal brain tumors. The prognosis of ETMR is poor and novel therapeutic approaches are desperately needed. Comprehension of ETMR tumor biology is currently based on only few previous molecular studies, which mainly focused on the analyses of nucleic acids. In this study, we explored integrated ETMR proteomics. METHODS Using mass spectrometry, proteome data were acquired from 16 ETMR and the ETMR cell line BT183. Proteome data were integrated with case-matched global DNA methylation data, publicly available transcriptome data, and proteome data of further embryonal and pediatric brain tumors. RESULTS Proteome-based cluster analyses grouped ETMR samples according to histomorphology, separating neuropil-rich tumors with neuronal signatures from primitive tumors with signatures relating to stemness and chromosome organization. Integrated proteomics showcased that ETMR and BT183 cells harbor proteasome regulatory proteins in abundance, implicating their strong dependency on the proteasome machinery to safeguard proteostasis. Indeed, in vitro assays using BT183 highlighted that ETMR tumor cells are highly vulnerable toward treatment with the CNS penetrant proteasome inhibitor Marizomib. CONCLUSIONS In summary, histomorphology stipulates the proteome signatures of ETMR, and proteasome regulatory proteins are pervasively abundant in these tumors. As validated in vitro, proteasome inhibition poses a promising therapeutic option in ETMR.
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Affiliation(s)
- Matthias Dottermusch
- Center for Molecular Neurobiology (ZMNH), University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- Institute of Neuropathology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Ali Biabani
- Section of Mass Spectrometric Proteomics, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Tasja Lempertz
- Center for Molecular Neurobiology (ZMNH), University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Yannis Schumann
- Chair for High Performance Computing, Helmut-Schmidt University, Hamburg, Germany
| | - Jelena Navolic
- Center for Molecular Neurobiology (ZMNH), University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Shweta Godbole
- Center for Molecular Neurobiology (ZMNH), University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Denise Obrecht
- Department of Pediatric Hematology and Oncology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Stephan Frank
- Division of Neuropathology, Institute of Medical Genetics and Pathology, University Hospital Basel, University of Basel, Basel, Switzerland
| | - Mario M Dorostkar
- Center for Neuropathology and Prion Research, Ludwig Maximilian University, Munich, Germany
| | - Hannah Voß
- Section of Mass Spectrometric Proteomics, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Hartmut Schlüter
- Section of Mass Spectrometric Proteomics, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Stefan Rutkowski
- Department of Pediatric Hematology and Oncology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Ulrich Schüller
- Institute of Neuropathology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- Department of Pediatric Hematology and Oncology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- Children’s Cancer Research Center Hamburg, Hamburg, Germany
| | - Julia E Neumann
- Center for Molecular Neurobiology (ZMNH), University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- Institute of Neuropathology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
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26
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Schmid K, Sehring J, Németh A, Harter PN, Weber KJ, Vengadeswaran A, Storf H, Seidemann C, Karki K, Fischer P, Dohmen H, Selignow C, von Deimling A, Grau S, Schröder U, Plate KH, Stein M, Uhl E, Acker T, Amsel D. DistSNE: Distributed computing and online visualization of DNA methylation-based central nervous system tumor classification. Brain Pathol 2024; 34:e13228. [PMID: 38012085 PMCID: PMC11007060 DOI: 10.1111/bpa.13228] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2023] [Accepted: 11/10/2023] [Indexed: 11/29/2023] Open
Abstract
The current state-of-the-art analysis of central nervous system (CNS) tumors through DNA methylation profiling relies on the tumor classifier developed by Capper and colleagues, which centrally harnesses DNA methylation data provided by users. Here, we present a distributed-computing-based approach for CNS tumor classification that achieves a comparable performance to centralized systems while safeguarding privacy. We utilize the t-distributed neighborhood embedding (t-SNE) model for dimensionality reduction and visualization of tumor classification results in two-dimensional graphs in a distributed approach across multiple sites (DistSNE). DistSNE provides an intuitive web interface (https://gin-tsne.med.uni-giessen.de) for user-friendly local data management and federated methylome-based tumor classification calculations for multiple collaborators in a DataSHIELD environment. The freely accessible web interface supports convenient data upload, result review, and summary report generation. Importantly, increasing sample size as achieved through distributed access to additional datasets allows DistSNE to improve cluster analysis and enhance predictive power. Collectively, DistSNE enables a simple and fast classification of CNS tumors using large-scale methylation data from distributed sources, while maintaining the privacy and allowing easy and flexible network expansion to other institutes. This approach holds great potential for advancing human brain tumor classification and fostering collaborative precision medicine in neuro-oncology.
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Affiliation(s)
- Kai Schmid
- Institute of Neuropathology, Justus‐Liebig University GiessenGiessenGermany
| | - Jannik Sehring
- Institute of Neuropathology, Justus‐Liebig University GiessenGiessenGermany
| | - Attila Németh
- Institute of Neuropathology, Justus‐Liebig University GiessenGiessenGermany
| | - Patrick N. Harter
- Neurological Institute (Edinger Institute)University Hospital FrankfurtFrankfurtGermany
- Present address:
Center for Neuropathology and Prion ResearchUniversity Hospital of MunichMunichGermany
| | - Katharina J. Weber
- Neurological Institute (Edinger Institute)University Hospital FrankfurtFrankfurtGermany
- German Cancer Consortium (DKTK)HeidelbergGermany
- German Cancer Research Center (DKFZ)HeidelbergGermany
- Frankfurt Cancer Institute (FCI)FrankfurtGermany
- University Cancer Center (UCT) FrankfurtFrankfurtGermany
| | - Abishaa Vengadeswaran
- Medical Informatics Group (MIG), Goethe University FrankfurtUniversity Hospital FrankfurtFrankfurt am MainGermany
| | - Holger Storf
- Medical Informatics Group (MIG), Goethe University FrankfurtUniversity Hospital FrankfurtFrankfurt am MainGermany
| | | | - Kapil Karki
- DIZ MarburgPhillips University MarburgMarburgGermany
| | - Patrick Fischer
- Institute for Medical InformaticsJustus‐Liebig UniversityGiessenGermany
- Department of Neuropathology, German Cancer Research Center (DKFZ)Universitätsklinikum Heidelberg, and CCU NeuropathologyHeidelbergGermany
| | - Hildegard Dohmen
- Institute of Neuropathology, Justus‐Liebig University GiessenGiessenGermany
| | - Carmen Selignow
- Institute of Neuropathology, Justus‐Liebig University GiessenGiessenGermany
| | | | - Stefan Grau
- Department of NeurosurgeryHospital FuldaFuldaGermany
| | - Uwe Schröder
- Department of NeurosurgeryMVZ Frankfurt/OderFrankfurtGermany
| | - Karl H. Plate
- Neurological Institute (Edinger Institute)University Hospital FrankfurtFrankfurtGermany
| | - Marco Stein
- Department of NeurosurgeryUniversity Hospital Giessen und Marburg Location GiessenGiessenGermany
| | - Eberhard Uhl
- Department of NeurosurgeryUniversity Hospital Giessen und Marburg Location GiessenGiessenGermany
| | - Till Acker
- Institute of Neuropathology, Justus‐Liebig University GiessenGiessenGermany
| | - Daniel Amsel
- Institute of Neuropathology, Justus‐Liebig University GiessenGiessenGermany
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27
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Dombrowski AK, Gerken JE, Muller KR, Kessel P. Diffeomorphic Counterfactuals With Generative Models. IEEE Trans Pattern Anal Mach Intell 2024; 46:3257-3274. [PMID: 38055368 DOI: 10.1109/tpami.2023.3339980] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/08/2023]
Abstract
Counterfactuals can explain classification decisions of neural networks in a human interpretable way. We propose a simple but effective method to generate such counterfactuals. More specifically, we perform a suitable diffeomorphic coordinate transformation and then perform gradient ascent in these coordinates to find counterfactuals which are classified with great confidence as a specified target class. We propose two methods to leverage generative models to construct such suitable coordinate systems that are either exactly or approximately diffeomorphic. We analyze the generation process theoretically using Riemannian differential geometry and validate the quality of the generated counterfactuals using various qualitative and quantitative measures.
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28
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Gonçalves FG, Mahecha-Carvajal ME, Desa A, Yildiz H, Talbeya JK, Moreno LA, Viaene AN, Vossough A. Imaging of supratentorial intraventricular masses in children:a pictorial review- part 1. Neuroradiology 2024; 66:677-698. [PMID: 38466393 PMCID: PMC11031501 DOI: 10.1007/s00234-024-03314-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2023] [Accepted: 02/12/2024] [Indexed: 03/13/2024]
Abstract
PURPOSE This article is the first in a two-part series designed to provide a comprehensive overview of the range of supratentorial intraventricular masses observed in children. Our primary objective is to discuss the diverse types of intraventricular masses that originate not only from cells within the choroid plexus but also from other sources. METHODS In this article, we review relevant epidemiological data, the current genetics/molecular classification as outlined in the fifth edition of the World Health Organization's Classification of tumours of the Central Nervous System and noteworthy imaging findings. We conduct an exhaustive analysis of primary choroid plexus tumours as well as other conditions such as choroid plexus hyperplasia, choroid plexus cyst, choroid plexus xanthogranuloma, atypical teratoid rhabdoid tumour, meningioma, arteriovenous malformation and metastasis. RESULTS We comprehensively evaluated each supratentorial intraventricular mass, providing an in-depth analysis of their unique clinical and histological characteristics. The fifth edition of the World Health Organization Classification of Tumours of the Central Nervous System introduces major modifications. These important changes could potentially have a profound impact on the management strategies and subsequent outcomes of these tumours. CONCLUSION Intraventricular masses in children can arise from various sources. Surgical intervention is key for certain supratentorial intraventricular masses in paediatric patients, with preoperative neuroimaging essential to decide the best treatment approach, surgical or otherwise, as some cases may not require surgery.
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Affiliation(s)
| | | | - Aishwary Desa
- Drexel University College of Medicine Philadelphia, Philadelphia, PA, USA
| | - Harun Yildiz
- Department of Radiology, Dortcelik Children's Hospital, Bursa, Turkey
| | | | - Luz Angela Moreno
- Pediatric Imaging, Department of Radiology, Fundación Hospital La Misericordia, Universidad Nacional de Colombia, Bogotá, Colombia
| | - Angela N Viaene
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, USA
- Pathology Department, Children's Hospital of Philadelphia, Philadelphia, USA
| | - Arastoo Vossough
- Radiology Department, Children's Hospital of Philadelphia, Philadelphia, USA
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, USA
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29
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Mohammed I, Elbashir MK, Faggad AS. Singular Value Decomposition-Based Penalized Multinomial Regression for Classifying Imbalanced Medulloblastoma Subgroups Using Methylation Data. J Comput Biol 2024; 31:458-471. [PMID: 38752890 DOI: 10.1089/cmb.2023.0198] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/23/2024] Open
Abstract
Medulloblastoma (MB) is a molecularly heterogeneous brain malignancy with large differences in clinical presentation. According to genomic studies, there are at least four distinct molecular subgroups of MB: sonic hedgehog (SHH), wingless/INT (WNT), Group 3, and Group 4. The treatment and outcomes depend on appropriate classification. It is difficult for the classification algorithms to identify these subgroups from an imbalanced MB genomic data set, where the distribution of samples among the MB subgroups may not be equal. To overcome this problem, we used singular value decomposition (SVD) and group lasso techniques to find DNA methylation probe features that maximize the separation between the different imbalanced MB subgroups. We used multinomial regression as a classification method to classify the four different molecular subgroups of MB using the reduced DNA methylation data. Coordinate descent is used to solve our loss function associated with the group lasso, which promotes sparsity. By using SVD, we were able to reduce the 321,174 probe features to just 200 features. Less than 40 features were successfully selected after applying the group lasso, which we then used as predictors for our classification models. Our proposed method achieved an average overall accuracy of 99% based on fivefold cross-validation technique. Our approach produces improved classification performance compared with the state-of-the-art methods for classifying MB molecular subgroups.
