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Dufresne A, Attignon V, Ferrari A, Tonon L, Boyault S, Tabone‐Eglinger S, Cassier P, Trédan O, Corradini N, Vinceneux A, Swalduz A, Viari A, Chabaud S, Pérol D, Blay JY, Saintigny P. Added value of whole-exome and RNA sequencing in advanced and refractory cancer patients with no molecular-based treatment recommendation based on a 90-gene panel. Cancer Med 2024; 13:e7115. [PMID: 38553950 PMCID: PMC10980928 DOI: 10.1002/cam4.7115] [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] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2023] [Revised: 02/21/2024] [Accepted: 03/04/2024] [Indexed: 04/02/2024] Open
Abstract
INTRODUCTION The objective was to determine the added value of comprehensive molecular profile by whole-exome and RNA sequencing (WES/RNA-Seq) in advanced and refractory cancer patients who had no molecular-based treatment recommendation (MBTR) based on a more limited targeted gene panel (TGP) plus array-based comparative genomic hybridization (aCGH). MATERIALS AND METHODS In this retrospective analysis, we selected 50 patients previously included in the PROFILER trial (NCT01774409) for which no MBT could be recommended based on a targeted 90-gene panel and aCGH. For each patient, the frozen tumor sample mirroring the FFPE sample used for TGP/aCGH analysis were processed for WES and RNA-Seq. Data from TGP/aCGH were reanalyzed, and together with WES/RNA-Seq, findings were simultaneously discussed at a new molecular tumor board (MTB). RESULTS After exclusion of variants of unknown significance, a total of 167 somatic molecular alterations were identified in 50 patients (median: 3 [1-10]). Out of these 167 relevant molecular alterations, 51 (31%) were common to both TGP/aCGH and WES/RNA-Seq, 19 (11%) were identified by the TGP/aCGH only and 97 (58%) were identified by WES/RNA-Seq only, including two fusion transcripts in two patients. A MBTR was provided in 4/50 (8%) patients using the information from TGP/aCGH versus 9/50 (18%) patients using WES/RNA-Seq findings. Three patients had similar recommendations based on TGP/aCGH and WES/RNA-Seq. CONCLUSIONS In advanced and refractory cancer patients in whom no MBTR was recommended from TGP/aCGH, WES/RNA-Seq allowed to identify more alterations which may in turn, in a limited fraction of patients, lead to new MBTR.
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Affiliation(s)
| | | | - Anthony Ferrari
- Platform of Bioinformatics Gilles‐ThomasCentre Léon BérardLyonFrance
| | - Laurie Tonon
- Platform of Bioinformatics Gilles‐ThomasCentre Léon BérardLyonFrance
| | | | | | | | - Olivier Trédan
- Department of Medical OncologyCentre Léon BérardLyonFrance
| | - Nadège Corradini
- Department of Pediatric Oncology, Institute of Pediatric Hematology and OncologyCentre Leon BérardLyonFrance
| | | | | | - Alain Viari
- Platform of Bioinformatics Gilles‐ThomasCentre Léon BérardLyonFrance
| | - Sylvie Chabaud
- Department of Clinical ResearchCentre Léon BérardLyonFrance
| | - David Pérol
- Department of Clinical ResearchCentre Léon BérardLyonFrance
| | - Jean Yves Blay
- Department of Medical OncologyCentre Léon BérardLyonFrance
- Univ Lyon, Claude Bernard Lyon 1 University, INSERM 1052, CNRS 5286, Centre Léon BérardCancer Research Center of LyonLyonFrance
| | - Pierre Saintigny
- Department of Medical OncologyCentre Léon BérardLyonFrance
- Univ Lyon, Claude Bernard Lyon 1 University, INSERM 1052, CNRS 5286, Centre Léon BérardCancer Research Center of LyonLyonFrance
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De Blander H, Tonon L, Fauvet F, Pommier RM, Lamblot C, Benhassoun R, Angileri F, Gibert B, Rodriguez R, Ouzounova M, Morel AP, Puisieux A. Cooperative pro-tumorigenic adaptation to oncogenic RAS through epithelial-to-mesenchymal plasticity. Sci Adv 2024; 10:eadi1736. [PMID: 38354248 PMCID: PMC10866563 DOI: 10.1126/sciadv.adi1736] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/07/2023] [Accepted: 01/12/2024] [Indexed: 02/16/2024]
Abstract
In breast cancers, aberrant activation of the RAS/MAPK pathway is strongly associated with mesenchymal features and stemness traits, suggesting an interplay between this mitogenic signaling pathway and epithelial-to-mesenchymal plasticity (EMP). By using inducible models of human mammary epithelial cells, we demonstrate herein that the oncogenic activation of RAS promotes ZEB1-dependent EMP, which is necessary for malignant transformation. Notably, EMP is triggered by the secretion of pro-inflammatory cytokines from neighboring RAS-activated senescent cells, with a prominent role for IL-6 and IL-1α. Our data contrast with the common view of cellular senescence as a tumor-suppressive mechanism and EMP as a process promoting late stages of tumor progression in response to signals from the tumor microenvironment. We highlighted here a pro-tumorigenic cooperation of RAS-activated mammary epithelial cells, which leverages on oncogene-induced senescence and EMP to trigger cellular reprogramming and malignant transformation.
