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Mazzoleni A, Awuah WA, Sanker V, Bharadwaj HR, Aderinto N, Tan JK, Huang HYR, Poornaselvan J, Shah MH, Atallah O, Tawfik A, Elmanzalawi MEAE, Ghozlan SH, Abdul-Rahman T, Moyondafoluwa JA, Alexiou A, Papadakis M. Chromosomal instability: a key driver in glioma pathogenesis and progression. Eur J Med Res 2024; 29:451. [PMID: 39227895 PMCID: PMC11373396 DOI: 10.1186/s40001-024-02043-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2024] [Accepted: 08/26/2024] [Indexed: 09/05/2024] Open
Abstract
Chromosomal instability (CIN) is a pivotal factor in gliomas, contributing to their complexity, progression, and therapeutic challenges. CIN, characterized by frequent genomic alterations during mitosis, leads to genetic abnormalities and impacts cellular functions. This instability results from various factors, including replication errors and toxic compounds. While CIN's role is well documented in cancers like ovarian cancer, its implications for gliomas are increasingly recognized. CIN influences glioma progression by affecting key oncological pathways, such as tumor suppressor genes (e.g., TP53), oncogenes (e.g., EGFR), and DNA repair mechanisms. It drives tumor evolution, promotes inflammatory signaling, and affects immune interactions, potentially leading to poor clinical outcomes and treatment resistance. This review examines CIN's impact on gliomas through a narrative approach, analyzing data from PubMed/Medline, EMBASE, the Cochrane Library, and Scopus. It highlights CIN's role across glioma subtypes, from adult glioblastomas and astrocytomas to pediatric oligodendrogliomas and astrocytomas. Key findings include CIN's effect on tumor heterogeneity and its potential as a biomarker for early detection and monitoring. Emerging therapies targeting CIN, such as those modulating tumor mutation burden and DNA damage response pathways, show promise but face challenges. The review underscores the need for integrated therapeutic strategies and improved bioinformatics tools like CINdex to advance understanding and treatment of gliomas. Future research should focus on combining CIN-targeted therapies with immune modulation and personalized medicine to enhance patient outcomes.
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Affiliation(s)
- Adele Mazzoleni
- Barts and the London School of Medicine and Dentistry, London, UK
| | | | - Vivek Sanker
- Department Of Neurosurgery, Trivandrum Medical College, Trivandrum, India
| | | | - Nicholas Aderinto
- Internal Medicine Department, LAUTECH Teaching Hospital, Ogbomoso, Nigeria
| | | | - Helen Ye Rim Huang
- Royal College of Surgeons in Ireland, University of Medicine and Health Sciences, Dublin, Ireland
| | | | | | - Oday Atallah
- Department of Neurosurgery, Hannover Medical School, Carl-Neuberg-Strasse 1, 30625, Hannover, Germany
| | - Aya Tawfik
- Faculty of Biotechnology, October University for Modern Sciences and Arts (MSA), Giza, Egypt
| | | | - Sama Hesham Ghozlan
- Arab Academy for Science, Technology & Maritime Transport, Alexandria, Egypt
| | | | | | - Athanasios Alexiou
- University Centre for Research & Development, Chandigarh University, Chandigarh-Ludhiana Highway, Mohali, Punjab, India
- Funogen, Department of Research & Development, Athens, Greece
- Department of Research & Development, AFNP Med, 1030, Vienna, Austria
- Department of Science and Engineering, Novel Global Community Educational Foundation, Hebersham, NSW, 2770, Australia
| | - Marios Papadakis
- Department of Surgery II, University Hospital Witten-Herdecke, University of Witten-Herdecke, Heusnerstrasse 40, 42283, Wuppertal, Germany.
