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White K, Connor K, Meylan M, Bougoüin A, Salvucci M, Bielle F, O'Farrell AC, Sweeney K, Weng L, Bergers G, Dicker P, Ashley DM, Lipp ES, Low JT, Zhao J, Wen P, Prins R, Verreault M, Idbaih A, Biswas A, Prehn JHM, Lambrechts D, Arijs I, Lodi F, Dilcan G, Lamfers M, Leenstra S, Fabro F, Ntafoulis I, Kros JM, Cryan J, Brett F, Quissac E, Beausang A, MacNally S, O'Halloran P, Clerkin J, Bacon O, Kremer A, Chi Yen RT, Varn FS, Verhaak RGW, Sautès-Fridman C, Fridman WH, Byrne AT. Identification, validation and biological characterisation of novel glioblastoma tumour microenvironment subtypes: implications for precision immunotherapy. Ann Oncol 2023; 34:300-314. [PMID: 36494005 DOI: 10.1016/j.annonc.2022.11.008] [Citation(s) in RCA: 24] [Impact Index Per Article: 24.0] [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: 05/05/2022] [Revised: 11/14/2022] [Accepted: 11/15/2022] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND New precision medicine therapies are urgently required for glioblastoma (GBM). However, to date, efforts to subtype patients based on molecular profiles have failed to direct treatment strategies. We hypothesised that interrogation of the GBM tumour microenvironment (TME) and identification of novel TME-specific subtypes could inform new precision immunotherapy treatment strategies. MATERIALS AND METHODS A refined and validated microenvironment cell population (MCP) counter method was applied to >800 GBM patient tumours (GBM-MCP-counter). Specifically, partition around medoids (PAM) clustering of GBM-MCP-counter scores in the GLIOTRAIN discovery cohort identified three novel patient clusters, uniquely characterised by TME composition, functional orientation markers and immune checkpoint proteins. Validation was carried out in three independent GBM-RNA-seq datasets. Neoantigen, mutational and gene ontology analysis identified mutations and uniquely altered pathways across subtypes. The longitudinal Glioma Longitudinal AnalySiS (GLASS) cohort and three immunotherapy clinical trial cohorts [treatment with neoadjuvant/adjuvant anti-programmed cell death protein 1 (PD-1) or PSVRIPO] were further interrogated to assess subtype alterations between primary and recurrent tumours and to assess the utility of TME classifiers as immunotherapy biomarkers. RESULTS TMEHigh tumours (30%) displayed elevated lymphocyte, myeloid cell immune checkpoint, programmed cell death protein 1 (PD-1) and cytotoxic T-lymphocyte-associated protein 4 transcripts. TMEHigh/mesenchymal+ patients featured tertiary lymphoid structures. TMEMed (46%) tumours were enriched for endothelial cell gene expression profiles and displayed heterogeneous immune populations. TMELow (24%) tumours were manifest as an 'immune-desert' group. TME subtype transitions upon recurrence were identified in the longitudinal GLASS cohort. Assessment of GBM immunotherapy trial datasets revealed that TMEHigh patients receiving neoadjuvant anti-PD-1 had significantly increased overall survival (P = 0.04). Moreover, TMEHigh patients treated with adjuvant anti-PD-1 or oncolytic virus (PVSRIPO) showed a trend towards improved survival. CONCLUSIONS We have established a novel TME-based classification system for application in intracranial malignancies. TME subtypes represent canonical 'termini a quo' (starting points) to support an improved precision immunotherapy treatment approach.