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Affiliation(s)
- Hadrien De Blander
- Cancer Research Center of Lyon, Université de Lyon, Université Claude Bernard Lyon 1, INSERM 1052, CNRS 5286, Centre Léon Bérard, Equipe Labellisée Ligue Contre le Cancer, 69008, Lyon, France
- LabEx DEVweCAN, Université de Lyon, F-69000, Lyon, France
| | - Laurie Tonon
- Synergie Lyon Cancer, Plateforme de Bioinformatique ‘Gilles Thomas’, Centre Léon Bérard, Lyon, France
| | - Frédérique Fauvet
- Cancer Research Center of Lyon, Université de Lyon, Université Claude Bernard Lyon 1, INSERM 1052, CNRS 5286, Centre Léon Bérard, Equipe Labellisée Ligue Contre le Cancer, 69008, Lyon, France
- LabEx DEVweCAN, Université de Lyon, F-69000, Lyon, France
| | - Roxane M. Pommier
- Cancer Research Center of Lyon, Université de Lyon, Université Claude Bernard Lyon 1, INSERM 1052, CNRS 5286, Centre Léon Bérard, Equipe Labellisée Ligue Contre le Cancer, 69008, Lyon, France
- LabEx DEVweCAN, Université de Lyon, F-69000, Lyon, France
- Synergie Lyon Cancer, Plateforme de Bioinformatique ‘Gilles Thomas’, Centre Léon Bérard, Lyon, France
| | - Christelle Lamblot
- Cancer Research Center of Lyon, Université de Lyon, Université Claude Bernard Lyon 1, INSERM 1052, CNRS 5286, Centre Léon Bérard, Equipe Labellisée Ligue Contre le Cancer, 69008, Lyon, France
- LabEx DEVweCAN, Université de Lyon, F-69000, Lyon, France
| | - Rahma Benhassoun
- Cancer Research Center of Lyon, Université de Lyon, Université Claude Bernard Lyon 1, INSERM 1052, CNRS 5286, Centre Léon Bérard, Equipe Labellisée Ligue Contre le Cancer, 69008, Lyon, France
- LabEx DEVweCAN, Université de Lyon, F-69000, Lyon, France
| | - Francesca Angileri
- Cancer Research Center of Lyon, Université de Lyon, Université Claude Bernard Lyon 1, INSERM 1052, CNRS 5286, Centre Léon Bérard, Equipe Labellisée Ligue Contre le Cancer, 69008, Lyon, France
- LabEx DEVweCAN, Université de Lyon, F-69000, Lyon, France
| | - Benjamin Gibert
- LabEx DEVweCAN, Université de Lyon, F-69000, Lyon, France
- Gastroenterology and Technologies for Health Group, Centre de Recherche en Cancérologie de Lyon, INSERM U1052-CNRS5286, Université Lyon 1, 69008, Lyon, France
| | - Raphaël Rodriguez
- Equipe Labellisée Ligue Contre le Cancer, CNRS UMR 3666, INSERM U1143, Paris, France
- Institut Curie, PSL Research University, Paris, France
| | - Maria Ouzounova
- Cancer Research Center of Lyon, Université de Lyon, Université Claude Bernard Lyon 1, INSERM 1052, CNRS 5286, Centre Léon Bérard, Equipe Labellisée Ligue Contre le Cancer, 69008, Lyon, France
- LabEx DEVweCAN, Université de Lyon, F-69000, Lyon, France
| | - Anne-Pierre Morel
- Cancer Research Center of Lyon, Université de Lyon, Université Claude Bernard Lyon 1, INSERM 1052, CNRS 5286, Centre Léon Bérard, Equipe Labellisée Ligue Contre le Cancer, 69008, Lyon, France
- LabEx DEVweCAN, Université de Lyon, F-69000, Lyon, France
| | - Alain Puisieux
- Equipe Labellisée Ligue Contre le Cancer, CNRS UMR 3666, INSERM U1143, Paris, France
- Institut Curie, PSL Research University, Paris, France
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Kleijwegt C, Bressac F, Seurre C, Bouchereau W, Cohen C, Texier P, Simonet T, Schaeffer L, Lomonte P, Corpet A. Interplay between PML NBs and HIRA for H3.3 dynamics following type I interferon stimulus. eLife 2023; 12:e80156. [PMID: 37227756 PMCID: PMC10212570 DOI: 10.7554/elife.80156] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [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: 05/10/2022] [Accepted: 04/25/2023] [Indexed: 05/26/2023] Open
Abstract
Promyelocytic leukemia Nuclear Bodies (PML NBs) are nuclear membrane-less organelles physically associated with chromatin underscoring their crucial role in genome function. The H3.3 histone chaperone complex HIRA accumulates in PML NBs upon senescence, viral infection or IFN-I treatment in primary cells. Yet, the molecular mechanisms of this partitioning and its function in regulating histone dynamics have remained elusive. By using specific approaches, we identify intermolecular SUMO-SIM interactions as an essential mechanism for HIRA recruitment in PML NBs. Hence, we describe a role of PML NBs as nuclear depot centers to regulate HIRA distribution in the nucleus, dependent both on SP100 and DAXX/H3.3 levels. Upon IFN-I stimulation, PML is required for interferon-stimulated genes (ISGs) transcription and PML NBs become juxtaposed to ISGs loci at late time points of IFN-I treatment. HIRA and PML are necessary for the prolonged H3.3 deposition at the transcriptional end sites of ISGs, well beyond the peak of transcription. Though, HIRA accumulation in PML NBs is dispensable for H3.3 deposition on ISGs. We thus uncover a dual function for PML/PML NBs, as buffering centers modulating the nuclear distribution of HIRA, and as chromosomal hubs regulating ISGs transcription and thus HIRA-mediated H3.3 deposition at ISGs upon inflammatory response.