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2
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Kim D, Lee JH, Kim N, Lim DH, Song JH, Suh CO, Wee CW, Kim IA. Optimizing Recurrent Glioblastoma Salvage Treatment: A Multicenter Study Integrating Genetic Biomarkers From the Korean Radiation Oncology Group (21-02). Neurosurgery 2024; 95:584-595. [PMID: 38511935 DOI: 10.1227/neu.0000000000002903] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2023] [Accepted: 01/13/2024] [Indexed: 03/22/2024] Open
Abstract
BACKGROUND AND OBJECTIVES Few studies have used real-world patient data to compare overall treatment patterns and survival outcomes for recurrent glioblastoma (rGBM). This study aimed to evaluate postprogression survival (PPS) according to the treatment strategy for rGBM by incorporating biomarker analysis. METHODS We assessed 468 adult patients with rGBM who underwent standard temozolomide-based chemoradiation. The impact of predictors on PPS was evaluated in patients with isocitrate dehydrogenase wild-type rGBM (n = 439) using survival probability analysis. We identified patients who would benefit from reirradiation (re-RT) during the first progression. RESULTS Median PPS was 3.4, 13.8, 6.6, and 10.0 months in the best supportive care (n = 82), surgery (with/without adjuvant therapy, n = 112), chemotherapy alone (n = 170), and re-RT (with/without chemotherapy, n = 75) groups, respectively. After propensity score matching analysis of the cohort, both the surgery and re-RT groups had a significantly better PPS than the chemotherapy-only group; however, no significant difference was observed in PPS between the surgery and re-RT groups. In the surgery subgroup, surgery with chemotherapy ( P = .024) and surgery with radio(chemo)therapy ( P = .039) showed significantly improved PPS compared with surgery alone. In the no-surgery subgroup, radio(chemo)therapy showed significantly improved PPS compared with chemotherapy alone ( P = .047). Homozygous deletion of cyclin-dependent kinase inhibitor 2A/B, along with other clinical factors (performance score and progression-free interval), was significantly associated with the re-RT survival benefit. CONCLUSION Surgery combined with radio(chemo)therapy resulted in the best survival outcomes for rGBM. re-RT should also be considered for patients with rGBM at first recurrence. Furthermore, this study identified a specific genetic biomarker and clinical factors that may enhance the survival benefit of re-RT.
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Affiliation(s)
- Dowook Kim
- Department of Radiation Oncology, Seoul National University College of Medicine, Seoul , Korea
- Department of Radiation Oncology, Chungnam National University Hospital, Daejeon , Korea
| | - Joo Ho Lee
- Department of Radiation Oncology, Seoul National University College of Medicine, Seoul , Korea
- Department of Radiation Oncology, Seoul National University Hospital, Seoul , Korea
| | - Nalee Kim
- Department of Radiation Oncology, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul , Korea
| | - Do Hoon Lim
- Department of Radiation Oncology, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul , Korea
| | - Jin Ho Song
- Department of Radiation Oncology, Seoul St. Mary's Hospital, College of Medicine, The Catholic University, Seoul , Korea
| | - Chang-Ok Suh
- Department of Radiation Oncology, Bundang CHA Medical Center, CHA University, Seongnam , Korea
| | - Chan Woo Wee
- Department of Radiation Oncology, Yonsei Cancer Center, Heavy Ion Therapy Research Institute, Yonsei University College of Medicine, Seoul , Korea
| | - In Ah Kim
- Department of Radiation Oncology, Seoul National University College of Medicine, Seoul , Korea
- Department of Radiation Oncology, Seoul National University Bundang Hospital, Seongnam , Korea
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3
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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] [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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4
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Wang J, Xi YF, Zhao Q, Guo JH, Zhang Z, Zhang MB, Chang J, Wu YQ, Su W. CDKN2A promoter methylation enhances self-renewal of glioblastoma stem cells and confers resistance to carmustine. Mol Biol Rep 2024; 51:385. [PMID: 38438773 PMCID: PMC10912136 DOI: 10.1007/s11033-024-09247-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Accepted: 01/11/2024] [Indexed: 03/06/2024]