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Affiliation(s)
- Isra Mohammed
- Department of Statistics, Faculty of Mathematical and Computer Sciences, University of Gezira, Wad Madani, Sudan
| | - Murtada K Elbashir
- Department of Information Systems, College of Computer and Information Sciences, Jouf University, Sakaka, Saudi Arabia
- Department of Computer Science, Faculty of Mathematical and Computer Sciences, University of Gezira, Wad Madani, Sudan
| | - Areeg S Faggad
- Department of Molecular Biology, National Cancer Institute-University of Gezira, Wad Madani, Sudan
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30
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Uro‐Coste E, Tauziede‐Espariat A, Dubucs C, Chiforeanu DC, Siegfried A, Nicaise Y, Bauchet L, Riffaud L, Bielle F, Vasiljevic A, Appay R, Evrard S, Varlet P, Rigau V. Two novel tumours with NTRK2 fusion in the methylation class of extraventricular neurocytomas, including one intraventricular. Brain Pathol 2024; 34:e13223. [PMID: 37994695 PMCID: PMC11006991 DOI: 10.1111/bpa.13223] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2023] [Accepted: 10/30/2023] [Indexed: 11/24/2023] Open
Abstract
We report here about two novel tumours classified as extraventricular neurocytomas (EVN) using DNA-methylation profiling, associated with NTRK2 fusions instead of the usual FGFR1 alterations so far attributed to this tumoural entity. We present the second detailed case of an intraventricular presentation in the MC EVN. Our findings broaden the spectrum of MC EVN and have implications in terms of diagnosis, therapy and terminology.
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Affiliation(s)
- Emmanuelle Uro‐Coste
- Department of PathologyToulouse University HospitalToulouseFrance
- INSERM U1037, Cancer Research Center of Toulouse (CRCT)ToulouseFrance
| | - Arnault Tauziede‐Espariat
- GHU Psychiatrie et Neurosciences, Site Sainte‐Anne, Service de NeuropathologieParisFrance
- Institut de Psychiatrie et Neurosciences de Paris (IPNP), UMR_S1266, INSERM, Equipe IMA‐BRAIN (Imaging Biomarkers for Brain Development and Disorders)University of ParisParisFrance
| | - Charlotte Dubucs
- Department of PathologyToulouse University HospitalToulouseFrance
| | | | - Aurore Siegfried
- Department of PathologyToulouse University HospitalToulouseFrance
- INSERM U1037, Cancer Research Center of Toulouse (CRCT)ToulouseFrance
| | - Yvan Nicaise
- INSERM U1037, Cancer Research Center of Toulouse (CRCT)ToulouseFrance
| | - Luc Bauchet
- Department of NeurosurgeryMontpellier University HospitalMontpellierFrance
- Institute for Neuroscience of Montpellier (IGF), INSERM U1051Montpellier University HospitalMontpellierFrance
| | | | - Franck Bielle
- Department of Neuropathology, AP‐HPHôpitaux Universitaires Pitié‐Salpêtrière Charles FoixParisFrance
- Sorbonne University, UPMCUniversity of ParisParisFrance
- Brain and Spine Institute (ICM; INSERM, UMRS 1127; CNRS, UMR 7225)ParisFrance
| | - Alexandre Vasiljevic
- Department of NeuropathologyGroupe Hospitalier Est, Hospices Civils de LyonBronFrance
- Claude Bernard University Lyon 1LyonFrance
| | - Romain Appay
- APHM, CHU Timone, Service d'Anatomie Pathologique et de NeuropathologieMarseilleFrance
- Aix‐Marseille Univ, CNRS, INP, Inst NeurophysiopatholMarseilleFrance
| | - Solène Evrard
- Department of PathologyToulouse University HospitalToulouseFrance
- INSERM U1037, Cancer Research Center of Toulouse (CRCT)ToulouseFrance
| | - Pascale Varlet
- GHU Psychiatrie et Neurosciences, Site Sainte‐Anne, Service de NeuropathologieParisFrance
- Institut de Psychiatrie et Neurosciences de Paris (IPNP), UMR_S1266, INSERM, Equipe IMA‐BRAIN (Imaging Biomarkers for Brain Development and Disorders)University of ParisParisFrance
| | - Valérie Rigau
- Institute for Neuroscience of Montpellier (IGF), INSERM U1051Montpellier University HospitalMontpellierFrance
- Department of PathologyMontpellier University HospitalMontpellierFrance
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31
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Künstner A, Schwarting J, Witte HM, Xing P, Bernard V, Stölting S, Lohneis P, Janke F, Salehi M, Chen X, Kusch K, Sültmann H, Chteinberg E, Fischer A, Siebert R, von Bubnoff N, Merz H, Busch H, Feller AC, Gebauer N. Genome-wide DNA methylation-analysis of blastic plasmacytoid dendritic cell neoplasm identifies distinct molecular features. Leukemia 2024; 38:1086-1098. [PMID: 38600314 DOI: 10.1038/s41375-024-02240-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2023] [Revised: 03/27/2024] [Accepted: 03/28/2024] [Indexed: 04/12/2024]
Abstract
Blastic plasmacytoid dendritic cell neoplasm (BPDCN) constitutes a rare and aggressive malignancy originating from plasmacytoid dendritic cells (pDCs) with a primarily cutaneous tropism followed by dissemination to the bone marrow and other organs. We conducted a genome-wide analysis of the tumor methylome in an extended cohort of 45 BPDCN patients supplemented by WES and RNA-seq as well as ATAC-seq on selected cases. We determined the BPDCN DNA methylation profile and observed a dramatic loss of DNA methylation during malignant transformation from early and mature DCs towards BPDCN. DNA methylation profiles further differentiate between BPDCN, AML, CMML, and T-ALL exhibiting the most striking global demethylation, mitotic stress, and merely localized DNA hypermethylation in BPDCN resulting in pronounced inactivation of tumor suppressor genes by comparison. DNA methylation-based analysis of the tumor microenvironment by MethylCIBERSORT yielded two, prognostically relevant clusters (IC1 and IC2) with specific cellular composition and mutational spectra. Further, the transcriptional subgroups of BPDCN (C1 and C2) differ by DNA methylation signatures in interleukin/inflammatory signaling genes but also by higher transcription factor activity of JAK-STAT and NFkB signaling in C2 in contrast to an EZH2 dependence in C1-BPDCN. Our integrative characterization of BPDCN offers novel molecular insights and potential diagnostic applications.
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Affiliation(s)
- Axel Künstner
- Medical Systems Biology Group, University of Lübeck, Ratzeburger Allee 160, 23538, Lübeck, Germany
- University Cancer Center Schleswig-Holstein, University Hospital of Schleswig-Holstein, Campus Lübeck, 23538, Lübeck, Germany
| | - Julian Schwarting
- University Cancer Center Schleswig-Holstein, University Hospital of Schleswig-Holstein, Campus Lübeck, 23538, Lübeck, Germany
- Department of Hematology and Oncology, University Hospital of Schleswig-Holstein, Campus Lübeck, Ratzeburger Allee 160, 23538, Lübeck, Germany
- Hämatopathologie Lübeck, Consultation Centre for Lymph Node Pathology and Hematopathology, 23562, Lübeck, Germany
| | - Hanno M Witte
- University Cancer Center Schleswig-Holstein, University Hospital of Schleswig-Holstein, Campus Lübeck, 23538, Lübeck, Germany
- Department of Hematology and Oncology, University Hospital of Schleswig-Holstein, Campus Lübeck, Ratzeburger Allee 160, 23538, Lübeck, Germany
- Department of Hematology and Oncology, Federal Armed Forces Hospital Ulm, Oberer Eselsberg 40, 89081, Ulm, Germany
| | - Pengwei Xing
- Department of Immunology, Genetics and Pathology, Uppsala University, 751 85, Uppsala, Sweden
| | - Veronica Bernard
- Hämatopathologie Lübeck, Consultation Centre for Lymph Node Pathology and Hematopathology, 23562, Lübeck, Germany
| | - Stephanie Stölting
- Hämatopathologie Lübeck, Consultation Centre for Lymph Node Pathology and Hematopathology, 23562, Lübeck, Germany
| | - Philipp Lohneis
- Hämatopathologie Lübeck, Consultation Centre for Lymph Node Pathology and Hematopathology, 23562, Lübeck, Germany
| | - Florian Janke
- Division of Cancer Genome Research, German Cancer Research Center (DKFZ), 69120, Heidelberg, Germany
- German Cancer Consortium (DKTK), 69120, Heidelberg, Germany
| | - Maede Salehi
- Department of Immunology, Genetics and Pathology, Uppsala University, 751 85, Uppsala, Sweden
| | - Xingqi Chen
- Department of Immunology, Genetics and Pathology, Uppsala University, 751 85, Uppsala, Sweden
| | - Kathrin Kusch
- Hämatopathologie Lübeck, Consultation Centre for Lymph Node Pathology and Hematopathology, 23562, Lübeck, Germany
| | - Holger Sültmann
- Division of Cancer Genome Research, German Cancer Research Center (DKFZ), 69120, Heidelberg, Germany
- German Cancer Consortium (DKTK), 69120, Heidelberg, Germany
| | - Emil Chteinberg
- Institute of Human Genetics Ulm University and Ulm University Medical Center, 89081, Ulm, Germany
| | - Anja Fischer
- Institute of Human Genetics Ulm University and Ulm University Medical Center, 89081, Ulm, Germany
| | - Reiner Siebert
- Institute of Human Genetics Ulm University and Ulm University Medical Center, 89081, Ulm, Germany
| | - Nikolas von Bubnoff
- University Cancer Center Schleswig-Holstein, University Hospital of Schleswig-Holstein, Campus Lübeck, 23538, Lübeck, Germany
- Department of Hematology and Oncology, University Hospital of Schleswig-Holstein, Campus Lübeck, Ratzeburger Allee 160, 23538, Lübeck, Germany
| | - Hartmut Merz
- Hämatopathologie Lübeck, Consultation Centre for Lymph Node Pathology and Hematopathology, 23562, Lübeck, Germany
| | - Hauke Busch
- Medical Systems Biology Group, University of Lübeck, Ratzeburger Allee 160, 23538, Lübeck, Germany
- University Cancer Center Schleswig-Holstein, University Hospital of Schleswig-Holstein, Campus Lübeck, 23538, Lübeck, Germany
| | - Alfred C Feller
- Hämatopathologie Lübeck, Consultation Centre for Lymph Node Pathology and Hematopathology, 23562, Lübeck, Germany
| | - Niklas Gebauer
- University Cancer Center Schleswig-Holstein, University Hospital of Schleswig-Holstein, Campus Lübeck, 23538, Lübeck, Germany.
