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Naqvi AS, Corbett RJ, Seghal P, Conkrite KL, Rathi KS, Ennis BM, Hayer KE, Zhang B, Brown MA, Miller DP, Kraya AA, Coleman KL, Dybas JM, Geng Z, Blackden C, Arif S, Chroni A, Lahiri A, Hollawell ML, Storm PB, Haydar D, Foster JB, Koptyra M, Madsen PJ, Diskin SJ, Thomas-Tikhonenko A, Resnick AC, Rokita JL. Characterization of aberrant splicing in pediatric central nervous system tumors reveals CLK1 as a candidate oncogenic dependency. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2025:2024.08.03.606419. [PMID: 39149264 PMCID: PMC11326178 DOI: 10.1101/2024.08.03.606419] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/17/2024]
Abstract
Pediatric brain cancer is the leading cause of disease-related mortality in children, and many aggressive tumors still lack effective treatment strategies. We characterized aberrant alternative splicing across pediatric brain tumors, identifying pediatric high-grade gliomas (HGGs) among the most heterogeneous. Annotating these events with UniProt, we identified 11,940 splice events in 5,368 genes leading to potential protein function changes. We discovered CDC-like kinase 1 (CLK1) is aberrantly spliced to favor exon 4 inclusion, resulting in a gain of two phosphorylation sites and subsequent activation. Inhibition of CLK1 with Cirtuvivint significantly decreased both cell viability and proliferation in the pediatric HGG KNS-42 cell line. Morpholino-mediated depletion of CLK1 exon 4 splicing reduced RNA expression, protein abundance, and cell viability with concurrent differential expression of 78 cancer genes and differential splicing at functional sites in 193 cancer genes. Our findings highlight a dependency of pediatric HGGs on CLK1 and represent a promising therapeutic strategy.
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Affiliation(s)
- Ammar S Naqvi
- Center for Data-Driven Discovery in Biomedicine, Children's Hospital of Philadelphia, Philadelphia, PA, USA
- Division of Neurosurgery, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Ryan J Corbett
- Center for Data-Driven Discovery in Biomedicine, Children's Hospital of Philadelphia, Philadelphia, PA, USA
- Division of Neurosurgery, Children's Hospital of Philadelphia, Philadelphia, PA, USA
- Division of Oncology and Center for Childhood Cancer Research, Children's Hospital of Philadelphia, Philadelphia, PA
| | - Priyanka Seghal
- Division of Cancer Pathobiology, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Karina L Conkrite
- Division of Oncology and Center for Childhood Cancer Research, Children's Hospital of Philadelphia, Philadelphia, PA
| | - Komal S Rathi
- Center for Data-Driven Discovery in Biomedicine, Children's Hospital of Philadelphia, Philadelphia, PA, USA
- Division of Neurosurgery, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Brian M Ennis
- Center for Data-Driven Discovery in Biomedicine, Children's Hospital of Philadelphia, Philadelphia, PA, USA
- Division of Neurosurgery, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Katharina E Hayer
- Division of Oncology and Center for Childhood Cancer Research, Children's Hospital of Philadelphia, Philadelphia, PA
- Department of Biomedical and Health Informatics, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Bo Zhang
- Center for Data-Driven Discovery in Biomedicine, Children's Hospital of Philadelphia, Philadelphia, PA, USA
- Division of Neurosurgery, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Miguel A Brown
- Center for Data-Driven Discovery in Biomedicine, Children's Hospital of Philadelphia, Philadelphia, PA, USA
- Division of Neurosurgery, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Daniel P Miller
- Center for Data-Driven Discovery in Biomedicine, Children's Hospital of Philadelphia, Philadelphia, PA, USA
- Division of Neurosurgery, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Adam A Kraya
- Center for Data-Driven Discovery in Biomedicine, Children's Hospital of Philadelphia, Philadelphia, PA, USA
- Division of Neurosurgery, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Kaleem L Coleman
- Center for Cancer and Immunology Research, Children's National Hospital, Washington, D.C., USA
| | - Joseph M Dybas
- Center for Data-Driven Discovery in Biomedicine, Children's Hospital of Philadelphia, Philadelphia, PA, USA
- Division of Neurosurgery, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Zhuangzhuang Geng
- Center for Data-Driven Discovery in Biomedicine, Children's Hospital of Philadelphia, Philadelphia, PA, USA
- Division of Neurosurgery, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Christopher Blackden
- Center for Data-Driven Discovery in Biomedicine, Children's Hospital of Philadelphia, Philadelphia, PA, USA
- Division of Neurosurgery, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Shehbeel Arif