Abstract
BACKGROUND Glioblastoma, a highly aggressive form of brain cancer, poses significant challenges due to its resistance to therapy and high recurrence rates. This study aimed to investigate the expression and functional implications of CDKN2A, a key tumor suppressor gene, in glioblastoma cells, building upon the existing background of knowledge in this field. METHOD Quantitative reverse transcription PCR (qRT-PCR) analysis was performed to evaluate CDKN2A expression in U87 glioblastoma cells compared to normal human astrocytes (NHA). CDKN2A expression levels were manipulated using small interfering RNA (siRNA) and CDKN2A overexpression vector. Cell viability assays and carmustine sensitivity tests were conducted to assess the impact of CDKN2A modulation on glioblastoma cell viability and drug response. Sphere formation assays and western blot analysis were performed to investigate the role of CDKN2A in glioblastoma stem cell (GSC) self-renewal and pluripotency marker expression. Additionally, methylation-specific PCR (MSP) assays and demethylation treatment were employed to elucidate the mechanism of CDKN2A downregulation in U87 cells. RESULT CDKN2A expression was significantly reduced in glioblastoma cells compared to NHA. CDKN2A overexpression resulted in decreased cell viability and enhanced sensitivity to carmustine treatment. CDKN2A inhibition promoted self-renewal capacity and increased pluripotency marker expression in U87 cells. CDKN2A upregulation led to elevated protein levels of p16INK4a, p14ARF, P53, and P21, which are involved in cell cycle regulation. CDKN2A downregulation in U87 cells was associated with high promoter methylation, which was reversed by treatment with a demethylating agent. CONCLUSION Our findings demonstrate that CDKN2A downregulation in glioblastoma cells is associated with decreased cell viability, enhanced drug resistance, increased self-renewal capacity, and altered expression of pluripotency markers. The observed CDKN2A expression changes are mediated by promoter methylation. These results highlight the potential role of CDKN2A as a therapeutic target and prognostic marker in glioblastoma.
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Affiliation(s)
- Jing Wang
- Department of Pathology, Cancer Hospital Affiliated to Shanxi Medical University/Shanxi Province Cancer Hospital/ Shanxi Hospital Affiliated to Cancer Hospital Chinese Academy of Medical Sciences, Taiyuan, 030013, Shanxi, China
| | - Yan-Feng Xi
- Department of Pathology, Cancer Hospital Affiliated to Shanxi Medical University/Shanxi Province Cancer Hospital/ Shanxi Hospital Affiliated to Cancer Hospital Chinese Academy of Medical Sciences, Taiyuan, 030013, Shanxi, China
| | - Qi Zhao
- Department of Pathology, Cancer Hospital Affiliated to Shanxi Medical University/Shanxi Province Cancer Hospital/ Shanxi Hospital Affiliated to Cancer Hospital Chinese Academy of Medical Sciences, Taiyuan, 030013, Shanxi, China
| | - Jiang-Hong Guo
- Department of Pathology, Cancer Hospital Affiliated to Shanxi Medical University/Shanxi Province Cancer Hospital/ Shanxi Hospital Affiliated to Cancer Hospital Chinese Academy of Medical Sciences, Taiyuan, 030013, Shanxi, China
| | - Zhen Zhang
- Department of Pathology, Cancer Hospital Affiliated to Shanxi Medical University/Shanxi Province Cancer Hospital/ Shanxi Hospital Affiliated to Cancer Hospital Chinese Academy of Medical Sciences, Taiyuan, 030013, Shanxi, China
| | - Mao-Bai Zhang
- Department of Neurosurgery, Cancer Hospital Affiliated to Shanxi Medical University/Shanxi Province Cancer Hospital/ Shanxi Hospital Affiliated to Cancer Hospital Chinese Academy of Medical Sciences, Taiyuan, 030013, Shanxi, China
| | - Jiang Chang
- Department of Pathology, Cancer Hospital Affiliated to Shanxi Medical University/Shanxi Province Cancer Hospital/ Shanxi Hospital Affiliated to Cancer Hospital Chinese Academy of Medical Sciences, Taiyuan, 030013, Shanxi, China
| | - Yue-Qin Wu
- Department of Pathology, Cancer Hospital Affiliated to Shanxi Medical University/Shanxi Province Cancer Hospital/ Shanxi Hospital Affiliated to Cancer Hospital Chinese Academy of Medical Sciences, Taiyuan, 030013, Shanxi, China
| | - Wen Su
- Department of Medical Laboratory, Cancer Hospital Affiliated to Shanxi Medical University/Shanxi Province Cancer Hospital/ Shanxi Hospital Affiliated to Cancer Hospital Chinese Academy of Medical Sciences, Taiyuan, 030013, Shanxi, China.