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Affiliation(s)
- K White
- Department of Physiology and Medical Physics, Royal College of Surgeons in Ireland, Dublin, Ireland
| | - K Connor
- Department of Physiology and Medical Physics, Royal College of Surgeons in Ireland, Dublin, Ireland
| | - M Meylan
- Centre de Recherche des Cordeliers, INSERM, Sorbonne Université, USPC, Université de Paris, Paris, France
| | - A Bougoüin
- Centre de Recherche des Cordeliers, INSERM, Sorbonne Université, USPC, Université de Paris, Paris, France
| | - M Salvucci
- Department of Physiology and Medical Physics, Royal College of Surgeons in Ireland, Dublin, Ireland
| | - F Bielle
- Paris Brain Institute (ICM), CNRS UMR 7225, Inserm U 1127, UPMC-P6 UMR S 1127, Hôpital de la Pitié-Salpêtrière, Paris, France
| | - A C O'Farrell
- Department of Physiology and Medical Physics, Royal College of Surgeons in Ireland, Dublin, Ireland
| | - K Sweeney
- National Centre of Neurosurgery, Beaumont Hospital, Dublin, Ireland
| | - L Weng
- VIB-KU Leuven Center for Cancer Biology, Department of Oncology, Leuven, Belgium
| | - G Bergers
- VIB-KU Leuven Center for Cancer Biology, Department of Oncology, Leuven, Belgium
| | - P Dicker
- Epidemiology & Public Health, Royal College of Surgeons in Ireland, Dublin, Ireland
| | - D M Ashley
- Duke Cancer Institute, Duke University, Durham, USA
| | - E S Lipp
- Duke Cancer Institute, Duke University, Durham, USA
| | - J T Low
- Duke Cancer Institute, Duke University, Durham, USA
| | - J Zhao
- Department of Systems Biology at Columbia University, New York, USA
| | - P Wen
- Center for Neuro-Oncology, Dana-Farber Cancer Institute, Boston, USA
| | - R Prins
- Department of Medical and Molecular Pharmacology, David Geffen School of Medicine, University of California, Los Angeles, USA
| | - M Verreault
- Paris Brain Institute (ICM), CNRS UMR 7225, Inserm U 1127, UPMC-P6 UMR S 1127, Hôpital de la Pitié-Salpêtrière, Paris, France
| | - A Idbaih
- Sorbonne Université, Inserm, CNRS, UMR S 1127, Paris Brain Institute (ICM), AP-HP, Hôpitaux Universitaires La Pitié Salpêtrière-Charles Foix, Paris, France
| | - A Biswas
- Department of Physiology and Medical Physics, Royal College of Surgeons in Ireland, Dublin, Ireland
| | - J H M Prehn
- Department of Physiology and Medical Physics, Royal College of Surgeons in Ireland, Dublin, Ireland
| | - D Lambrechts
- Laboratory for Translational Genetics, Department of Human Genetics, Leuven, Belgium; VIB Center for Cancer Biology, Leuven, Belgium
| | - I Arijs
- Laboratory for Translational Genetics, Department of Human Genetics, Leuven, Belgium; VIB Center for Cancer Biology, Leuven, Belgium
| | - F Lodi
- Laboratory for Translational Genetics, Department of Human Genetics, Leuven, Belgium; VIB Center for Cancer Biology, Leuven, Belgium
| | - G Dilcan
- Laboratory for Translational Genetics, Department of Human Genetics, Leuven, Belgium; VIB Center for Cancer Biology, Leuven, Belgium
| | - M Lamfers
- Department of Neurosurgery, Brain Tumor Center, Erasmus University Medical Center, Rotterdam, the Netherlands
| | - S Leenstra
- Department of Neurosurgery, Brain Tumor Center, Erasmus University Medical Center, Rotterdam, the Netherlands
| | - F Fabro
- Department of Neurosurgery, Brain Tumor Center, Erasmus University Medical Center, Rotterdam, the Netherlands
| | - I Ntafoulis
- Department of Neurosurgery, Brain Tumor Center, Erasmus University Medical Center, Rotterdam, the Netherlands
| | - J M Kros
- Department of Pathology, Erasmus Medical Center, Rotterdam, the Netherlands
| | - J Cryan
- Department of Neuropathology, Beaumont Hospital, Dublin, Ireland
| | - F Brett
- Department of Neuropathology, Beaumont Hospital, Dublin, Ireland
| | - E Quissac
- Paris Brain Institute (ICM), CNRS UMR 7225, Inserm U 1127, UPMC-P6 UMR S 1127, Hôpital de la Pitié-Salpêtrière, Paris, France
| | - A Beausang
- Department of Neuropathology, Beaumont Hospital, Dublin, Ireland
| | - S MacNally
- National Centre of Neurosurgery, Beaumont Hospital, Dublin, Ireland
| | - P O'Halloran
- National Centre of Neurosurgery, Beaumont Hospital, Dublin, Ireland
| | - J Clerkin
- National Centre of Neurosurgery, Beaumont Hospital, Dublin, Ireland
| | - O Bacon
- Department of Neuropathology, Beaumont Hospital, Dublin, Ireland
| | - A Kremer
- Information Technology for Translational Medicine (ITTM), Luxembourg, Luxembourg
| | - R T Chi Yen
- Information Technology for Translational Medicine (ITTM), Luxembourg, Luxembourg
| | - F S Varn
- The Jackson Laboratory for Genomic Medicine, Farmington, USA
| | - R G W Verhaak
- The Jackson Laboratory for Genomic Medicine, Farmington, USA; Department of Neurosurgery, Cancer Center Amsterdam, Amsterdam University Medical Centers, VU University Medical Center, Amsterdam, the Netherlands
| | - C Sautès-Fridman
- Centre de Recherche des Cordeliers, INSERM, Sorbonne Université, USPC, Université de Paris, Paris, France
| | - W H Fridman
- Centre de Recherche des Cordeliers, INSERM, Sorbonne Université, USPC, Université de Paris, Paris, France
| | - A T Byrne
- Department of Physiology and Medical Physics, Royal College of Surgeons in Ireland, Dublin, Ireland.