- Center for Data-Driven Discovery in Biomedicine, Children's Hospital of Philadelphia, Philadelphia, PA, USA
- Division of Neurosurgery, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Antonia Chroni
- Center for Data-Driven Discovery in Biomedicine, Children's Hospital of Philadelphia, Philadelphia, PA, USA
- Division of Neurosurgery, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Aditya Lahiri
- Department of Biomedical and Health Informatics, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Madison L Hollawell
- Center for Data-Driven Discovery in Biomedicine, Children's Hospital of Philadelphia, Philadelphia, PA, USA
- Division of Neurosurgery, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Phillip B Storm
- Center for Data-Driven Discovery in Biomedicine, Children's Hospital of Philadelphia, Philadelphia, PA, USA
- Division of Neurosurgery, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Dalia Haydar
- Center for Cancer and Immunology Research, Children's National Hospital, Washington, D.C., USA
- Department of Pediatrics, The George Washington University School of Medicine and Health Sciences, Washington, D.C., USA
| | - Jessica B Foster
- Division of Oncology and Center for Childhood Cancer Research, Children's Hospital of Philadelphia, Philadelphia, PA
- Department of Pediatrics, University of Pennsylvania, Philadelphia, PA, USA
| | - Mateusz Koptyra
- Center for Data-Driven Discovery in Biomedicine, Children's Hospital of Philadelphia, Philadelphia, PA, USA
- Division of Neurosurgery, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Peter J Madsen
- Center for Data-Driven Discovery in Biomedicine, Children's Hospital of Philadelphia, Philadelphia, PA, USA
- Division of Neurosurgery, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Sharon J Diskin
- Division of Oncology and Center for Childhood Cancer Research, Children's Hospital of Philadelphia, Philadelphia, PA
- Department of Biomedical and Health Informatics, Children's Hospital of Philadelphia, Philadelphia, PA, USA
- Department of Pediatrics, University of Pennsylvania, Philadelphia, PA, USA
| | - Andrei Thomas-Tikhonenko
- Division of Oncology and Center for Childhood Cancer Research, Children's Hospital of Philadelphia, Philadelphia, PA
- Division of Cancer Pathobiology, Children's Hospital of Philadelphia, Philadelphia, PA, USA
- Department of Pediatrics, University of Pennsylvania, Philadelphia, PA, USA
- Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Adam C Resnick
- Center for Data-Driven Discovery in Biomedicine, Children's Hospital of Philadelphia, Philadelphia, PA, USA
- Division of Neurosurgery, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Jo Lynne Rokita
- Center for Data-Driven Discovery in Biomedicine, Children's Hospital of Philadelphia, Philadelphia, PA, USA
- Division of Neurosurgery, Children's Hospital of Philadelphia, Philadelphia, PA, USA
- Center for Cancer and Immunology Research, Children's National Hospital, Washington, D.C., USA
- Department of Pediatrics, The George Washington University School of Medicine and Health Sciences, Washington, D.C., USA
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Valerio J, Borro M, Proietti E, Pisciotta L, Olarinde IO, Fernandez Gomez M, Alvarez Pinzon AM. Systematic Review and Clinical Insights: The Role of the Ketogenic Diet in Managing Glioblastoma in Cancer Neuroscience. J Pers Med 2024; 14:929. [PMID: 39338183 PMCID: PMC11433106 DOI: 10.3390/jpm14090929] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2024] [Revised: 08/02/2024] [Accepted: 08/24/2024] [Indexed: 09/30/2024] Open
Abstract
Recent scientific research has shown that the ketogenic diet may have potential benefits in a variety of medical fields, which has led to the diet receiving a substantial amount of attention. Clinical and experimental research on brain tumors has shown that the ketogenic diet has a satisfactory safety profile. This safety profile has been established in a variety of applications, including the management of obesity and the treatment of drug-resistant epileptic cases. However, in human studies, the impact of ketogenic therapy on the growth of tumors and the life expectancy of patients has not provided results that are well characterized. Consequently, our purpose is to improve the comprehension of these features by succinctly presenting the developments and conclusions that have been gained from the most recent study that pertains to this non-pharmacological technique. According to the findings of our study, patients with brain tumors who stick to a ketogenic diet are more likely to experience improved survival rates. However, it is required to conduct additional research on humans in order to more accurately define the anti-tumor efficiency of this diet as well as the underlying processes that support the therapeutic effects of this dieting regimen.