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5
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van der Meulen M, Ramos RC, Voisin MR, Patil V, Wei Q, Singh O, Climans SA, Kalidindi N, Or R, Aldape K, Diamandis P, Munoz DG, Zadeh G, Mason WP. Differences in methylation profiles between long-term survivors and short-term survivors of IDH-wild-type glioblastoma. Neurooncol Adv 2024; 6:vdae001. [PMID: 38312227 PMCID: PMC10838123 DOI: 10.1093/noajnl/vdae001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2024] Open
Abstract
Background Patients with glioblastoma (GBM) have a median overall survival (OS) of approximately 16 months. However, approximately 5% of patients survive >5 years. This study examines the differences in methylation profiles between long-term survivors (>5 years, LTS) and short-term survivors (<1 year, STS) with isocitrate dehydrogenase (IDH)-wild-type GBMs. Methods In a multicenter retrospective analysis, we identified 25 LTS with a histologically confirmed GBM. They were age- and sex-matched to an STS. The methylation profiles of all 50 samples were analyzed with EPIC 850k, classified according to the DKFZ methylation classifier, and the methylation profiles of LTS versus STS were compared. Results After methylation profiling, 16/25 LTS and 23/25 STS were confirmed to be IDH-wild-type GBMs, all with +7/-10 signature. LTS had significantly increased O6-methylguanine methyltransferase (MGMT) promoter methylation and higher prevalence of FGFR3-TACC3 fusion (P = .03). STS were more likely to exhibit CDKN2A/B loss (P = .01) and higher frequency of NF1 (P = .02) mutation. There were no significant CpGs identified between LTS versus STS at an adjusted P-value of .05. Unadjusted analyses identified key pathways involved in both LTS and STS. The most common pathways were the Hippo signaling pathway and the Wnt pathway in LTS, and GPCR ligand binding and cell-cell signaling in STS. Conclusions A small group of patients with IDH-wild-type GBM survive more than 5 years. While there are few differences in the global methylation profiles of LTS compared to STS, our study highlights potential pathways involved in GBMs with a good or poor prognosis.
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Affiliation(s)
- Matthijs van der Meulen
- Department of Medicine, Divisions of Neurology and Medical Oncology, Princess Margaret Cancer Centre, University of Toronto, Toronto, Ontario, Canada
- Department of Neurology, Medisch Spectrum Twente, Enschede, The Netherlands
| | - Ronald C Ramos
- Department of Medicine, Divisions of Neurology and Medical Oncology, Princess Margaret Cancer Centre, University of Toronto, Toronto, Ontario, Canada
- Division of Neurology, Department of Medicine, McMaster University, Hamilton, Ontario, Canada
| | - Mathew R Voisin
- Division of Neurosurgery, Department of Surgery, University of Toronto, Toronto, Ontario, Canada
| | - Vikas Patil
- MacFeeters Hamilton Centre for Neuro-Oncology Research, Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Qingxia Wei
- MacFeeters Hamilton Centre for Neuro-Oncology Research, Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Olivia Singh
- MacFeeters Hamilton Centre for Neuro-Oncology Research, Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Seth A Climans
- Department of Medicine, Divisions of Neurology and Medical Oncology, Princess Margaret Cancer Centre, University of Toronto, Toronto, Ontario, Canada
- Department of Oncology, London Regional Cancer Program, London, Ontario, Canada
| | - Navya Kalidindi
- Division of Neurology, Department of Medicine, McMaster University, Hamilton, Ontario, Canada
| | - Rosemarylin Or
- Department of Neurology, The Medical City, Pasig, Philippines
| | - Ken Aldape
- Neuro-Oncology Branch, National Cancer Institute, National Institute of Health, Bethesda, Maryland, USA