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Flanagan L, Kehoe J, Fay J, Bacon O, Lindner AU, Kay EW, Deasy J, McNamara DA, Prehn JHM. High levels of X-linked Inhibitor-of-Apoptosis Protein (XIAP) are indicative of radio chemotherapy resistance in rectal cancer. Radiat Oncol 2015; 10:131. [PMID: 26071313 PMCID: PMC4480907 DOI: 10.1186/s13014-015-0437-1] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2015] [Accepted: 06/05/2015] [Indexed: 01/04/2023] Open
Abstract
BACKGROUND The mainstay of treatment in rectal cancer is neoadjuvant radio chemotherapy prior to surgery, in an attempt to downstage the tumour, allowing for more complete removal during surgery. In 40 % of cases however, this neoadjuvant radio chemotherapy fails to achieve tumour regression, partly due insufficient apoptosis signaling. X-linked Inhibitor of Apoptosis Protein (XIAP) is an anti-apoptotic protein that has been reported to contribute to disease progression and chemotherapy resistance. METHODS We obtained rectal biopsy normal and matched tumour tissue from 29 rectal cancer patients with varying degrees of tumour regression, and using Western blot, examined anti-apoptotic XIAP and pro-apoptotic Smac protein levels in these tissues, with the aim to examine whether disturbed XIAP/Smac levels may be an indicator of neoadjuvant radio chemotherapy resistance. Expression of inhibitor of apoptosis proteins cIAP-1 and cIAP-2 was also examined. RESULTS We found that levels of XIAP increased in accordance with the degree of radio chemotherapy resistance of the tissue. Levels of this protein were also significantly higher in tumour tissue, compared to matched normal tissue in highly resistant tissue. In contrast, Smac protein levels did not increase with radio chemotherapy resistance, and the protein was similarly expressed in normal and tumour tissue, indicating a shift in the balance of these proteins. Post treatment surgical resection tissue was available for 8 patients. When we compared matched tissue pre- and post- radio chemotherapy we found that XIAP levels increased significantly during treatment in both normal and tumour tissue, while Smac levels did not change. cIAP-1 and cIAP-2 levels were not differentially expressed in varying degrees of radio chemotherapy resistance, and neoadjuvant therapy did not alter expression of these proteins. CONCLUSION These data indicate that disturbance of the XIAP/Smac balance may be a driver of radio chemotherapy resistance, and hence high levels of XIAP may be a useful indicator of neoadjuvant radio chemotherapy resistance in rectal cancer. Moreover, as XIAP levels increase with radio chemotherapy it is possible that a subset of more resistant tumour cells survive this treatment and may be resistant to further adjuvant treatment. Patients with resistant tumours highly expressing XIAP may benefit from alternative treatment strategies, such as Smac mimetics post neoadjuvant radio chemotherapy.
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Affiliation(s)
- L Flanagan
- Department of Physiology and Medical Physics, Royal College of Surgeons in Ireland, 123 St. Stephen's Green, Dublin 2, Ireland. .,Centre for Systems Medicine, Royal College of Surgeons in Ireland, 123 St. Stephen's Green, Dublin 2, Ireland.
| | - J Kehoe
- Department of Physiology and Medical Physics, Royal College of Surgeons in Ireland, 123 St. Stephen's Green, Dublin 2, Ireland. .,Departments of Pathology, Beaumont Hospital, Dublin 9, Ireland. .,Departments of Surgery, Beaumont Hospital, Dublin 9, Ireland.
| | - J Fay
- Departments of Pathology, Beaumont Hospital, Dublin 9, Ireland.
| | - O Bacon
- Department of Physiology and Medical Physics, Royal College of Surgeons in Ireland, 123 St. Stephen's Green, Dublin 2, Ireland.
| | - A U Lindner
- Department of Physiology and Medical Physics, Royal College of Surgeons in Ireland, 123 St. Stephen's Green, Dublin 2, Ireland. .,Centre for Systems Medicine, Royal College of Surgeons in Ireland, 123 St. Stephen's Green, Dublin 2, Ireland.
| | - E W Kay
- Departments of Pathology, Beaumont Hospital, Dublin 9, Ireland.
| | - J Deasy
- Departments of Surgery, Beaumont Hospital, Dublin 9, Ireland.
| | - D A McNamara
- Departments of Surgery, Beaumont Hospital, Dublin 9, Ireland.
| | - J H M Prehn
- Department of Physiology and Medical Physics, Royal College of Surgeons in Ireland, 123 St. Stephen's Green, Dublin 2, Ireland. .,Centre for Systems Medicine, Royal College of Surgeons in Ireland, 123 St. Stephen's Green, Dublin 2, Ireland.
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