- Department of Hematology and Oncology, University Hospital of Schleswig-Holstein, Campus Lübeck, Ratzeburger Allee 160, 23538, Lübeck, Germany.
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32
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Abe E, Suzuki M, Ichimura K, Arakawa A, Satomi K, Ogino I, Hara T, Iwamuro H, Ohara Y, Kondo A. Implications of DNA Methylation Classification in Diagnosing Ependymoma. World Neurosurg 2024; 185:e1019-e1029. [PMID: 38479644 DOI: 10.1016/j.wneu.2024.03.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2024] [Revised: 03/02/2024] [Accepted: 03/04/2024] [Indexed: 04/04/2024]
Abstract
BACKGROUND Ependymoma is a central nervous system (CNS) tumor that arises from the ependymal cells of the brain's ventricles and spinal cord. The histopathology of ependymomas is indistinguishable regardless of the site of origin, and the prognosis varies. Recent studies have revealed that the development site and prognosis reflect the genetic background. In this study, we used genome-wide DNA methylation array analysis to investigate the epigenetic background of ependymomas from different locations treated at our hospital. METHODS Four cases of posterior fossa ependymomas and 11 cases of spinal ependymomas were analyzed. RESULTS DNA methylation profiling using the DKFZ methylation classifier showed that the methylation diagnoses of the 2 cases differed from the histopathological diagnoses, and 2 cases could not be classified. Tumor that spread from the brain to the spinal cord was molecularly distinguishable from other primary spinal tumors. CONCLUSIONS Although adding DNA methylation classification to conventional diagnostic methods may be helpful, the diagnosis in some cases remains undetermined. This may affect decision-making regarding treatment strategies and follow-up. Further investigations are required to improve the diagnostic accuracy of these tumors.
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Affiliation(s)
- Eiji Abe
- Department of Neurosurgery, Juntendo University Graduate School of Medicine, Tokyo, Japan.
| | - Mario Suzuki
- Department of Neurosurgery, Juntendo University Graduate School of Medicine, Tokyo, Japan
| | - Koichi Ichimura
- Department of Neurosurgery, Juntendo University Graduate School of Medicine, Tokyo, Japan; Department of Brain Disease Translational Research, Juntendo University Graduate School of Medicine, Tokyo, Japan
| | - Atsushi Arakawa
- Department of Human Pathology, Juntendo University Graduate School of Medicine, Tokyo, Japan
| | - Kaishi Satomi
- Department of Pathology, Kyorin University Faculty of Medicine, Tokyo, Japan
| | - Ikuko Ogino
- Department of Neurosurgery, Juntendo University Graduate School of Medicine, Tokyo, Japan
| | - Takeshi Hara
- Department of Neurosurgery, Juntendo University Graduate School of Medicine, Tokyo, Japan
| | - Hirokazu Iwamuro
- Department of Neurosurgery, Juntendo University Graduate School of Medicine, Tokyo, Japan
| | - Yukoh Ohara
- Department of Neurosurgery, Juntendo University Graduate School of Medicine, Tokyo, Japan
| | - Akihide Kondo
- Department of Neurosurgery, Juntendo University Graduate School of Medicine, Tokyo, Japan
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33
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Korbonits M, Blair JC, Boguslawska A, Ayuk J, Davies JH, Druce MR, Evanson J, Flanagan D, Glynn N, Higham CE, Jacques TS, Sinha S, Simmons I, Thorp N, Swords FM, Storr HL, Spoudeas HA. Consensus guideline for the diagnosis and management of pituitary adenomas in childhood and adolescence: Part 1, general recommendations. Nat Rev Endocrinol 2024; 20:278-289. [PMID: 38336897 DOI: 10.1038/s41574-023-00948-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 12/19/2023] [Indexed: 02/12/2024]
Abstract
Tumours of the anterior part of the pituitary gland represent just 1% of all childhood (aged <15 years) intracranial neoplasms, yet they can confer high morbidity and little evidence and guidance is in place for their management. Between 2014 and 2022, a multidisciplinary expert group systematically developed the first comprehensive clinical practice consensus guideline for children and young people under the age 19 years (hereafter referred to as CYP) presenting with a suspected pituitary adenoma to inform specialist care and improve health outcomes. Through robust literature searches and a Delphi consensus exercise with an international Delphi consensus panel of experts, the available scientific evidence and expert opinions were consolidated into 74 recommendations. Part 1 of this consensus guideline includes 17 pragmatic management recommendations related to clinical care, neuroimaging, visual assessment, histopathology, genetics, pituitary surgery and radiotherapy. While in many aspects the care for CYP is similar to that of adults, key differences exist, particularly in aetiology and presentation. CYP with suspected pituitary adenomas require careful clinical examination, appropriate hormonal work-up, dedicated pituitary imaging and visual assessment. Consideration should be given to the potential for syndromic disease and genetic assessment. Multidisciplinary discussion at both the local and national levels can be key for management. Surgery should be performed in specialist centres. The collection of outcome data on novel modalities of medical treatment, surgical intervention and radiotherapy is essential for optimal future treatment.
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Affiliation(s)
- Márta Korbonits
- Centre for Endocrinology, William Harvey Research Institute, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, London, UK.
| | | | - Anna Boguslawska
- Department of Endocrinology, Jagiellonian University Medical College, Krakow, Poland
| | - John Ayuk
- University Hospitals Birmingham NHS Foundation Trust, Birmingham, UK
| | - Justin H Davies
- University Hospital Southampton NHS Foundation Trust, Southampton, UK
| | - Maralyn R Druce
- Centre for Endocrinology, William Harvey Research Institute, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, London, UK
| | - Jane Evanson
- Neuroradiology, Barts Health NHS Trust, London, UK
| | | | - Nigel Glynn
- Centre for Endocrinology, William Harvey Research Institute, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, London, UK
| | | | - Thomas S Jacques
- Great Ormond Street Institute of Child Health, University College London, London, UK
- Great Ormond Street Hospital for Children NHS Foundation Trust, London, UK
| | - Saurabh Sinha
- Sheffield Children's and Sheffield Teaching Hospitals NHS Foundation Trust, Sheffield, UK
| | - Ian Simmons
- The Leeds Teaching Hospitals NHS Trust, Leeds, UK
| | - Nicky Thorp
- The Christie NHS Foundation Trust, Manchester, UK
| | | | - Helen L Storr
- Centre for Endocrinology, William Harvey Research Institute, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, London, UK
| | - Helen A Spoudeas
- Great Ormond Street Hospital for Children NHS Foundation Trust, London, UK
- University College London Hospitals NHS Foundation Trust, London, UK
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34
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Klubíčková N, Dermawan JK, Mosaieby E, Martínek P, Vaněček T, Hájková V, Ptáková N, Grossmann P, Šteiner P, Švajdler M, Kinkor Z, Michalová K, Szepe P, Plank L, Hederová S, Kolenová A, Spasov NJ, Kosemehmetoglu K, Pažanin L, Špůrková Z, Baník M, Baumruk L, Meyer A, Kalmykova A, Koshyk O, Michal M, Michal M. Comprehensive clinicopathological, molecular, and methylation analysis of mesenchymal tumors with NTRK and other kinase gene aberrations. J Pathol 2024; 263:61-73. [PMID: 38332737 DOI: 10.1002/path.6260] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2023] [Revised: 12/13/2023] [Accepted: 01/04/2024] [Indexed: 02/10/2024]
Abstract
Alterations in kinase genes such as NTRK1/2/3, RET, and BRAF underlie infantile fibrosarcoma (IFS), the emerging entity 'NTRK-rearranged spindle cell neoplasms' included in the latest WHO classification, and a growing set of tumors with overlapping clinical and pathological features. In this study, we conducted a comprehensive clinicopathological and molecular analysis of 22 cases of IFS and other kinase gene-altered spindle cell neoplasms affecting both pediatric and adult patients. Follow-up periods for 16 patients ranged in length from 10 to 130 months (mean 38 months). Six patients were treated with targeted therapy, achieving a partial or complete response in five cases. Overall, three cases recurred and one metastasized. Eight patients were free of disease, five were alive with disease, and two patients died. All cases showed previously reported morphological patterns. Based on the cellularity and level of atypia, cases were divided into three morphological grade groups. S100 protein and CD34 were at least focally positive in 12/22 and 14/22 cases, respectively. Novel PWWP2A::RET, NUMA1::RET, ITSN1::RAF1, and CAPZA2::MET fusions, which we report herein in mesenchymal tumors for the first time, were detected by RNA sequencing. Additionally, the first uterine case with BRAF and EGFR mutations and CD34 and S100 co-expression is described. DNA sequencing performed in 13 cases uncovered very rare additional genetic aberrations. The CNV profiles showed that high-grade tumors demonstrate a significantly higher percentage of copy number gains and losses across the genome compared with low- and intermediate-grade tumors. Unsupervised clustering of the tumors' methylation profiles revealed that in 8/9 cases, the methylation profiles clustered with the IFS methylation class, irrespective of their clinicopathological or molecular features. © 2024 The Authors. The Journal of Pathology published by John Wiley & Sons Ltd on behalf of The Pathological Society of Great Britain and Ireland.
