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Kohe S, Bennett C, Burté F, Adiamah M, Rose H, Worthington L, Scerif F, MacPherson L, Gill S, Hicks D, Schwalbe EC, Crosier S, Storer L, Lourdusamy A, Mitra D, Morgan PS, Dineen RA, Avula S, Pizer B, Wilson M, Davies N, Tennant D, Bailey S, Williamson D, Arvanitis TN, Grundy RG, Clifford SC, Peet AC. Metabolite profiles of medulloblastoma for rapid and non-invasive detection of molecular disease groups. EBioMedicine 2024; 100:104958. [PMID: 38184938 PMCID: PMC10808898 DOI: 10.1016/j.ebiom.2023.104958] [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: 08/04/2023] [Revised: 12/13/2023] [Accepted: 12/21/2023] [Indexed: 01/09/2024] Open
Abstract
BACKGROUND The malignant childhood brain tumour, medulloblastoma, is classified clinically into molecular groups which guide therapy. DNA-methylation profiling is the current classification 'gold-standard', typically delivered 3-4 weeks post-surgery. Pre-surgery non-invasive diagnostics thus offer significant potential to improve early diagnosis and clinical management. Here, we determine tumour metabolite profiles of the four medulloblastoma groups, assess their diagnostic utility using tumour tissue and potential for non-invasive diagnosis using in vivo magnetic resonance spectroscopy (MRS). METHODS Metabolite profiles were acquired by high-resolution magic-angle spinning NMR spectroscopy (MAS) from 86 medulloblastomas (from 59 male and 27 female patients), previously classified by DNA-methylation array (WNT (n = 9), SHH (n = 22), Group3 (n = 21), Group4 (n = 34)); RNA-seq data was available for sixty. Unsupervised class-discovery was performed and a support vector machine (SVM) constructed to assess diagnostic performance. The SVM classifier was adapted to use only metabolites (n = 10) routinely quantified from in vivo MRS data, and re-tested. Glutamate was assessed as a predictor of overall survival. FINDINGS Group-specific metabolite profiles were identified; tumours clustered with good concordance to their reference molecular group (93%). GABA was only detected in WNT, taurine was low in SHH and lipids were high in Group3. The tissue-based metabolite SVM classifier had a cross-validated accuracy of 89% (100% for WNT) and, adapted to use metabolites routinely quantified in vivo, gave a combined classification accuracy of 90% for SHH, Group3 and Group4. Glutamate predicted survival after incorporating known risk-factors (HR = 3.39, 95% CI 1.4-8.1, p = 0.025). INTERPRETATION Tissue metabolite profiles characterise medulloblastoma molecular groups. Their combination with machine learning can aid rapid diagnosis from tissue and potentially in vivo. Specific metabolites provide important information; GABA identifying WNT and glutamate conferring poor prognosis. FUNDING Children with Cancer UK, Cancer Research UK, Children's Cancer North and a Newcastle University PhD studentship.
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Affiliation(s)
- Sarah Kohe
- Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham, UK; Birmingham Children's Hospital, Birmingham, UK
| | - Christopher Bennett
- Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham, UK; Birmingham Children's Hospital, Birmingham, UK
| | - Florence Burté
- Wolfson Childhood Cancer Research Centre, Newcastle University Centre for Cancer, Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne, UK
| | - Magretta Adiamah
- Wolfson Childhood Cancer Research Centre, Newcastle University Centre for Cancer, Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne, UK
| | - Heather Rose
- Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham, UK; Birmingham Children's Hospital, Birmingham, UK
| | - Lara Worthington
- Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham, UK; Birmingham Children's Hospital, Birmingham, UK; RRPPS, University Hospital Birmingham, Birmingham, UK
| | - Fatma Scerif
- Wolfson Childhood Cancer Research Centre, Newcastle University Centre for Cancer, Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne, UK
| | | | - Simrandip Gill
- Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham, UK; Birmingham Children's Hospital, Birmingham, UK
| | - Debbie Hicks
- Wolfson Childhood Cancer Research Centre, Newcastle University Centre for Cancer, Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne, UK
| | - Edward C Schwalbe
- Wolfson Childhood Cancer Research Centre, Newcastle University Centre for Cancer, Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne, UK; Department of Applied Sciences, Northumbria University, Newcastle upon Tyne, UK
| | - Stephen Crosier
- Wolfson Childhood Cancer Research Centre, Newcastle University Centre for Cancer, Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne, UK
| | - Lisa Storer