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Affiliation(s)
- Jose Valerio
- Neurosurgery Oncology Center of Excellence, Neurosurgery Department, Miami Neuroscience Center at Larkin, South Miami, FL 33143, USA
| | - Matteo Borro
- Internal Medicine Unit, Department of Internal Medicine, IRCCS Ospedale Policlinico San Martino, Largo R. Benzi 10, 16132 Genova, Italy
| | - Elisa Proietti
- Department of Internal Medicine (DIMI), University of Genova, Viale Benedetto XV, 6, 16132 Genova, Italy
| | - Livia Pisciotta
- Department of Internal Medicine (DIMI), University of Genova, Viale Benedetto XV, 6, 16132 Genova, Italy
- Operative Unit of Dietetics and Clinical Nutrition, Department of Internal Medicine, IRCCS Ospedale Policlinico San Martino, Largo R. Benzi 10, 16132 Genova, Italy
| | - Immanuel O Olarinde
- Neurosurgery Department, Latino America Valerio Foundation, Weston, FL 33331, USA
| | | | - Andres Mauricio Alvarez Pinzon
- MCIFAU Cancer Center of Excellence, Memorial Cancer Institute, Memorial Healthcare System, Hollywood, FL 33021, USA
- Cancer Neuroscience Program, The Institute of Neuroscience of Castilla y León (INCYL), Universidad de Salamanca, 37007 Salamanca, Spain
- Institute for Human Health and Disease Intervention, Division of Research, FAU Charles E. Schmidt College of Medicine, Florida Atlantic University, Boca Raton, FL 33431, USA
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Lucke-Wold B, Rangwala BS, Shafique MA, Siddiq MA, Mustafa MS, Danish F, Nasrullah RMU, Zainab N, Haseeb A. Focus on current and emerging treatment options for glioma: A comprehensive review. World J Clin Oncol 2024; 15:482-495. [PMID: 38689623 PMCID: PMC11056857 DOI: 10.5306/wjco.v15.i4.482] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/22/2023] [Revised: 01/22/2024] [Accepted: 02/28/2024] [Indexed: 04/22/2024] Open
Abstract
This comprehensive review delves into the current updates and challenges associated with the management of low-grade gliomas (LGG), the predominant primary tumors in the central nervous system. With a general incidence rate of 5.81 per 100000, gliomas pose a significant global concern, necessitating advancements in treatment techniques to reduce mortality and morbidity. This review places a particular focus on immunotherapies, discussing promising agents such as Zotiraciclib and Lerapolturev. Zotiraciclib, a CDK9 inhibitor, has demonstrated efficacy in glioblastoma treatment in preclinical and clinical studies, showing its potential as a therapeutic breakthrough. Lerapolturev, a viral immunotherapy, induces inflammation in glioblastoma and displays positive outcomes in both adult and pediatric patients. Exploration of immunotherapy extends to Pembrolizumab, Nivolumab, and Entrectinib, revealing the challenges and variabilities in patient responses. Despite promising preclinical data, the monoclonal antibody Depatuxizumab has proven ineffective in glioblastoma treatment, emphasizing the critical need to understand resistance mechanisms. The review also covers the success of radiation therapy in pediatric LGG, with evolving techniques, such as proton therapy, showing potential improvements in patient quality of life. Surgical treatment is discussed in the context of achieving a balance between preserving the patient's quality of life and attaining gross total resection, with the extent of surgical resection significantly influencing the survival outcomes. In addition to advancements in cancer vaccine development, this review highlights the evolving landscape of LGG treatment, emphasizing a shift toward personalized and targeted therapies. Ongoing research is essential for refining strategies and enhancing outcomes in the management of LGG.