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Affiliation(s)
- Natálie Klubíčková
- Department of Pathology, Faculty of Medicine in Pilsen, Charles University, Pilsen, Czech Republic
- Bioptical Laboratory Ltd, Pilsen, Czech Republic
| | - Josephine K Dermawan
- Robert J. Tomsich Pathology and Laboratory Medicine Institute, Cleveland Clinic, Cleveland, OH, USA
| | - Elaheh Mosaieby
- Department of Pathology, Faculty of Medicine in Pilsen, Charles University, Pilsen, Czech Republic
- Bioptical Laboratory Ltd, Pilsen, Czech Republic
| | | | | | | | - Nikola Ptáková
- Bioptical Laboratory Ltd, Pilsen, Czech Republic
- Department of Biology and Medical Genetics, Second Faculty of Medicine, Charles University and Motol University Hospital, Prague, Czech Republic
| | | | - Petr Šteiner
- Bioptical Laboratory Ltd, Pilsen, Czech Republic
| | - Marián Švajdler
- Department of Pathology, Faculty of Medicine in Pilsen, Charles University, Pilsen, Czech Republic
- Bioptical Laboratory Ltd, Pilsen, Czech Republic
| | | | - Květoslava Michalová
- Department of Pathology, Faculty of Medicine in Pilsen, Charles University, Pilsen, Czech Republic
- Bioptical Laboratory Ltd, Pilsen, Czech Republic
| | - Peter Szepe
- Institute of Pathological Anatomy, Jessenius Faculty of Medicine in Martin, Comenius University, Martin, Slovakia
| | - Lukáš Plank
- Institute of Pathological Anatomy, Jessenius Faculty of Medicine in Martin, Comenius University, Martin, Slovakia
| | - Stanislava Hederová
- Department of Pediatric Hematology and Oncology, National Institute of Children's Diseases and Medical Faculty, Comenius University, Bratislava, Slovakia
| | - Alexandra Kolenová
- Department of Pediatric Hematology and Oncology, National Institute of Children's Diseases and Medical Faculty, Comenius University, Bratislava, Slovakia
| | - Neofit Juriev Spasov
- Department of Pediatrics and Medical Genetics, Oncohematology Unit, Medical University Plovdiv, University Hospital Sveti Georgi, Plovdiv, Bulgaria
| | | | - Leo Pažanin
- Department of Pathology, Sestre Milosrdnice University Hospital Center, Zagreb, Croatia
| | - Zuzana Špůrková
- Department of Pathology, Na Bulovce Hospital, Prague, Czech Republic
| | - Martin Baník
- Department of Pathology, Regional Hospital Karlovy Vary, Karlovy Vary, Czech Republic
| | - Luděk Baumruk
- Department of Pathology, Regional Hospital Příbram, Příbram, Czech Republic
| | - Anders Meyer
- Department of Pathology, University of Kansas, Kansas City, KS, USA
| | | | - Olena Koshyk
- Medical Laboratory CSD Health Care Ltd, Kyiv, Ukraine
| | - Michal Michal
- Department of Pathology, Faculty of Medicine in Pilsen, Charles University, Pilsen, Czech Republic
- Bioptical Laboratory Ltd, Pilsen, Czech Republic
| | - Michael Michal
- Department of Pathology, Faculty of Medicine in Pilsen, Charles University, Pilsen, Czech Republic
- Bioptical Laboratory Ltd, Pilsen, Czech Republic
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35
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Hermsen M, Bossi P, Capper D, Fleming J, Haybaeck J, Martinez-Balibrea E, Nuyts S, Skalova A, Thomson D, Trama A, Turri-Zanoni M, Verillaud B, Woods R, von Buchwald C, Lechner M. The European Network for Sinonasal Cancer Research (EUSICA) - A pan-European initiative targeting a group of orphan tumours. Eur J Cancer 2024; 202:113939. [PMID: 38447380 DOI: 10.1016/j.ejca.2024.113939] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2024] [Accepted: 01/31/2024] [Indexed: 03/08/2024]
Affiliation(s)
- Mario Hermsen
- Dept Head and Neck Cancer, Instituto de Investigación Sanitaria del Principado de Asturias, Oviedo, Spain.
| | - Paolo Bossi
- Department of Biomedical Sciences, Humanitas University, Via Rita Levi Montalcini 4, Pieve Emanuele, Milan 20072, Italy; IRCCS Humanitas Research Hospital, Via Manzoni 56, Rozzano, Milan 20089, Italy
| | - David Capper
- Department of Neuropathology, Charité - Universitätsmedizin Berlin (corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin), Berlin, Germany; German Cancer Consortium (DKTK), Partner Site Berlin, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | | | - Johannes Haybaeck
- Diagnostic & Research Center for Molecular BioMedicine, Institute of Pathology, Medical University of Graz, Graz, Styria, Austria; Department of Pathology, Saint Vincent Hospital Zams, Zams, Tyrol, Austria; Department of Pathology, University Medical Centre Maribor, Maribor, Styria, Slovenia
| | - Eva Martinez-Balibrea
- ProCURE program, Catalan Institute of Oncology and CARE program, Germans Trias i Pujol Research Institute (IGTP) Ctra. De Can Ruti, cami de les escoles s/n, Badalona 08916, Spain
| | - Sandra Nuyts
- Laboratory of Experimental Radiotherapy, Department of Oncology, KU Leuven, Department of Radiation Oncology, Leuven Cancer Institute, University Hospitals, Leuven 3000, Belgium
| | - Alena Skalova
- Department of Pathology, Charles University, Faculty of Medicine in Plzen, Plzen, Czech Republic
| | - David Thomson
- The Christie NHS Foundation Trust, Manchester, UK; The University of Manchester, Manchester, UK
| | - Annalisa Trama
- Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | - Mario Turri-Zanoni
- Unit of Otorhinolaryngology and Head & Neck Surgery, Department of Biotechnology and Life Sciences, ASST Lariana, University of Insubria, Como, Italy
| | | | - Robbie Woods
- Department of Otolaryngology - Head and Neck Surgery, Beaumont Hospital / Royal College of Surgeons in Ireland, Dublin, Ireland
| | - Christian von Buchwald
- Department of ORL, Head & Neck Surgery and Audiology, Rigshospitalet, University of Copenhagen, Copenhagen, Denmark
| | - Matt Lechner
- Division of Surgery and Interventional Science and UCL Cancer Institute, University College London, London, UK.
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36
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Liu Y, Ali H, Khan F, Pang L, Chen P. Epigenetic regulation of tumor-immune symbiosis in glioma. Trends Mol Med 2024; 30:429-442. [PMID: 38453529 PMCID: PMC11081824 DOI: 10.1016/j.molmed.2024.02.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2023] [Revised: 02/01/2024] [Accepted: 02/14/2024] [Indexed: 03/09/2024]
Abstract
Glioma is a type of aggressive and incurable brain tumor. Patients with glioma are highly resistant to all types of therapies, including immunotherapies. Epigenetic reprogramming is a key molecular hallmark in tumors across cancer types, including glioma. Mounting evidence highlights a pivotal role of epigenetic regulation in shaping tumor biology and therapeutic responses through mechanisms involving both glioma cells and immune cells, as well as their symbiotic interactions in the tumor microenvironment (TME). In this review, we discuss the molecular mechanisms of epigenetic regulation that impacts glioma cell biology and tumor immunity in both a cell-autonomous and non-cell-autonomous manner. Moreover, we provide an overview of potential therapeutic approaches that can disrupt epigenetic-regulated tumor-immune symbiosis in the glioma TME.
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Affiliation(s)
- Yang Liu
- Department of Neurological Surgery, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Heba Ali
- Department of Neurological Surgery, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Fatima Khan
- Department of Neurological Surgery, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Lizhi Pang
- Department of Neurological Surgery, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Peiwen Chen
- Department of Neurological Surgery, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA.
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37
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Parker M, Kazemi F, Krishnakumar A, Horowitz MA, Myneni S, Liu A, Schreck KC, Lucas CHG, Mukherjee D. Availability and utilization of molecular testing for primary central nervous system tumors among US hospitals. J Neuropathol Exp Neurol 2024:nlae035. [PMID: 38687613 DOI: 10.1093/jnen/nlae035] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/02/2024] Open
Abstract
Advanced molecular testing has increasingly become an integral component for accurate diagnosis of central nervous system (CNS) tumors. We sought to establish the current state of molecular testing availability and approaches for the diagnosis of CNS tumors in US hospitals that conduct high volumes of CNS tumor resections. We distributed a 16-item survey inquiring about molecular testing approaches for CNS tumors to 115 neuropathologists at US hospitals with neurosurgery residency programs. Thirty-five neuropathologists (30.4%) responded to the survey, all of whom indicated their institutions perform molecular testing on CNS tumor tissue. The most commonly offered tests were MGMT methylation profiling and next-generation sequencing. Fourteen respondents (40%) indicated that their institution is able to test for and report all of the molecular alterations included in our survey. Nine (25.7%) respondents indicated that molecular testing is performed as standard of care for all patients with resected CNS tumors. Our results suggest that even in academic hospitals with a high volume of CNS tumor resections, molecular testing for these tumors is limited. Continued initiatives are necessary to expand the availability of molecular testing for CNS tumors to ensure diagnostic accuracy and guide targeted therapy.
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Affiliation(s)
- Megan Parker
- Department of Neurosurgery, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Foad Kazemi
- Department of Neurosurgery, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Asha Krishnakumar
- School of Medicine, Virginia Commonwealth University, Richmond, Virginia, USA
| | - Melanie A Horowitz
- Department of Neurosurgery, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Saket Myneni
- Department of Neurosurgery, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Abby Liu
- Department of Neurosurgery, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Karisa C Schreck
- Department of Neurology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, Baltimore, Maryland, USA
| | - Calixto-Hope G Lucas
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Debraj Mukherjee
- Department of Neurosurgery, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
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38
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Lee MK, Azizgolshani N, Zhang Z, Perreard L, Kolling FW, Nguyen LN, Zanazzi GJ, Salas LA, Christensen BC. Associations in cell type-specific hydroxymethylation and transcriptional alterations of pediatric central nervous system tumors. Nat Commun 2024; 15:3635. [PMID: 38688903 PMCID: PMC11061294 DOI: 10.1038/s41467-024-47943-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2023] [Accepted: 04/16/2024] [Indexed: 05/02/2024] Open
Abstract
Although intratumoral heterogeneity has been established in pediatric central nervous system tumors, epigenomic alterations at the cell type level have largely remained unresolved. To identify cell type-specific alterations to cytosine modifications in pediatric central nervous system tumors, we utilize a multi-omic approach that integrated bulk DNA cytosine modification data (methylation and hydroxymethylation) with both bulk and single-cell RNA-sequencing data. We demonstrate a large reduction in the scope of significantly differentially modified cytosines in tumors when accounting for tumor cell type composition. In the progenitor-like cell types of tumors, we identify a preponderance differential Cytosine-phosphate-Guanine site hydroxymethylation rather than methylation. Genes with differential hydroxymethylation, like histone deacetylase 4 and insulin-like growth factor 1 receptor, are associated with cell type-specific changes in gene expression in tumors. Our results highlight the importance of epigenomic alterations in the progenitor-like cell types and its role in cell type-specific transcriptional regulation in pediatric central nervous system tumors.
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Affiliation(s)
- Min Kyung Lee
- Department of Epidemiology, Geisel School of Medicine at Dartmouth, Lebanon, NH, USA.
| | - Nasim Azizgolshani
- Department of Epidemiology, Geisel School of Medicine at Dartmouth, Lebanon, NH, USA
- Department of Surgery, Columbia University Medical Center, New York, NY, USA
| | - Ze Zhang
- Department of Epidemiology, Geisel School of Medicine at Dartmouth, Lebanon, NH, USA
| | - Laurent Perreard
- Dartmouth Cancer Center, Geisel School of Medicine at Dartmouth, Lebanon, NH, USA
| | - Fred W Kolling
- Dartmouth Cancer Center, Geisel School of Medicine at Dartmouth, Lebanon, NH, USA
| | - Lananh N Nguyen
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, Canada
| | - George J Zanazzi
- Dartmouth Cancer Center, Geisel School of Medicine at Dartmouth, Lebanon, NH, USA
- Department of Pathology and Laboratory Medicine, Geisel School of Medicine at Dartmouth, Lebanon, NH, USA
| | - Lucas A Salas
- Department of Epidemiology, Geisel School of Medicine at Dartmouth, Lebanon, NH, USA
| | - Brock C Christensen
- Department of Epidemiology, Geisel School of Medicine at Dartmouth, Lebanon, NH, USA.