- Children's Brain Tumour Research Centre, Queen's Medical Centre, University of Nottingham, Nottingham, UK
| | - Ambarasu Lourdusamy
- Children's Brain Tumour Research Centre, Queen's Medical Centre, University of Nottingham, Nottingham, UK
| | - Dipyan Mitra
- Wolfson Childhood Cancer Research Centre, Newcastle University Centre for Cancer, Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne, UK
| | - Paul S Morgan
- Children's Brain Tumour Research Centre, Queen's Medical Centre, University of Nottingham, Nottingham, UK
| | - Robert A Dineen
- Radiological Sciences, Division of Clinical Neuroscience, University of Nottingham, Nottingham, UK; Sir Peter Mansfield Imaging Centre, University of Nottingham, Nottingham, UK
| | | | | | - Martin Wilson
- Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham, UK; Birmingham Children's Hospital, Birmingham, UK
| | - Nigel Davies
- RRPPS, University Hospital Birmingham, Birmingham, UK
| | - Daniel Tennant
- Institute of Metabolism and Systems Research, University of Birmingham, UK
| | - Simon Bailey
- Wolfson Childhood Cancer Research Centre, Newcastle University Centre for Cancer, Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne, UK
| | - Daniel Williamson
- Wolfson Childhood Cancer Research Centre, Newcastle University Centre for Cancer, Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne, UK
| | - Theodoros N Arvanitis
- Department of Electronic, Electrical and Systems Engineering, University of Birmingham, UK
| | - Richard G Grundy
- Children's Brain Tumour Research Centre, Queen's Medical Centre, University of Nottingham, Nottingham, UK
| | - Steven C Clifford
- Wolfson Childhood Cancer Research Centre, Newcastle University Centre for Cancer, Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne, UK.
| | - Andrew C Peet
- Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham, UK; Birmingham Children's Hospital, Birmingham, UK.
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Adiamah M, Lindsey JC, Burté F, Kohe S, Morcavallo A, Blair H, Hill RM, Singh M, Crosier S, Zhang T, Maddocks O, Peet A, Chesler L, Hickson I, Maxwell R, Clifford SC. MEDB-79. MYC-driven upregulation of the de novo serine and glycine pathway is a novel therapeutic target for Group 3 MYC-amplified Medulloblastoma. Neuro Oncol 2022. [PMCID: PMC9164881 DOI: 10.1093/neuonc/noac079.453] [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] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
Despite advances in the molecular sub-classification and risk-stratification of medulloblastoma (MB), a subset of tumours remain refractory to current multimodal therapies. Group 3 (MBGroup3) patients represent around 25% of MBs, and amplification and elevated expression of MYC in this group correlates with dismal clinical outcomes. Since direct targeting of MYC remains elusive, understanding and exploiting metabolic dependencies in MYC-amplified MBGroup3 may reveal novel therapeutic opportunities. We engineered three independent regulable MYC-amplified MBGroup3 cell-based models, each harbouring doxycycline-inducible anti-MYC shRNAs (two independent species) or a non-silencing shRNA control. In all three models, MYC knockdown (KD) revealed persistent MYC-dependent cancer phenotypes, reduction in proliferation and cell cycle progression. We utilised 1H high-resolution magic angle spectroscopy (HRMAS) and stable isotope-resolved metabolomics to assess changes in intracellular metabolites and pathway dynamics when MYC expression was modulated. Profiling revealed consistent MYC-dependent changes in metabolite concentrations across models. Notably, glycine was consistently accumulated following MYC KD suggesting altered pathway dynamics. 13C-glucose tracing further revealed a reduction in glucose-derived serine and glycine (de novo synthesis) following MYC KD which was attributable to lower expression of PHGDH, the rate-limiting enzyme of this pathway. Furthermore, in human primary tumours, elevated expression of PHGDH was associated with MYC amplification and poorer survival outcomes. MYC expressing cells showed greater sensitivity to pharmacological inhibition of PHGDH compared to MYC KD (MBGroup3) and MBSHH subgroup cell lines in vitro. Critically, targeting PHGDH in vivo, using MYC-dependent xenografts and genetically engineered mouse models, consistently slowed tumour progression and increased survival. In summary, metabolic profiling has uncovered MYC-dependent metabolic alterations and revealed the de novo serine/glycine synthesis pathway as a novel and clinically relevant therapeutic target in MYC-amplified MBGroup3. Together, these findings reveal metabolic vulnerabilities of MYC-amplified MBGroup3 which represent novel therapeutic opportunities for this poor-prognosis disease group.