| | - Phedias Diamandis
- Department of Laboratory Medicine and Pathobiology, Princess Margaret Cancer Centre, Toronto, Ontario, Canada
| | - David G Munoz
- Department of Laboratory Medicine, St. Michaels Hospital, Toronto, Ontario, Canada
| | - Gelareh Zadeh
- Division of Neurosurgery, Department of Surgery, University of Toronto, Toronto, Ontario, Canada
- MacFeeters Hamilton Centre for Neuro-Oncology Research, Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Warren P Mason
- Department of Medicine, Divisions of Neurology and Medical Oncology, Princess Margaret Cancer Centre, University of Toronto, Toronto, Ontario, Canada
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Cabezas-Camarero S, Pérez-Alfayate R, Polidura C, Gómez-Ruiz MN, Gil-Martínez L, Casado-Fariñas I, Bartolomé J, Pérez-Segura P. Durable benefit and slowdown in tumor growth dynamics with erdafitinib in a FGFR3-TACC3 fusion-positive IDH-wild type glioblastoma. Neurooncol Adv 2024; 6:vdae139. [PMID: 39211518 PMCID: PMC11358818 DOI: 10.1093/noajnl/vdae139] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/04/2024] Open
Abstract
FGFR3-TACC3 fusion-positive IDH-wild-type (IDH-WT) glioblastoma (GB) is a rare GB subtype occurring in approximately 3% of cases. It is clinical behavior and molecular profile is different from those of fusion-negative IDH-WT GBs. Evidence on the role of FGFR inhibitors in FGFR-altered gliomas is limited. We present the case of a patient with a FGFR3-TACC3 fusion-positive IDH-WT GB that at its second recurrence was treated with the FGFR inhibitor erdafitinib through a compassionate use program. Although no objective response was achieved, an overt deceleration in tumor growth was evidenced and the patient remained on treatment for 5.5 months.
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Affiliation(s)
- Santiago Cabezas-Camarero
- Medical Oncology Department, IOB Institute of Oncology-Madrid, Madrid, Spain
- Medical Oncology Department, Instituto de Investigación Sanitaria San Carlos (IdISSC), Hospital Clínico Universitario San Carlos, Madrid, Spain
| | | | - Carmen Polidura
- Radiology Department, Hospital Clínico Universitario San Carlos, Madrid, Spain
| | | | - Lidia Gil-Martínez
- Radiology Department, Hospital Clínico Universitario San Carlos, Madrid, Spain
| | | | - Jorge Bartolomé
- Medical Oncology Department, Instituto de Investigación Sanitaria San Carlos (IdISSC), Hospital Clínico Universitario San Carlos, Madrid, Spain
| | - Pedro Pérez-Segura
- Medical Oncology Department, IOB Institute of Oncology-Madrid, Madrid, Spain
- Medical Oncology Department, Instituto de Investigación Sanitaria San Carlos (IdISSC), Hospital Clínico Universitario San Carlos, Madrid, Spain
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7
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Tillmanns N, Lost J, Tabor J, Vasandani S, Vetsa S, Marianayagam N, Yalcin K, Erson-Omay EZ, von Reppert M, Jekel L, Merkaj S, Ramakrishnan D, Avesta A, de Oliveira Santo ID, Jin L, Huttner A, Bousabarah K, Ikuta I, Lin M, Aneja S, Turowski B, Aboian M, Moliterno J. Application of novel PACS-based informatics platform to identify imaging based predictors of CDKN2A allelic status in glioblastomas. Sci Rep 2023; 13:22942. [PMID: 38135704 PMCID: PMC10746716 DOI: 10.1038/s41598-023-48918-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2023] [Accepted: 12/01/2023] [Indexed: 12/24/2023] Open
Abstract