- Department of Molecular and Systems Biology, Geisel School of Medicine at Dartmouth, Lebanon, NH, USA.
- Department of Community and Family Medicine, Geisel School of Medicine at Dartmouth, Lebanon, NH, USA.
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39
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Miele E, Anghileri E, Calatozzolo C, Lazzarini E, Patrizi S, Ciolfi A, Pedace L, Patanè M, Abballe L, Paterra R, Maddaloni L, Barresi S, Mastronuzzi A, Petruzzi A, Tramacere I, Farinotti M, Gurrieri L, Pirola E, Scarpelli M, Lombardi G, Villani V, Simonelli M, Merli R, Salmaggi A, Tartaglia M, Silvani A, DiMeco F, Calistri D, Lamperti E, Locatelli F, Indraccolo S, Pollo B. Clinicopathological and molecular landscape of 5-year IDH-wild-type glioblastoma survivors: A multicentric retrospective study. Cancer Lett 2024; 588:216711. [PMID: 38423245 DOI: 10.1016/j.canlet.2024.216711] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2023] [Revised: 01/19/2024] [Accepted: 02/05/2024] [Indexed: 03/02/2024]
Abstract
Five-year glioblastoma (GBM) survivors (LTS) are the minority of the isocitrate dehydrogenase (IDH)-wild-type GBM patients, and their molecular fingerprint is still largely unexplored. This multicenter retrospective study analyzed a large LTS-GBM cohort from nine Italian institutions and molecularly characterized a subgroup of patients by mutation, DNA methylation (DNAm) and copy number variation (CNV) profiling, comparing it to standard survival GBM. Mutation scan allowed the identification of pathogenic variants in most cases, showing a similar mutational spectrum in both groups, and highlighted TP53 as the most commonly mutated gene in the LTS group. We confirmed DNAm as a valuable tool for GBM classification with a diagnostic refinement by using brain tumor classifier v12.5. LTS were more heterogeneous with more cases classified as diffuse pediatric high-grade glioma subtypes and having peculiar CNVs. We observed a global higher methylation in CpG islands and in gene promoters of LTS with methylation levels of distinct gene promoters correlating with prognosis.
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Affiliation(s)
- Evelina Miele
- Department of Onco-Hematology, Cell Therapy, Gene Therapies and Hemopoietic Transplant, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Elena Anghileri
- Neuro-Oncology Unit, Fondazione IRCCS Istituto Neurologico Carlo Besta (FINCB), Milan, Italy.
| | - Chiara Calatozzolo
- Neuropathology Unit, Fondazione IRCCS Istituto Neurologico Carlo Besta, Milan, Italy
| | - Elisabetta Lazzarini
- Basic and Translational Oncology Unit, Istituto Oncologico Veneto (IOV)-IRCCS, Padua, Italy
| | - Sara Patrizi
- Department of Onco-Hematology, Cell Therapy, Gene Therapies and Hemopoietic Transplant, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Andrea Ciolfi
- Molecular Genetics and Functional Genomics Research Unit, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Lucia Pedace
- Department of Onco-Hematology, Cell Therapy, Gene Therapies and Hemopoietic Transplant, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Monica Patanè
- Neuropathology Unit, Fondazione IRCCS Istituto Neurologico Carlo Besta, Milan, Italy
| | - Luana Abballe
- Department of Onco-Hematology, Cell Therapy, Gene Therapies and Hemopoietic Transplant, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Rosina Paterra
- Neuro-Oncology Unit, Fondazione IRCCS Istituto Neurologico Carlo Besta (FINCB), Milan, Italy
| | - Luisa Maddaloni
- Neuro-Oncology Unit, Fondazione IRCCS Istituto Neurologico Carlo Besta (FINCB), Milan, Italy
| | - Sabina Barresi
- Pathology Unit, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Angela Mastronuzzi
- Department of Onco-Hematology, Cell Therapy, Gene Therapies and Hemopoietic Transplant, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Alessandra Petruzzi
- Neuro-Oncology Unit, Fondazione IRCCS Istituto Neurologico Carlo Besta (FINCB), Milan, Italy
| | - Irene Tramacere
- Department of Research and Clinical Development, Fondazione IRCCS Istituto Neurologico Carlo Besta, Milan, Italy
| | - Mariangela Farinotti
- Neuroepidemiology-Brain Cancer Registry, Fondazione IRCCS Istituto Neurologico Carlo Besta, Milan, Italy
| | - Lorena Gurrieri
- Osteoncology and Rare Tumors Center, IRCCS Istituto Romagnolo Per Lo Studio Dei Tumori (IRST) Dino Amadori, Meldola, Italy
| | - Elena Pirola
- Department of Neurosurgery Unit, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy
| | - Mauro Scarpelli
- Neurology Unit, Azienda Ospedaliera Universitaria Integrata Verona, Italy
| | - Giuseppe Lombardi
- Medical Oncology Unit 1, Istituto Oncologico Veneto IOV-IRCCS, Padua, Italy
| | - Veronica Villani
- Neuro-Oncology Unit, IRCCS Istituto Nazionale Tumori Regina Elena, Rome, Italy
| | - Matteo Simonelli
- Department of Oncology and Hematology Unit, IRCCS Humanitas Research Hospital, Rozzano, Italy; Department of Biomedical Sciences, Humanitas University, Pieve Emanuele, Milan, Italy
| | - Rossella Merli
- Neurosurgery Unit, ASST Papa Giovanni XXIII, Bergamo, Italy
| | | | - Marco Tartaglia
- Molecular Genetics and Functional Genomics Research Unit, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Antonio Silvani
- Neuro-Oncology Unit, Fondazione IRCCS Istituto Neurologico Carlo Besta (FINCB), Milan, Italy
| | - Francesco DiMeco
- Department of Neurosurgery, Fondazione IRCCS Istituto Neurologico Carlo Besta, Milan, Italy; Department of Neurological Surgery, John Hopkins Medical School, Baltimore, MD, USA
| | - Daniele Calistri
- Biosciences Laboratory, Istituto Scientifico Romagnolo per lo Studio e la Cura dei Tumori (IRST) IRCCS, Meldola, FC, Italy
| | - Elena Lamperti
- Neuro-Oncology Unit, Fondazione IRCCS Istituto Neurologico Carlo Besta (FINCB), Milan, Italy
| | - Franco Locatelli
- Department of Onco-Hematology, Cell Therapy, Gene Therapies and Hemopoietic Transplant, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy; Department of Life Sciences and Public Health, Catholic University of the Sacred Heart, Rome, Italy
| | - Stefano Indraccolo
- Basic and Translational Oncology Unit, Istituto Oncologico Veneto (IOV)-IRCCS, Padua, Italy; Department of Surgery Oncology and Gastroenterology, University of Padua, Padua, Italy
| | - Bianca Pollo
- Neuropathology Unit, Fondazione IRCCS Istituto Neurologico Carlo Besta, Milan, Italy
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40
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Lee SM, Loo C, Prasasya R, Bartolomei M, Kohli R, Zhou W. Low-input and single-cell methods for Infinium DNA methylation BeadChips. Nucleic Acids Res 2024; 52:e38. [PMID: 38407446 PMCID: PMC11040145 DOI: 10.1093/nar/gkae127] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2023] [Revised: 01/29/2024] [Accepted: 02/10/2024] [Indexed: 02/27/2024] Open
Abstract
The Infinium BeadChip is the most widely used DNA methylome assay technology for population-scale epigenome profiling. However, the standard workflow requires over 200 ng of input DNA, hindering its application to small cell-number samples, such as primordial germ cells. We developed experimental and analysis workflows to extend this technology to suboptimal input DNA conditions, including ultra-low input down to single cells. DNA preamplification significantly enhanced detection rates to over 50% in five-cell samples and ∼25% in single cells. Enzymatic conversion also substantially improved data quality. Computationally, we developed a method to model the background signal's influence on the DNA methylation level readings. The modified detection P-value calculation achieved higher sensitivities for low-input datasets and was validated in over 100 000 public diverse methylome profiles. We employed the optimized workflow to query the demethylation dynamics in mouse primordial germ cells available at low cell numbers. Our data revealed nuanced chromatin states, sex disparities, and the role of DNA methylation in transposable element regulation during germ cell development. Collectively, we present comprehensive experimental and computational solutions to extend this widely used methylation assay technology to applications with limited DNA.
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Affiliation(s)
- Sol Moe Lee
- Center for Computational and Genomic Medicine, The Children's Hospital of Philadelphia, PA 19104, USA
| | - Christian E Loo
- Graduate Group in Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Rexxi D Prasasya
- Department of Cell and Developmental Biology, Epigenetics Institute, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
| | - Marisa S Bartolomei
- Department of Cell and Developmental Biology, Epigenetics Institute, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
| | - Rahul M Kohli
- Department of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Wanding Zhou
- Center for Computational and Genomic Medicine, The Children's Hospital of Philadelphia, PA 19104, USA
- Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
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41
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Afflerbach AK, Albers A, Appelt A, Schweizer L, Paulus W, Bockmayr M, Schüller U, Thomas C. Nanopore sequencing from formalin-fixed paraffin-embedded specimens for copy-number profiling and methylation-based CNS tumor classification. Acta Neuropathol 2024; 147:74. [PMID: 38642165 PMCID: PMC11032293 DOI: 10.1007/s00401-024-02731-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2024] [Revised: 04/08/2024] [Accepted: 04/09/2024] [Indexed: 04/22/2024]
Affiliation(s)
- Ann-Kristin Afflerbach
- Department of Pediatric Hematology and Oncology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- Research Institute Children's Cancer Center Hamburg, Hamburg, Germany
- Institute for Tumor Biology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Anne Albers
- Institute of Neuropathology, University Hospital Münster, Pottkamp 2, 48149, Münster, Germany
| | - Anton Appelt
- Department of Pediatric Hematology and Oncology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- Research Institute Children's Cancer Center Hamburg, Hamburg, Germany
| | - Leonille Schweizer
- Institute of Neurology (Edinger Institute), University Hospital Frankfurt, Goethe University, Frankfurt Am Main, Germany
- German Cancer Research Center (DKFZ), German Cancer Consortium (DKTK), Partner Site Frankfurt/Mainz, Heidelberg, Germany
- Frankfurt Cancer Institute (FCI), Frankfurt Am Main, Germany
| | - Werner Paulus
- Institute of Neuropathology, University Hospital Münster, Pottkamp 2, 48149, Münster, Germany
| | - Michael Bockmayr
- Department of Pediatric Hematology and Oncology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- Research Institute Children's Cancer Center Hamburg, Hamburg, Germany
- bAIome - Center for Biomedical AI, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Ulrich Schüller
- Department of Pediatric Hematology and Oncology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- Research Institute Children's Cancer Center Hamburg, Hamburg, Germany
- Institute of Neuropathology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Christian Thomas
- Institute of Neuropathology, University Hospital Münster, Pottkamp 2, 48149, Münster, Germany.