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Affiliation(s)
- Magretta Adiamah
- Newcastle University Centre for Cancer, Newcastle University , Newcastle , United Kingdom
| | - Janet C Lindsey
- Newcastle University Centre for Cancer, Newcastle University , Newcastle , United Kingdom
| | - Florence Burté
- Newcastle University Centre for Cancer, Newcastle University , Newcastle , United Kingdom
| | - Sarah Kohe
- Institute of Cancer and Genomic Sciences, University of Birmingham , Birmingham , United Kingdom
| | - Alaide Morcavallo
- Division of Clinical Studies, Institute of Cancer Research , London , United Kingdom
| | - Helen Blair
- Newcastle University Centre for Cancer, Newcastle University , Newcastle , United Kingdom
| | - Rebecca M Hill
- Newcastle University Centre for Cancer, Newcastle University , Newcastle , United Kingdom
| | - Mankaran Singh
- Newcastle University Centre for Cancer, Newcastle University , Newcastle , United Kingdom
| | - Stephen Crosier
- Newcastle University Centre for Cancer, Newcastle University , Newcastle , United Kingdom
| | - Tong Zhang
- Institute of Cancer Sciences, University of Glasgow , Glasgow , United Kingdom
| | - Oliver Maddocks
- Institute of Cancer Sciences, University of Glasgow , Glasgow , United Kingdom
| | - Andrew Peet
- Institute of Cancer and Genomic Sciences, University of Birmingham , Birmingham , United Kingdom
| | - Louis Chesler
- Division of Clinical Studies, Institute of Cancer Research , London , United Kingdom
| | - Ian Hickson
- Newcastle University Centre for Cancer, Newcastle University , Newcastle , United Kingdom
| | - Ross Maxwell
- Newcastle University Centre for Cancer, Newcastle University , Newcastle , United Kingdom
| | - Steven C Clifford
- Newcastle University Centre for Cancer, Newcastle University , Newcastle , United Kingdom
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Kohe SE, Babourina-Brooks B, Scerif F, Hicks D, Schwalbe EC, Crosier S, Lindsey J, Adiamah M, Storer LCD, Lourdusamy A, Gill SK, Bennett CD, Wilson M, Avula S, Mitra D, Dineen R, Bailey S, Williamson D, Grundy RG, Clifford SC, Peet AC. MBRS-29. IN-VIVO METABOLITE PROFILES FOR THE NON-INVASIVE AND RAPID IDENTIFICATION OF MOLECULAR SUBGROUP IN MEDULLOBLASTOMA. Neuro Oncol 2018. [DOI: 10.1093/neuonc/noy059.474] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Affiliation(s)
- Sarah E Kohe
- Institute of Cancer and Genomic SciencesUniversity of Birmingham, Birmingham, UK
- Birmingham Womens and Childrens NHS Foundation Trust, Birmingham, UK
| | - Ben Babourina-Brooks
- Institute of Cancer and Genomic SciencesUniversity of Birmingham, Birmingham, UK
- Birmingham Womens and Childrens NHS Foundation Trust, Birmingham, UK
| | - Fatma Scerif
- Northern Institute for Cancer Research, Newcastle University, Newcastle, UK
| | - Debbie Hicks
- Northern Institute for Cancer Research, Newcastle University, Newcastle, UK
| | - Ed C Schwalbe
- Northern Institute for Cancer Research, Newcastle University, Newcastle, UK
| | - Stephen Crosier
- Northern Institute for Cancer Research, Newcastle University, Newcastle, UK
| | - Janet Lindsey
- Northern Institute for Cancer Research, Newcastle University, Newcastle, UK
| | - Magretta Adiamah
- Northern Institute for Cancer Research, Newcastle University, Newcastle, UK
| | - Lisa C D Storer
- Children’s Brain Tumour Research Centre, University of Nottingham, Nottingham, UK
| | - Anbarasu Lourdusamy
- Children’s Brain Tumour Research Centre, University of Nottingham, Nottingham, UK
| | - Simrandip K Gill
- Institute of Cancer and Genomic SciencesUniversity of Birmingham, Birmingham, UK