Gliomas with CDKN2A mutations are known to have worse prognosis but imaging features of these gliomas are unknown. Our goal is to identify CDKN2A specific qualitative imaging biomarkers in glioblastomas using a new informatics workflow that enables rapid analysis of qualitative imaging features with Visually AcceSAble Rembrandtr Images (VASARI) for large datasets in PACS. Sixty nine patients undergoing GBM resection with CDKN2A status determined by whole-exome sequencing were included. GBMs on magnetic resonance images were automatically 3D segmented using deep learning algorithms incorporated within PACS. VASARI features were assessed using FHIR forms integrated within PACS. GBMs without CDKN2A alterations were significantly larger (64 vs. 30%, p = 0.007) compared to tumors with homozygous deletion (HOMDEL) and heterozygous loss (HETLOSS). Lesions larger than 8 cm were four times more likely to have no CDKN2A alteration (OR: 4.3; 95% CI 1.5-12.1; p < 0.001). We developed a novel integrated PACS informatics platform for the assessment of GBM molecular subtypes and show that tumors with HOMDEL are more likely to have radiographic evidence of pial invasion and less likely to have deep white matter invasion or subependymal invasion. These imaging features may allow noninvasive identification of CDKN2A allele status.
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Affiliation(s)
- Niklas Tillmanns
- Brain Tumor Research Group, Department of Radiology and Biomedical Imaging, Yale School of Medicine, 333 Cedar Street, PO Box 208042, New Haven, CT, 06520, USA
- Department of Diagnostic and Interventional Radiology, Medical Faculty, University Dusseldorf, 40225, Dusseldorf, Germany
| | - Jan Lost
- Brain Tumor Research Group, Department of Radiology and Biomedical Imaging, Yale School of Medicine, 333 Cedar Street, PO Box 208042, New Haven, CT, 06520, USA
| | - Joanna Tabor
- Department of Neurosurgery, Yale School of Medicine, New Haven, CT, USA
| | - Sagar Vasandani
- Department of Neurosurgery, Yale School of Medicine, New Haven, CT, USA
| | - Shaurey Vetsa
- Department of Neurosurgery, Yale School of Medicine, New Haven, CT, USA
| | | | - Kanat Yalcin
- Department of Neurosurgery, Yale School of Medicine, New Haven, CT, USA
| | | | - Marc von Reppert
- Brain Tumor Research Group, Department of Radiology and Biomedical Imaging, Yale School of Medicine, 333 Cedar Street, PO Box 208042, New Haven, CT, 06520, USA
| | - Leon Jekel
- Brain Tumor Research Group, Department of Radiology and Biomedical Imaging, Yale School of Medicine, 333 Cedar Street, PO Box 208042, New Haven, CT, 06520, USA
| | - Sara Merkaj
- Brain Tumor Research Group, Department of Radiology and Biomedical Imaging, Yale School of Medicine, 333 Cedar Street, PO Box 208042, New Haven, CT, 06520, USA
| | - Divya Ramakrishnan
- Brain Tumor Research Group, Department of Radiology and Biomedical Imaging, Yale School of Medicine, 333 Cedar Street, PO Box 208042, New Haven, CT, 06520, USA
| | - Arman Avesta
- Department of Radiation Oncology, Yale School of Medicine, 333 Cedar Street, PO Box 208042, New Haven, CT, 06520, USA
| | - Irene Dixe de Oliveira Santo
- Brain Tumor Research Group, Department of Radiology and Biomedical Imaging, Yale School of Medicine, 333 Cedar Street, PO Box 208042, New Haven, CT, 06520, USA
| | - Lan Jin
- R&D, Sema4, 333 Ludlow Street, North Tower, 8th Floor, Stamford, CT, 06902, USA
| | - Anita Huttner
- Department of Pathology, Yale School of Medicine, New Haven, CT, USA
| | | | - Ichiro Ikuta
- Department of Radiology, Mayo Clinic Arizona, 5711 E Mayo Blvd, Phoenix, AZ, 85054, USA
| | - MingDe Lin
- Brain Tumor Research Group, Department of Radiology and Biomedical Imaging, Yale School of Medicine, 333 Cedar Street, PO Box 208042, New Haven, CT, 06520, USA
- Visage Imaging, Inc., 12625 High Bluff Dr, Suite 205, San Diego, CA, 92130, USA
| | - Sanjay Aneja
- Department of Neurosurgery, Yale School of Medicine, New Haven, CT, USA
| | - Bernd Turowski
- Department of Diagnostic and Interventional Radiology, Medical Faculty, University Dusseldorf, 40225, Dusseldorf, Germany
| | - Mariam Aboian
- Brain Tumor Research Group, Department of Radiology and Biomedical Imaging, Yale School of Medicine, 333 Cedar Street, PO Box 208042, New Haven, CT, 06520, USA.