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Schniederjan MJ, Potnis C, Vasudevaraja V, Moser CD, Watson B, Snuderl M, MacDonald T, Rogers BB. DNA Methylation Profiles Are Stable in H3 K27M-Mutant Diffuse Midline Glioma Neurosphere Cell Lines. Children (Basel) 2024; 11:492. [PMID: 38671709 PMCID: PMC11049299 DOI: 10.3390/children11040492] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/05/2024] [Revised: 04/02/2024] [Accepted: 04/12/2024] [Indexed: 04/28/2024]
Abstract
Diffuse midline gliomas are among the deadliest human cancers and have had little progress in treatment in the last 50 years. Cell cultures of these tumors have been developed recently, but the degree to which such cultures retain the characteristics of the source tumors is unknown. DNA methylation profiling offers a powerful tool to look at genome-wide epigenetic changes that are biologically meaningful and can help assess the similarity of cultured tumor cells to their in vivo progenitors. Paraffinized diagnostic tissue from three diffuse intrinsic pontine gliomas with H3 K27M mutations was compared with subsequent passages of neurosphere cell cultures from those tumors. Each cell line was passaged 3-4 times and analyzed with DNA methylation arrays and standard algorithms that provided a comparison of diagnostic classification and cluster analysis. All samples tested maintained high classifier scores and clustered within the reference group of H3 K27M-mutant diffuse midline gliomas. There was a gain of 1q in all cell lines, with two cell lines initially manifesting the gain of 1q only during culture. In vitro cell cultures of H3 K27M-mutant gliomas maintain high degrees of similarity in DNA methylation profiles to their source tumor, confirming their fidelity even with some chromosomal changes.
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Affiliation(s)
- Matthew J. Schniederjan
- Department of Pathology, Children’s Healthcare of Atlanta, Atlanta, GA 30342, USA (B.W.)
- Department of Pathology, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Cahil Potnis
- Department of Pathology, Children’s Healthcare of Atlanta, Atlanta, GA 30342, USA (B.W.)
| | - Varshini Vasudevaraja
- Department of Biomedical Informatics, New York University Langone Health, New York, NY 10016, USA;
| | - Catherine D. Moser
- Department of Pathology, Children’s Healthcare of Atlanta, Atlanta, GA 30342, USA (B.W.)
| | - Bethany Watson
- Department of Pathology, Children’s Healthcare of Atlanta, Atlanta, GA 30342, USA (B.W.)
| | - Matija Snuderl
- Department of Neuropathology, New York University Langone Health, New York, NY 10016, USA
| | - Tobey MacDonald
- Department of Pediatrics, Aflac Cancer and Blood Disorders Center, Children’s Healthcare of Atlanta, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Beverly B. Rogers
- Department of Pathology, Children’s Healthcare of Atlanta, Atlanta, GA 30342, USA (B.W.)
- Department of Pathology, Emory University School of Medicine, Atlanta, GA 30322, USA
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Raj A, Petreaca RC, Mirzaei G. Multi-Omics Integration for Liver Cancer Using Regression Analysis. Curr Issues Mol Biol 2024; 46:3551-3562. [PMID: 38666952 PMCID: PMC11049490 DOI: 10.3390/cimb46040222] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2024] [Revised: 04/11/2024] [Accepted: 04/16/2024] [Indexed: 04/28/2024] Open
Abstract
Genetic biomarkers have played a pivotal role in the classification, prognostication, and guidance of clinical cancer therapies. Large-scale and multi-dimensional analyses of entire cancer genomes, as exemplified by projects like The Cancer Genome Atlas (TCGA), have yielded an extensive repository of data that holds the potential to unveil the underlying biology of these malignancies. Mutations stand out as the principal catalysts of cellular transformation. Nonetheless, other global genomic processes, such as alterations in gene expression and chromosomal re-arrangements, also play crucial roles in conferring cellular immortality. The incorporation of multi-omics data specific to cancer has demonstrated the capacity to enhance our comprehension of the molecular mechanisms underpinning carcinogenesis. This report elucidates how the integration of comprehensive data on methylation, gene expression, and copy number variations can effectively facilitate the unsupervised clustering of cancer samples. We have identified regressors that can effectively classify tumor and normal samples with an optimal integration of RNA sequencing, DNA methylation, and copy number variation while also achieving significant p-values. Further, these regressors were trained using linear and logistic regression with k-means clustering. For comparison, we employed autoencoder- and stacking-based omics integration and computed silhouette scores to evaluate the clusters. The proof of concept is illustrated using liver cancer data. Our analysis serves to underscore the feasibility of unsupervised cancer classification by considering genetic markers beyond mutations, thereby emphasizing the clinical relevance of additional global cellular parameters that contribute to the transformative process in cells. This work is clinically relevant because changes in gene expression and genomic re-arrangements have been shown to be signatures of cellular transformation across cancers, as well as in liver cancers.
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Affiliation(s)
- Aditya Raj
- Department of Electrical and Computer Engineering, The Ohio State University, Columbus, OH 43210, USA;
| | - Ruben C. Petreaca
- Department of Molecular Genetics, The Ohio State University, Marion, OH 43302, USA;
- Cancer Biology Program, The Ohio State University James Comprehensive Cancer Center, Columbus, OH 43210, USA
| | - Golrokh Mirzaei
- Department of Computer Science and Engineering, The Ohio State University, Marion, OH 43302, USA
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Pećina-Šlaus N, Hrašćan R. Glioma Stem Cells-Features for New Therapy Design. Cancers (Basel) 2024; 16:1557. [PMID: 38672638 PMCID: PMC11049195 DOI: 10.3390/cancers16081557] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2024] [Revised: 04/11/2024] [Accepted: 04/16/2024] [Indexed: 04/28/2024] Open
Abstract
On a molecular level, glioma is very diverse and presents a whole spectrum of specific genetic and epigenetic alterations. The tumors are unfortunately resistant to available therapies and the survival rate is low. The explanation of significant intra- and inter-tumor heterogeneity and the infiltrative capability of gliomas, as well as its resistance to therapy, recurrence and aggressive behavior, lies in a small subset of tumor-initiating cells that behave like stem cells and are known as glioma cancer stem cells (GCSCs). They are responsible for tumor plasticity and are influenced by genetic drivers. Additionally, GCSCs also display greater migratory abilities. A great effort is under way in order to find ways to eliminate or neutralize GCSCs. Many different treatment strategies are currently being explored, including modulation of the tumor microenvironment, posttranscriptional regulation, epigenetic modulation and immunotherapy.
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Affiliation(s)
- Nives Pećina-Šlaus
- Laboratory of Neuro-Oncology, Croatian Institute for Brain Research, School of Medicine, University of Zagreb, Šalata 12, 10000 Zagreb, Croatia
- Department of Biology, School of Medicine, University of Zagreb, Šalata 3, 10000 Zagreb, Croatia
| | - Reno Hrašćan
- Department of Biochemical Engineering, Faculty of Food Technology and Biotechnology, University of Zagreb, 10000 Zagreb, Croatia;
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Morales-Vargas B, Saad H, Refai D, Schniederjan M, Abdullaev Z, Aldape K, Abedalthagafi M. A case of myxopapillary ependymoma with predominant giant cell morphology: A rare entity with comprehensive genomic profiling and review of literature. Neuropathology 2024. [PMID: 38639066 DOI: 10.1111/neup.12977] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2023] [Revised: 04/03/2024] [Accepted: 04/08/2024] [Indexed: 04/20/2024]
Abstract
In the evolving landscape of ependymoma classification, which integrates histological, molecular, and anatomical context, we detail a rare case divergent from the usual histopathological spectrum. We present the case of a 37-year-old man with symptomatic spinal cord compression at the L3-L4 level. Neuroradiological evaluation revealed an intradural, encapsulated mass. Histologically, the tumor displayed atypical features: bizarre pleomorphic giant cells, intranuclear inclusions, mitotic activity, and a profusion of eosinophilic cytoplasm with hyalinized vessels, deviating from the characteristic perivascular pseudorosettes or myxopapillary patterns. Immunohistochemical staining bolstered this divergence, marking the tumor cells positive for glial fibrillary acidic protein and epithelial membrane antigen with a characteristic ring-like pattern, and CD99 but negative for Olig-2. These markers, alongside methylation profiling, facilitated its classification as a myxopapillary ependymoma (MPE), despite the atypical histologic features. This profile underscores the necessity of a multifaceted diagnostic process, especially when histological presentation is uncommon, confirming the critical role of immunohistochemistry and molecular diagnostics in classifying morphologically ambiguous ependymomas and exemplifying the histological diversity within MPEs.
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Affiliation(s)
- Bryan Morales-Vargas
- Pathology and Laboratory Medicine, Emory University School of Medicine, Atlanta, Georgia, USA
| | - Hassan Saad
- Department of Neurological Surgery, Emory University School of Medicine, Atlanta, Georgia, USA
| | - Daniel Refai
- Department of Neurological Surgery, Emory University School of Medicine, Atlanta, Georgia, USA
| | - Matthew Schniederjan
- Pathology and Laboratory Medicine, Emory University School of Medicine, Atlanta, Georgia, USA
| | - Zied Abdullaev
- Laboratory of Pathology, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland, USA
| | - Kenneth Aldape
- Laboratory of Pathology, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland, USA
| | - Malak Abedalthagafi
- Pathology and Laboratory Medicine, Emory University School of Medicine, Atlanta, Georgia, USA
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46
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Donev K, Sundararajan V, Johnson D, Balan J, Chambers M, Paulson VA, Scherpelz KP, Abdullaev Z, Quezado M, Cimino PJ, Pratt D, Valerio E, Alves de Castro JV, Carraro DM, Torrezan GT, Wolff BM, Kulikowski LD, Costa FD, Aldape K, Ida CM. Diffuse hemispheric glioma with H3 p.K28M (K27M) mutation: Unusual non-midline presentation of diffuse midline glioma, H3 K27M-altered? J Neuropathol Exp Neurol 2024; 83:357-364. [PMID: 38447592 PMCID: PMC11029465 DOI: 10.1093/jnen/nlae018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/08/2024] Open
Abstract
Diffuse midline glioma, H3 K27-altered (DMG-H3 K27) is an aggressive group of diffuse gliomas that predominantly occurs in pediatric patients, involves midline structures, and displays loss of H3 p.K28me3 (K27me3) expression by immunohistochemistry and characteristic genetic/epigenetic profile. Rare examples of a diffuse glioma with an H3 p.K28M (K27M) mutation and without involvement of the midline structures, so-called "diffuse hemispheric glioma with H3 p.K28M (K27M) mutation" (DHG-H3 K27), have been reported. Herein, we describe 2 additional cases of radiologically confirmed DHG-H3 K27 and summarize previously reported cases. We performed histological, immunohistochemical, molecular, and DNA methylation analysis and provided clinical follow-up in both cases. Overall, DHG-H3 K27 is an unusual group of diffuse gliomas that shows similar clinical, histopathological, genomic, and epigenetic features to DMG-H3 K27 as well as enrichment for activating alterations in MAPK pathway genes. These findings suggest that DHG-H3 K27 is closely related to DMG-H3 K27 and may represent an unusual presentation of DMG-H3 K27 without apparent midline involvement and with frequent MAPK pathway activation. Detailed reports of additional cases with clinical follow-up will be important to expand our understanding of this unusual group of diffuse gliomas and to better define the clinical outcome and how to classify DHG-H3 K27.