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Affiliation(s)
- Constance Kleijwegt
- University of Lyon, Université Claude Bernard Lyon 1, CNRS UMR 5261, INSERM U 1315, LabEx DEVweCAN, Institut NeuroMyoGène (INMG), Pathophysiology and Genetics of the Neuron and Muscle (PGNM) laboratory, team Chromatin Dynamics, Nuclear Domains, VirusLyonFrance
| | - Florent Bressac
- University of Lyon, Université Claude Bernard Lyon 1, CNRS UMR 5261, INSERM U 1315, LabEx DEVweCAN, Institut NeuroMyoGène (INMG), Pathophysiology and Genetics of the Neuron and Muscle (PGNM) laboratory, team Chromatin Dynamics, Nuclear Domains, VirusLyonFrance
| | - Coline Seurre
- University of Lyon, Université Claude Bernard Lyon 1, CNRS UMR 5261, INSERM U 1315, LabEx DEVweCAN, Institut NeuroMyoGène (INMG), Pathophysiology and Genetics of the Neuron and Muscle (PGNM) laboratory, team Chromatin Dynamics, Nuclear Domains, VirusLyonFrance
| | - Wilhelm Bouchereau
- University of Lyon, Université Claude Bernard Lyon 1, CNRS UMR 5261, INSERM U 1315, LabEx DEVweCAN, Institut NeuroMyoGène (INMG), Pathophysiology and Genetics of the Neuron and Muscle (PGNM) laboratory, team Chromatin Dynamics, Nuclear Domains, VirusLyonFrance
| | - Camille Cohen
- University of Lyon, Université Claude Bernard Lyon 1, CNRS UMR 5261, INSERM U 1315, LabEx DEVweCAN, Institut NeuroMyoGène (INMG), Pathophysiology and Genetics of the Neuron and Muscle (PGNM) laboratory, team Chromatin Dynamics, Nuclear Domains, VirusLyonFrance
| | - Pascale Texier
- University of Lyon, Université Claude Bernard Lyon 1, CNRS UMR 5261, INSERM U 1315, LabEx DEVweCAN, Institut NeuroMyoGène (INMG), Pathophysiology and Genetics of the Neuron and Muscle (PGNM) laboratory, team Chromatin Dynamics, Nuclear Domains, VirusLyonFrance
| | - Thomas Simonet
- Univ Lyon, Université Claude Bernard Lyon 1, CNRS UMR 5310, INSERM U 1217, Institut NeuroMyoGène (INMG), team Nerve-Muscle interactionsLyonFrance
| | - Laurent Schaeffer
- Univ Lyon, Université Claude Bernard Lyon 1, CNRS UMR 5310, INSERM U 1217, Institut NeuroMyoGène (INMG), team Nerve-Muscle interactionsLyonFrance
| | - Patrick Lomonte
- University of Lyon, Université Claude Bernard Lyon 1, CNRS UMR 5261, INSERM U 1315, LabEx DEVweCAN, Institut NeuroMyoGène (INMG), Pathophysiology and Genetics of the Neuron and Muscle (PGNM) laboratory, team Chromatin Dynamics, Nuclear Domains, VirusLyonFrance
| | - Armelle Corpet
- University of Lyon, Université Claude Bernard Lyon 1, CNRS UMR 5261, INSERM U 1315, LabEx DEVweCAN, Institut NeuroMyoGène (INMG), Pathophysiology and Genetics of the Neuron and Muscle (PGNM) laboratory, team Chromatin Dynamics, Nuclear Domains, VirusLyonFrance
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