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Hernández-Verdin I, Kirasic E, Wienand K, Mokhtari K, Eimer S, Loiseau H, Rousseau A, Paillassa J, Ahle G, Lerintiu F, Uro-Coste E, Oberic L, Figarella-Branger D, Chinot O, Gauchotte G, Taillandier L, Marolleau JP, Polivka M, Adam C, Ursu R, Schmitt A, Barillot N, Nichelli L, Lozano-Sánchez F, Ibañez-Juliá MJ, Peyre M, Mathon B, Abada Y, Charlotte F, Davi F, Stewart C, de Reyniès A, Choquet S, Soussain C, Houillier C, Chapuy B, Hoang-Xuan K, Alentorn A. Molecular and clinical diversity in primary central nervous system lymphoma. Ann Oncol 2023; 34:186-199. [PMID: 36402300 DOI: 10.1016/j.annonc.2022.11.002] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [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: 08/31/2022] [Accepted: 11/08/2022] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND Primary central nervous system lymphoma (PCNSL) is a rare and distinct entity within diffuse large B-cell lymphoma presenting with variable response rates probably to underlying molecular heterogeneity. PATIENTS AND METHODS To identify and characterize PCNSL heterogeneity and facilitate clinical translation, we carried out a comprehensive multi-omic analysis [whole-exome sequencing, RNA sequencing (RNA-seq), methylation sequencing, and clinical features] in a discovery cohort of 147 fresh-frozen (FF) immunocompetent PCNSLs and a validation cohort of formalin-fixed, paraffin-embedded (FFPE) 93 PCNSLs with RNA-seq and clinico-radiological data. RESULTS Consensus clustering of multi-omic data uncovered concordant classification of four robust, non-overlapping, prognostically significant clusters (CS). The CS1 and CS2 groups presented an immune-cold hypermethylated profile but a distinct clinical behavior. The 'immune-hot' CS4 group, enriched with mutations increasing the Janus kinase (JAK)-signal transducer and activator of transcription (STAT) and nuclear factor-κB activity, had the most favorable clinical outcome, while the heterogeneous-immune CS3 group had the worse prognosis probably due to its association with meningeal infiltration and enriched HIST1H1E mutations. CS1 was characterized by high Polycomb repressive complex 2 activity and CDKN2A/B loss leading to higher proliferation activity. Integrated analysis on proposed targets suggests potential use of immune checkpoint inhibitors/JAK1 inhibitors for CS4, cyclin D-Cdk4,6 plus phosphoinositide 3-kinase (PI3K) inhibitors for CS1, lenalidomide/demethylating drugs for CS2, and enhancer of zeste 2 polycomb repressive complex 2 subunit (EZH2) inhibitors for CS3. We developed an algorithm to identify the PCNSL subtypes using RNA-seq data from either FFPE or FF tissue. CONCLUSIONS The integration of genome-wide data from multi-omic data revealed four molecular patterns in PCNSL with a distinctive prognostic impact that provides a basis for future clinical stratification and subtype-based targeted interventions.
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Affiliation(s)
- I Hernández-Verdin
- Institut du Cerveau-Paris Brain Institute-ICM, Inserm, Sorbonne Université, CNRS, Paris, France
| | - E Kirasic
- Institut du Cerveau-Paris Brain Institute-ICM, Inserm, Sorbonne Université, CNRS, Paris, France
| | - K Wienand
- Department of Hematology and Medical Oncology, University Medical Center Göttingen, Göttingen, Germany; Department of Hematology, Oncology and Cancer Immunology, Campus Benjamin Franklin, Charité-Universitätsmedizin Berlin, Berlin, Germany; Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
| | - K Mokhtari
- Institut du Cerveau-Paris Brain Institute-ICM, Inserm, Sorbonne Université, CNRS, Paris, France; Department of Neuropathology, Groupe Hospitalier Pitié Salpêtrière, APHP, Paris, France
| | - S Eimer
- Department of Pathology, CHU de Bordeaux, Hôpital Pellegrin, Bordeaux, France
| | - H Loiseau
- Department of Neurosurgery, Bordeaux University Hospital Center, Pellegrin Hospital, Bordeaux, France; EA 7435-IMOTION, University of Bordeaux, Bordeaux, France
| | - A Rousseau
- Department of Pathology, PBH, CHU Angers, Angers, France; CRCINA, Université de Nantes-université d'Angers, Angers, France
| | - J Paillassa
- Department of Hematology, CHU Angers, Angers, France
| | - G Ahle
- Department of Neurology, Hôpitaux Civils de Colmar, Colmar, France
| | - F Lerintiu
- Department of Neuropathology, Hôpitaux Civils de Colmar, Strasbourg, France
| | - E Uro-Coste