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Affiliation(s)
- Kliment Donev
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Scottsdale, Arizona, USA
| | - Vanitha Sundararajan
- OhioHealth Riverside Methodist Hospital, Columbus, Ohio, USA
- CORPath Pathology Services, Columbus, Ohio, USA
| | - Derek Johnson
- Department of Radiology, Mayo Clinic, Rochester, Minnesota, USA
| | - Jagadheshwar Balan
- Department of Quantitative Health Sciences, Mayo Clinic, Rochester, Minnesota, USA
| | - Meagan Chambers
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, Washington, USA
| | - Vera A Paulson
- Department of Laboratory Medicine and Pathology, Genetics and Solid Tumor Laboratory, University of Washington, Seattle, Washington, USA
| | - Kathryn P Scherpelz
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, Washington, USA
| | - Zied Abdullaev
- Laboratory of Pathology, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland, USA
| | - Martha Quezado
- Laboratory of Pathology, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland, USA
| | - Patrick J Cimino
- Laboratory of Pathology, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland, USA
| | - Drew Pratt
- Laboratory of Pathology, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland, USA
| | - Ediel Valerio
- Department of Pathology, A.C. Camargo Cancer Center, Sao Paulo, Brazil
| | | | - Dirce Maria Carraro
- Genomics and Molecular Biology Group, International Center of Research CIPE, A.C. Camargo Cancer Center, Sao Paulo, Brazil
- National Institute of Science and Technology in Oncogenomics (INCITO), Sao Paulo, Brazil
| | - Giovana Tardin Torrezan
- Genomics and Molecular Biology Group, International Center of Research CIPE, A.C. Camargo Cancer Center, Sao Paulo, Brazil
- National Institute of Science and Technology in Oncogenomics (INCITO), Sao Paulo, Brazil
| | - Beatriz Martins Wolff
- Cytogenomic Laboratory, Department of Pathology, Faculdade de Medicina FMUSP, Universidade de Sao Paulo, Sao Paulo, Brazil
| | - Leslie Domenici Kulikowski
- Cytogenomic Laboratory, Department of Pathology, Faculdade de Medicina FMUSP, Universidade de Sao Paulo, Sao Paulo, Brazil
| | - Felipe D’Almeida Costa
- Laboratory of Pathology, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland, USA
- Dasa Laboratories, Sao Paulo, Brazil
| | - Kenneth Aldape
- Laboratory of Pathology, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland, USA
| | - Cristiane M Ida
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota, USA
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Pedace L, Pizzi S, Abballe L, Vinci M, Antonacci C, Patrizi S, Nardini C, Del Bufalo F, Rossi S, Pericoli G, Gianno F, Besharat ZM, Tiberi L, Mastronuzzi A, Ferretti E, Tartaglia M, Locatelli F, Ciolfi A, Miele E. Evaluating cell culture reliability in pediatric brain tumor primary cells through DNA methylation profiling. NPJ Precis Oncol 2024; 8:92. [PMID: 38637626 PMCID: PMC11026496 DOI: 10.1038/s41698-024-00578-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2023] [Accepted: 03/13/2024] [Indexed: 04/20/2024] Open
Abstract
In vitro models of pediatric brain tumors (pBT) are instrumental for better understanding the mechanisms contributing to oncogenesis and testing new therapies; thus, ideally, they should recapitulate the original tumor. We applied DNA methylation (DNAm) and copy number variation (CNV) profiling to characterize 241 pBT samples, including 155 tumors and 86 pBT-derived cell cultures, considering serum vs serum-free conditions, late vs early passages, and dimensionality (2D vs 3D cultures). We performed a t-SNE classification and identified differentially methylated regions in tumors compared to cell models. Early cell cultures recapitulate the original tumor, but serum media and 2D culturing were demonstrated to significantly contribute to the divergence of DNAm profiles from the parental ones. All divergent cells clustered together acquiring a common deregulated epigenetic signature suggesting a shared selective pressure. We identified a set of hypomethylated genes shared among unfaithful cells converging on response to growth factors and migration pathways, such as signaling cascade activation, tissue organization, and cellular migration. In conclusion, DNAm and CNV are informative tools that should be used to assess the recapitulation of pBT-cells from parental tumors.
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Affiliation(s)
- Lucia Pedace
- Onco-Hematology, Cell Therapy, Gene Therapies and Hemopoietic Transplant, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Simone Pizzi
- Molecular Genetics and Functional Genomics, Bambino Gesù Children's Hospital, IRCCS, 00146, Rome, Italy
| | - Luana Abballe
- Onco-Hematology, Cell Therapy, Gene Therapies and Hemopoietic Transplant, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Maria Vinci
- Onco-Hematology, Cell Therapy, Gene Therapies and Hemopoietic Transplant, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Celeste Antonacci
- Onco-Hematology, Cell Therapy, Gene Therapies and Hemopoietic Transplant, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Sara Patrizi
- Onco-Hematology, Cell Therapy, Gene Therapies and Hemopoietic Transplant, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Claudia Nardini
- Onco-Hematology, Cell Therapy, Gene Therapies and Hemopoietic Transplant, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Francesca Del Bufalo
- Onco-Hematology, Cell Therapy, Gene Therapies and Hemopoietic Transplant, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Sabrina Rossi
- Pathology Unit, Department of Laboratories, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Giulia Pericoli
- Onco-Hematology, Cell Therapy, Gene Therapies and Hemopoietic Transplant, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Francesca Gianno
- Department of Radiological, Oncological and Anatomic Pathology, Sapienza University, Rome, Italy
| | | | - Luca Tiberi
- Armenise-Harvard Laboratory of Brain Disorders and Cancer, Department of Cellular, Computational and Integrative Biology (CIBIO), University of Trento, Trento, Italy
| | - Angela Mastronuzzi
- Onco-Hematology, Cell Therapy, Gene Therapies and Hemopoietic Transplant, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Elisabetta Ferretti
- Department of Experimental Medicine, "Sapienza" University, 00161, Rome, Italy
| | - Marco Tartaglia
- Molecular Genetics and Functional Genomics, Bambino Gesù Children's Hospital, IRCCS, 00146, Rome, Italy
| | - Franco Locatelli
- Onco-Hematology, Cell Therapy, Gene Therapies and Hemopoietic Transplant, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Andrea Ciolfi
- Molecular Genetics and Functional Genomics, Bambino Gesù Children's Hospital, IRCCS, 00146, Rome, Italy.
| | - Evelina Miele
- Onco-Hematology, Cell Therapy, Gene Therapies and Hemopoietic Transplant, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy.
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Nuechterlein N, Shelbourn A, Szulzewsky F, Arora S, Casad M, Pattwell S, Merino-Galan L, Sulman E, Arowa S, Alvinez N, Jung M, Brown D, Tang K, Jackson S, Stoica S, Chittaboina P, Banasavadi-Siddegowda YK, Wirsching HG, Stella N, Shapiro L, Paddison P, Patel AP, Gilbert MR, Abdullaev Z, Aldape K, Pratt D, Holland EC, Cimino PJ. Haploinsufficiency of phosphodiesterase 10A activates PI3K/AKT signaling independent of PTEN to induce an aggressive glioma phenotype. Genes Dev 2024; 38:273-288. [PMID: 38589034 PMCID: PMC11065166 DOI: 10.1101/gad.351350.123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2023] [Accepted: 03/27/2024] [Indexed: 04/10/2024]
Abstract
Glioblastoma is universally fatal and characterized by frequent chromosomal copy number alterations harboring oncogenes and tumor suppressors. In this study, we analyzed exome-wide human glioblastoma copy number data and found that cytoband 6q27 is an independent poor prognostic marker in multiple data sets. We then combined CRISPR-Cas9 data, human spatial transcriptomic data, and human and mouse RNA sequencing data to nominate PDE10A as a potential haploinsufficient tumor suppressor in the 6q27 region. Mouse glioblastoma modeling using the RCAS/tv-a system confirmed that Pde10a suppression induced an aggressive glioma phenotype in vivo and resistance to temozolomide and radiation therapy in vitro. Cell culture analysis showed that decreased Pde10a expression led to increased PI3K/AKT signaling in a Pten-independent manner, a response blocked by selective PI3K inhibitors. Single-nucleus RNA sequencing from our mouse gliomas in vivo, in combination with cell culture validation, further showed that Pde10a suppression was associated with a proneural-to-mesenchymal transition that exhibited increased cell adhesion and decreased cell migration. Our results indicate that glioblastoma patients harboring PDE10A loss have worse outcomes and potentially increased sensitivity to PI3K inhibition.