- , New Haven, USA.
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Kałuzińska-Kołat Ż, Kołat D, Kośla K, Płuciennik E, Bednarek AK. Molecular landscapes of glioblastoma cell lines revealed a group of patients that do not benefit from WWOX tumor suppressor expression. Front Neurosci 2023; 17:1260409. [PMID: 37781246 PMCID: PMC10540236 DOI: 10.3389/fnins.2023.1260409] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2023] [Accepted: 08/28/2023] [Indexed: 10/03/2023] Open
Abstract
Introduction Glioblastoma (GBM) is notorious for its clinical and molecular heterogeneity, contributing to therapeutic failure and a grim prognosis. WWOX is one of the tumor suppressor genes important in nervous tissue or related pathologies, which was scarcely investigated in GBM for reliable associations with prognosis or disease progression despite known alterations. Recently, we observed a phenotypic heterogeneity between GBM cell lines (U87MG, T98G, U251MG, DBTRG-05MG), among which the anti-GBM activity of WWOX was generally corresponding, but colony growth and formation were inconsistent in DBTRG-05MG. This prompted us to investigate the molecular landscapes of these cell lines, intending to translate them into the clinical context. Methods U87MG/T98G/U251MG/DBTRG-05MG were subjected to high-throughput sequencing, and obtained data were explored via weighted gene co-expression network analysis, differential expression analysis, functional annotation, and network building. Following the identification of the most relevant DBTRG-distinguishing driver genes, data from GBM patients were employed for, e.g., differential expression analysis, survival analysis, and principal component analysis. Results Although most driver genes were unique for each cell line, some were inversely regulated in DBTRG-05MG. Alongside driver genes, the differentially-expressed genes were used to build a WWOX-related network depicting protein-protein interactions in U87MG/T98G/U251MG/DBTRG-05MG. This network revealed processes distinctly regulated in DBTRG-05MG, e.g., microglia proliferation or neurofibrillary tangle assembly. POLE4 and HSF2BP were selected as DBTRG-discriminating driver genes based on the gene significance, module membership, and fold-change. Alongside WWOX, POLE4 and HSF2BP expression was used to stratify patients into cell lines-resembling groups that differed in, e.g., prognosis and treatment response. Some differences from a WWOX-related network were certified in patients, revealing genes that clarify clinical outcomes. Presumably, WWOX overexpression in DBTRG-05MG resulted in expression profile change resembling that of patients with inferior prognosis and drug response. Among these patients, WWOX may be inaccessible for its partners and does not manifest its anti-cancer activity, which was proposed in the literature but not regarding glioblastoma or concerning POLE4 and HSF2BP. Conclusion Cell lines data enabled the identification of patients among which, despite high expression of WWOX tumor suppressor, no advantageous outcomes were noted due to the cancer-promoting profile ensured by other genes.
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Affiliation(s)
| | - Damian Kołat
- Department of Molecular Carcinogenesis, Medical University of Lodz, Lodz, Poland
| | - Katarzyna Kośla
- Department of Molecular Carcinogenesis, Medical University of Lodz, Lodz, Poland
| | | | - Andrzej K. Bednarek
- Department of Molecular Carcinogenesis, Medical University of Lodz, Lodz, Poland
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