- Department of Pathology, CHU de Toulouse, IUC-Oncopole, Toulouse, France; INSERM U1037, Cancer Research Center of Toulouse (CRCT), Toulouse, France; Université Toulouse III Paul Sabatier, Toulouse, France
| | - L Oberic
- Department of Hematology, IUC Toulouse Oncopole, Toulouse, France
| | - D Figarella-Branger
- Neuropathology Department, University Hospital Timone, Aix Marseille University, Marseille, France; Inst Neurophysiopathol, CNRS, INP, Aix-Marseille University, Marseille, France
| | - O Chinot
- Department of Neuro-oncology, CHU Timone, APHM, Marseille, France; Institute of NeuroPhysiopathology, CNRS, INP, Aix-Marseille University, Marseille, France
| | - G Gauchotte
- Department of Biopathology, CHRU Nancy, CHRU/ICL, Bâtiment BBB, Vandoeuvre-lès-Nancy, France; Department of Legal Medicine, CHRU Nancy, Vandoeuvre-lès-Nancy, France; INSERM U1256, University of Lorraine, Vandoeuvre-lès-Nancy, France; Centre de Ressources Biologiques, BB-0033-00035, CHRU, Nancy, France
| | - L Taillandier
- Department of Neuro-oncology, CHRU-Nancy, Université de Lorraine, Nancy, France
| | - J-P Marolleau
- Department of Hematology, CHU Amiens-Picardie, Amiens, France
| | - M Polivka
- Department of Anatomopathology, Lariboisière Hospital, Assistance Publique-Hopitaux de Paris, University of Paris, Paris, France
| | - C Adam
- Pathology Department, Bicêtre University Hospital, Public Hospital Network of Paris, Le Kremlin Bicêtre, France
| | - R Ursu
- Department of Neurology, Université de Paris, AP-HP, Hôpital Saint Louis, Paris, France
| | - A Schmitt
- Department of Hematology, Institut Bergonié Hospital, Bordeaux, France
| | - N Barillot
- Institut du Cerveau-Paris Brain Institute-ICM, Inserm, Sorbonne Université, CNRS, Paris, France
| | - L Nichelli
- Department of Neuroradiology, Sorbonne Université, Assistance Publique-Hôpitaux de Paris, Groupe Hospitalier Pitié-Salpêtrière-Charles Foix, Paris, France
| | - F Lozano-Sánchez
- Department of Neurology-2, Sorbonne Université, Assistance Publique-Hôpitaux de Paris, Groupe Hospitalier Pitié-Salpêtrière-Charles Foix, Paris, France
| | | | - M Peyre
- Institut du Cerveau-Paris Brain Institute-ICM, Inserm, Sorbonne Université, CNRS, Paris, France; Department of Neurosurgery, Sorbonne Université, Assistance Publique-Hôpitaux de Paris, Groupe Hospitalier Pitié-Salpêtrière-Charles Foix, Paris, France
| | - B Mathon
- Institut du Cerveau-Paris Brain Institute-ICM, Inserm, Sorbonne Université, CNRS, Paris, France; Department of Neurosurgery, Sorbonne Université, Assistance Publique-Hôpitaux de Paris, Groupe Hospitalier Pitié-Salpêtrière-Charles Foix, Paris, France
| | - Y Abada
- Department of Neurology-2, Sorbonne Université, Assistance Publique-Hôpitaux de Paris, Groupe Hospitalier Pitié-Salpêtrière-Charles Foix, Paris, France
| | - F Charlotte
- Department Pathology, Hôpital Pitié-Salpêtrière and Sorbonne University, Paris, France
| | - F Davi
- Department Hematology, APHP, Hôpital Pitié-Salpêtrière and Sorbonne University, Paris, France
| | - C Stewart
- Department Broad Institute of MIT and Harvard, Cambridge, USA
| | - A de Reyniès
- Department INSERM UMR_S1138-Centre de Recherche des Cordeliers-Université Pierre et Marie Curie et Université Paris Descartes, Paris, France
| | - S Choquet
- Department Pathology, Hôpital Pitié-Salpêtrière and Sorbonne University, Paris, France
| | - C Soussain
- Department Hematology Unit, Institut Curie, Saint-Cloud, France
| | - C Houillier
- Department of Neurology-2, Sorbonne Université, Assistance Publique-Hôpitaux de Paris, Groupe Hospitalier Pitié-Salpêtrière-Charles Foix, Paris, France
| | - B Chapuy
- Department of Hematology and Medical Oncology, University Medical Center Göttingen, Göttingen, Germany; Department of Hematology, Oncology and Cancer Immunology, Campus Benjamin Franklin, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - K Hoang-Xuan
- Institut du Cerveau-Paris Brain Institute-ICM, Inserm, Sorbonne Université, CNRS, Paris, France; Department of Neurology-2, Sorbonne Université, Assistance Publique-Hôpitaux de Paris, Groupe Hospitalier Pitié-Salpêtrière-Charles Foix, Paris, France
| | - A Alentorn
- Institut du Cerveau-Paris Brain Institute-ICM, Inserm, Sorbonne Université, CNRS, Paris, France; Department of Neurology-2, Sorbonne Université, Assistance Publique-Hôpitaux de Paris, Groupe Hospitalier Pitié-Salpêtrière-Charles Foix, Paris, France.
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