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Affiliation(s)
- Nicholas Nuechterlein
- Neuropathology Unit, Surgical Neurology Branch, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, Maryland 20814, USA
| | - Allison Shelbourn
- Neuropathology Unit, Surgical Neurology Branch, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, Maryland 20814, USA
| | - Frank Szulzewsky
- Human Biology Division, Fred Hutchinson Cancer Center, Seattle, Washington 98109, USA
| | - Sonali Arora
- Human Biology Division, Fred Hutchinson Cancer Center, Seattle, Washington 98109, USA
| | - Michelle Casad
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, Washington 98195, USA
| | - Siobhan Pattwell
- Ben Towne Center for Childhood Cancer Research, Seattle Children's Research Institute, Seattle, Washington 98145, USA
| | - Leyre Merino-Galan
- Ben Towne Center for Childhood Cancer Research, Seattle Children's Research Institute, Seattle, Washington 98145, USA
| | - Erik Sulman
- Department of Radiation Oncology, New York University Grossman School of Medicine, New York, New York 11220, USA
| | - Sumaita Arowa
- Neuropathology Unit, Surgical Neurology Branch, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, Maryland 20814, USA
| | - Neriah Alvinez
- Neuropathology Unit, Surgical Neurology Branch, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, Maryland 20814, USA
| | - Miyeon Jung
- Neurosurgical Oncology Unit, Surgical Neurology Branch, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, Maryland 20814, USA
| | - Desmond Brown
- Neurosurgical Oncology Unit, Surgical Neurology Branch, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, Maryland 20814, USA
| | - Kayen Tang
- Developmental Therapeutics and Pharmacology Unit, Surgical Neurology Branch, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, Maryland 20814, USA
| | - Sadhana Jackson
- Developmental Therapeutics and Pharmacology Unit, Surgical Neurology Branch, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, Maryland 20814, USA
| | - Stefan Stoica
- Neurosurgery Unit for Pituitary and Inheritable Diseases, Surgical Neurology Branch, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, Maryland 20814, USA
| | - Prashant Chittaboina
- Neurosurgery Unit for Pituitary and Inheritable Diseases, Surgical Neurology Branch, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, Maryland 20814, USA
| | - Yeshavanth K Banasavadi-Siddegowda
- Molecular and Therapeutics Unit, Surgical Neurology Branch, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, Maryland 20814, USA
| | - Hans-Georg Wirsching
- Department of Neurology, University Hospital, University of Zurich, Zurich 8091, Switzerland
| | - Nephi Stella
- Department of Pharmacology, University of Washington, Seattle, Washington 98195, USA
| | - Linda Shapiro
- Paul G. Allen School of Computer Science and Engineering, University of Washington, Seattle, Washington 98195, USA
| | - Patrick Paddison
- Human Biology Division, Fred Hutchinson Cancer Center, Seattle, Washington 98109, USA
| | - Anoop P Patel
- Department of Neurosurgery, Preston Robert Tisch Brain Tumor Center, Duke University, Durham, North Carolina 27710, USA
| | - Mark R Gilbert
- Neuro-Oncology Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland 20814, USA
| | - Zied Abdullaev
- Laboratory of Pathology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland 20814, USA
| | - Kenneth Aldape
- Laboratory of Pathology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland 20814, USA
| | - Drew Pratt
- Laboratory of Pathology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland 20814, USA
| | - Eric C Holland
- Human Biology Division, Fred Hutchinson Cancer Center, Seattle, Washington 98109, USA
| | - Patrick J Cimino
- Neuropathology Unit, Surgical Neurology Branch, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, Maryland 20814, USA;
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49
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Zhang J, Chen J, Zhang Y, Chen L, Mo W, Yang Q, Zhang M, Liu H. Exploring TSPAN4 promoter methylation as a diagnostic biomarker for tuberculosis. Front Genet 2024; 15:1380828. [PMID: 38680421 PMCID: PMC11048481 DOI: 10.3389/fgene.2024.1380828] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2024] [Accepted: 04/01/2024] [Indexed: 05/01/2024] Open
Abstract
Background Tuberculosis (TB), caused by Mycobacterium tuberculosis (Mtb), is a persistent infectious disease threatening human health. The existing diagnostic methods still have significant shortcomings, including a low positivity rate in pathogen-based diagnoses and the inability of immunological diagnostics to detect active TB. Hence, it is urgent to develop new techniques to detect TB more accurate and earlier. This research aims to scrutinize and authenticate DNA methylation markers suitable for tuberculosis diagnosis. Concurrently, Providing a new approach for tuberculosis diagnosis. Methods Blood samples from patients with newly diagnosed tuberculosis and healthy controls (HC) were utilized in this study. Examining methylation microarray data from 40 whole blood samples (22TB + 18HC), we employed two procedures: signature gene methylated position analysis and signature region methylated position analysis to pinpoint distinctive methylated positions. Based on the screening results, diagnostic classifiers are constructed through machine learning, and validation was conducted through pyrosequencing in a separate queue (22TB + 18HC). Culminating in the development of a new tuberculosis diagnostic method via quantitative real-time methylation specific PCR (qMSP). Results The combination of the two procedures revealed a total of 10 methylated positions, all of which were located in the promoter region. These 10 signature methylated positions facilitated the construction of a diagnostic classifier, exhibiting robust diagnostic accuracy in both cross-validation and external test sets. The LDA model demonstrated the best classification performance, achieving an AUC of 0.83, specificity of 0.8, and sensitivity of 0.86 on the external test set. Furthermore, the validation of signature methylated positions through pyrosequencing demonstrated high agreement with screening outcomes. Additionally, qMSP detection of 2 potential hypomethylated positions (cg04552852 and cg12464638) exhibited promising results, yielding an AUC of 0.794, specificity of 0.720, and sensitivity of 0.816. Conclusion Our study demonstrates that the validated signature methylated positions through pyrosequencing emerge as plausible biomarkers for tuberculosis diagnosis. The specific methylation markers in the TSPAN4 gene, identified in whole blood samples, hold promise for improving tuberculosis diagnosis. This approach could significantly enhance diagnostic accuracy and speed, offering a new avenue for early detection and treatment.
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Affiliation(s)
- Jiahao Zhang
- National Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
- State Key Laboratory of Respiratory Health and Multimorbidity, NHC Key Laboratory of Systems Biology of Pathogens, National Institute of Pathogen Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
- National Institute of Pathogen Biology and Center for Tuberculosis Research, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Jilong Chen
- National Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
- State Key Laboratory of Respiratory Health and Multimorbidity, NHC Key Laboratory of Systems Biology of Pathogens, National Institute of Pathogen Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
- National Institute of Pathogen Biology and Center for Tuberculosis Research, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Yan Zhang
- National Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
- State Key Laboratory of Respiratory Health and Multimorbidity, NHC Key Laboratory of Systems Biology of Pathogens, National Institute of Pathogen Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
- National Institute of Pathogen Biology and Center for Tuberculosis Research, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Liuchi Chen
- National Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
- State Key Laboratory of Respiratory Health and Multimorbidity, NHC Key Laboratory of Systems Biology of Pathogens, National Institute of Pathogen Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
- National Institute of Pathogen Biology and Center for Tuberculosis Research, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Weiwei Mo
- National Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
- State Key Laboratory of Respiratory Health and Multimorbidity, NHC Key Laboratory of Systems Biology of Pathogens, National Institute of Pathogen Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
- National Institute of Pathogen Biology and Center for Tuberculosis Research, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Qianting Yang
- Shenzhen Clinical Research Center for Tuberculosis, Shenzhen, China
- National Clinical Research Center for Infectious Disease, Shenzhen Third People’s Hospital, The Second Affiliated Hospital, School of Medicine, Institute for Hepatology, Southern University of Science and Technology, Shenzhen, China
| | - Mingxia Zhang
- Shenzhen Clinical Research Center for Tuberculosis, Shenzhen, China
- National Clinical Research Center for Infectious Disease, Shenzhen Third People’s Hospital, The Second Affiliated Hospital, School of Medicine, Institute for Hepatology, Southern University of Science and Technology, Shenzhen, China
| | - Haiying Liu
- National Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
- State Key Laboratory of Respiratory Health and Multimorbidity, NHC Key Laboratory of Systems Biology of Pathogens, National Institute of Pathogen Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
- National Institute of Pathogen Biology and Center for Tuberculosis Research, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
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50
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Kibe Y, Ohka F, Aoki K, Yamaguchi J, Motomura K, Ito E, Takeuchi K, Nagata Y, Ito S, Mizutani N, Shiba Y, Maeda S, Nishikawa T, Shimizu H, Saito R. Pediatric-type high-grade gliomas with PDGFRA amplification in adult patients with Li-Fraumeni syndrome: clinical and molecular characterization of three cases. Acta Neuropathol Commun 2024; 12:57. [PMID: 38605367 PMCID: PMC11010357 DOI: 10.1186/s40478-024-01762-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2024] [Accepted: 03/22/2024] [Indexed: 04/13/2024] Open
Abstract
Li-Fraumeni syndrome (LFS) is an autosomal dominant tumor predisposition syndrome caused by heterozygous germline mutations or deletions in the TP53 tumor suppressor gene. Central nervous system tumors, such as choroid plexus tumors, medulloblastomas, and diffuse gliomas, are frequently found in patients with LFS. Although molecular profiles of diffuse gliomas that develop in pediatric patients with LFS have been elucidated, those in adults are limited. Recently, diffuse gliomas have been divided into pediatric- and adult-type gliomas, based on their distinct molecular profiles. In the present study, we investigated the molecular profiles of high-grade gliomas in three adults with LFS. These tumors revealed characteristic histopathological findings of high-grade glioma or glioblastoma and harbored wild-type IDH1/2 according to whole exome sequencing (WES). However, these tumors did not exhibit the key molecular alterations of glioblastoma, IDH-wildtype such as TERT promoter mutation, EGFR amplification, or chromosome 7 gain and 10 loss. Although WES revealed no other characteristic gene mutations or copy number alterations in high-grade gliomas, such as those in histone H3 genes, PDGFRA amplification was found in all three cases together with uniparental disomy of chromosome 17p, where the TP53 gene is located. DNA methylation analyses revealed that all tumors exhibited DNA methylation profiles similar to those of pediatric-type high-grade glioma H3-wildtype and IDH-wildtype (pHGG H3-/IDH-wt), RTK1 subtype. These data suggest that high-grade gliomas developed in adult patients with LFS may be involved in pHGG H3-/IDH-wt. PDGFRA and homozygous alterations in TP53 may play pivotal roles in the development of this type of glioma in adult patients with LFS.
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Affiliation(s)
- Yuji Kibe
- Department of Neurosurgery, Nagoya University Graduate School of Medicine, 65 Tsurumai-cho, Showa-ku, Nagoya, 466-8550, Japan
| | - Fumiharu Ohka
- Department of Neurosurgery, Nagoya University Graduate School of Medicine, 65 Tsurumai-cho, Showa-ku, Nagoya, 466-8550, Japan.
| | - Kosuke Aoki
- Department of Neurosurgery, Nagoya University Graduate School of Medicine, 65 Tsurumai-cho, Showa-ku, Nagoya, 466-8550, Japan
| | - Junya Yamaguchi
- Department of Neurosurgery, Nagoya University Graduate School of Medicine, 65 Tsurumai-cho, Showa-ku, Nagoya, 466-8550, Japan
| | - Kazuya Motomura
- Department of Neurosurgery, Nagoya University Graduate School of Medicine, 65 Tsurumai-cho, Showa-ku, Nagoya, 466-8550, Japan
| | - Eiji Ito
- Department of Neurosurgery, Nagoya University Graduate School of Medicine, 65 Tsurumai-cho, Showa-ku, Nagoya, 466-8550, Japan
| | - Kazuhito Takeuchi
- Department of Neurosurgery, Nagoya University Graduate School of Medicine, 65 Tsurumai-cho, Showa-ku, Nagoya, 466-8550, Japan
| | - Yuichi Nagata
- Department of Neurosurgery, Nagoya University Graduate School of Medicine, 65 Tsurumai-cho, Showa-ku, Nagoya, 466-8550, Japan
| | - Satoshi Ito
- Department of Neurosurgery, Konan Kosei Hospital, 137 Oomatsubara, Takaya-cho, Konan, 483-8703, Japan
| | - Nobuhiko Mizutani
- Department of Neurosurgery, Konan Kosei Hospital, 137 Oomatsubara, Takaya-cho, Konan, 483-8703, Japan
| | - Yoshiki Shiba
- Department of Neurosurgery, Nagoya University Graduate School of Medicine, 65 Tsurumai-cho, Showa-ku, Nagoya, 466-8550, Japan
| | - Sachi Maeda
- Department of Neurosurgery, Nagoya University Graduate School of Medicine, 65 Tsurumai-cho, Showa-ku, Nagoya, 466-8550, Japan
| | - Tomohide Nishikawa
- Department of Neurosurgery, Nagoya University Graduate School of Medicine, 65 Tsurumai-cho, Showa-ku, Nagoya, 466-8550, Japan
| | - Hiroki Shimizu
- Department of Neurosurgery, Nagoya University Graduate School of Medicine, 65 Tsurumai-cho, Showa-ku, Nagoya, 466-8550, Japan
| | - Ryuta Saito
- Department of Neurosurgery, Nagoya University Graduate School of Medicine, 65 Tsurumai-cho, Showa-ku, Nagoya, 466-8550, Japan
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