- Birmingham Womens and Childrens NHS Foundation Trust, Birmingham, UK
| | - Christopher D Bennett
- Institute of Cancer and Genomic SciencesUniversity of Birmingham, Birmingham, UK
- Birmingham Womens and Childrens NHS Foundation Trust, Birmingham, UK
| | - Martin Wilson
- Institute of Cancer and Genomic SciencesUniversity of Birmingham, Birmingham, UK
- Birmingham Womens and Childrens NHS Foundation Trust, Birmingham, UK
| | | | - Dipayan Mitra
- Newcastle Hospitals NHS Foundation Trust, Newcastle, UK
| | - Rob Dineen
- Children’s Brain Tumour Research Centre, University of Nottingham, Nottingham, UK
| | - Simon Bailey
- Northern Institute for Cancer Research, Newcastle University, Newcastle, UK
- Great North Children’s Hospital, Newcastle, UK
| | - Daniel Williamson
- Northern Institute for Cancer Research, Newcastle University, Newcastle, UK
| | - Richard G Grundy
- Children’s Brain Tumour Research Centre, University of Nottingham, Nottingham, UK
| | - Steven C Clifford
- Northern Institute for Cancer Research, Newcastle University, Newcastle, UK
| | - Andrew C Peet
- Institute of Cancer and Genomic SciencesUniversity of Birmingham, Birmingham, UK
- Birmingham Womens and Childrens NHS Foundation Trust, Birmingham, UK
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James AD, Patel W, Butt Z, Adiamah M, Dakhel R, Latif A, Uggenti C, Swanton E, Imamura H, Siriwardena AK, Bruce JIE. The Plasma Membrane Calcium Pump in Pancreatic Cancer Cells Exhibiting the Warburg Effect Relies on Glycolytic ATP. J Biol Chem 2015; 290:24760-71. [PMID: 26294767 PMCID: PMC4598988 DOI: 10.1074/jbc.m115.668707] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2015] [Indexed: 12/15/2022] Open
Abstract
Evidence suggests that the plasma membrane Ca2+-ATPase (PMCA), which is critical for maintaining a low intracellular Ca2+ concentration ([Ca2+]i), utilizes glycolytically derived ATP in pancreatic ductal adenocarcinoma (PDAC) and that inhibition of glycolysis in PDAC cell lines results in ATP depletion, PMCA inhibition, and an irreversible [Ca2+]i overload. We explored whether this is a specific weakness of highly glycolytic PDAC by shifting PDAC cell (MIA PaCa-2 and PANC-1) metabolism from a highly glycolytic phenotype toward mitochondrial metabolism and assessing the effects of mitochondrial versus glycolytic inhibitors on ATP depletion, PMCA inhibition, and [Ca2+]i overload. The highly glycolytic phenotype of these cells was first reversed by depriving MIA PaCa-2 and PANC-1 cells of glucose and supplementing with α-ketoisocaproate or galactose. These culture conditions resulted in a significant decrease in both glycolytic flux and proliferation rate, and conferred resistance to ATP depletion by glycolytic inhibition while sensitizing cells to mitochondrial inhibition. Moreover, in direct contrast to cells exhibiting a high glycolytic rate, glycolytic inhibition had no effect on PMCA activity and resting [Ca2+]i in α-ketoisocaproate- and galactose-cultured cells, suggesting that the glycolytic dependence of the PMCA is a specific vulnerability of PDAC cells exhibiting the Warburg phenotype.
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Affiliation(s)
| | | | | | | | | | | | - Carolina Uggenti
- the Faculty of Medical and Human Sciences, University of Manchester, Manchester M13 9PT, United Kingdom
| | | | - Hiromi Imamura
- the Hakubi Center for Advanced Research and Graduate School of Biostudies, Kyoto University, Kyoto 606-8501, Japan, and
| | - Ajith K Siriwardena
- the Hepatobiliary Surgery Unit, Manchester Royal Infirmary, Manchester M13 9NT, United Kingdom
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