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Affiliation(s)
- Brandon Lucke-Wold
- Department of Neurosurgery, University of Florida, Gainesville, FL 32608, United States
| | | | | | - Mohammad Arham Siddiq
- Department of Neurosurgery, Jinnah Sindh Medical University, Karachi 75510, Pakistan
| | | | - Fnu Danish
- Department of Neurosurgery, Jinnah Sindh Medical University, Karachi 75510, Pakistan
| | | | - Noor Zainab
- Department of Neurosurgery, Army Medical College, Rawalpindi 46000, Pakistan
| | - Abdul Haseeb
- Department of Neurosurgery, Jinnah Sindh Medical University, Karachi 75510, Pakistan
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Hargrave DR, Terashima K, Hara J, Kordes UR, Upadhyaya SA, Sahm F, Bouffet E, Packer RJ, Witt O, Sandalic L, Kieloch A, Russo M, Cohen KJ. Phase II Trial of Dabrafenib Plus Trametinib in Relapsed/Refractory BRAF V600-Mutant Pediatric High-Grade Glioma. J Clin Oncol 2023; 41:5174-5183. [PMID: 37643378 PMCID: PMC10666989 DOI: 10.1200/jco.23.00558] [Citation(s) in RCA: 31] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2023] [Revised: 05/16/2023] [Accepted: 06/28/2023] [Indexed: 08/31/2023] Open
Abstract
PURPOSE BRAF V600 mutation is detected in 5%-10% of pediatric high-grade gliomas (pHGGs), and effective treatments are limited. In previous trials, dabrafenib as monotherapy or in combination with trametinib demonstrated activity in children and adults with relapsed/refractory BRAF V600-mutant HGG. METHODS This phase II study evaluated dabrafenib plus trametinib in patients with relapsed/refractory BRAF V600-mutant pHGG. The primary objective was overall response rate (ORR) by independent review by Response Assessment in Neuro-Oncology criteria. Secondary objectives included ORR by investigator determination, duration of response (DOR), progression-free survival, overall survival (OS), and safety. RESULTS A total of 41 pediatric patients with previously treated BRAF V600-mutant HGG were enrolled. At primary analysis, median follow-up was 25.1 months, and 51% of patients remained on treatment. Sixteen of 20 discontinuations were due to progressive disease in this relapsed/refractory pHGG population. Independently assessed ORR was 56% (95% CI, 40 to 72). Median DOR was 22.2 months (95% CI, 7.6 months to not reached [NR]). Fourteen deaths were reported. Median OS was 32.8 months (95% CI, 19.2 months to NR). The most common all-cause adverse events (AEs) were pyrexia (51%), headache (34%), and dry skin (32%). Two patients (5%) had AEs (both rash) leading to discontinuation. CONCLUSION In relapsed/refractory BRAF V600-mutant pHGG, dabrafenib plus trametinib improved ORR versus previous trials of chemotherapy in molecularly unselected patients with pHGG and was associated with durable responses and encouraging survival. These findings suggest that dabrafenib plus trametinib is a promising targeted therapy option for children and adolescents with relapsed/refractory BRAF V600-mutant HGG.
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Affiliation(s)
- Darren R Hargrave
- UCL Great Ormond Street Institute of Child Health, London, United Kingdom
| | - Keita Terashima
- National Center for Child Health and Development, Tokyo, Japan
| | | | - Uwe R Kordes
- University Medical Center Eppendorf, Hamburg, Germany
| | | | - Felix Sahm
- Department of Neuropathology, University Hospital Heidelberg, Heidelberg, Germany
- CCU Neuropathology, German Consortium for Translational Cancer Research (DKTK), German Cancer Research Center (DKFZ), Heidelberg University Hospital, Heidelberg, Germany
- Hopp Children's Cancer Center (KiTZ), German Cancer Research Center (DKFZ), Heidelberg University Hospital, Heidelberg, Germany
| | - Eric Bouffet
- The Hospital for Sick Children, University of Toronto, Toronto, ON, Canada
| | | | - Olaf Witt
- Hopp Children's Cancer Center (KiTZ), German Cancer Research Center (DKFZ), Heidelberg University Hospital, Heidelberg, Germany
| | | | | | - Mark Russo
- Novartis Pharmaceuticals Corporation, East Hanover, NJ
| | - Kenneth J Cohen
- The Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, Baltimore, MD
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