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Lucibello F, Lalanne AI, Le Gac AL, Soumare A, Aflaki S, Cyrta J, Dubreuil L, Mestdagh M, Salou M, Houy A, Ekwegbara C, Jamet C, Gardrat S, Le Ven A, Bernardeau K, Cassoux N, Matet A, Malaise D, Pierron G, Piperno-Neumann S, Stern MH, Rodrigues M, Lantz O. Divergent local and systemic antitumor response in primary uveal melanomas. J Exp Med 2024; 221:e20232094. [PMID: 38563818 PMCID: PMC10986814 DOI: 10.1084/jem.20232094] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2023] [Revised: 02/08/2024] [Accepted: 03/11/2024] [Indexed: 04/04/2024] Open
Abstract
Uveal melanoma (UM) is the most common cancer of the eye. The loss of chromosome 3 (M3) is associated with a high risk of metastases. M3 tumors are more infiltrated by T-lymphocytes than low-risk disomic-3 (D3) tumors, contrasting with other tumor types in which T cell infiltration correlates with better prognosis. Whether these T cells represent an antitumor response and how these T cells would be primed in the eye are both unknown. Herein, we characterized the T cells infiltrating primary UMs. CD8+ and Treg cells were more abundant in M3 than in D3 tumors. CD39+PD-1+CD8+ T cells were enriched in M3 tumors, suggesting specific responses to tumor antigen (Ag) as confirmed using HLA-A2:Melan-A tetramers. scRNAseq-VDJ analysis of T cells evidenced high numbers of proliferating CD39+PD1+CD8+ clonal expansions, suggesting in situ antitumor Ag responses. TCRseq and tumor-Ag tetramer staining characterized the recirculation pattern of the antitumor responses in M3 and D3 tumors. Thus, tumor-Ag responses occur in localized UMs, raising the question of the priming mechanisms in the absence of known lymphatic drainage.
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Affiliation(s)
- Francesca Lucibello
- Department of Immunity and Cancer, Inserm U932, Paris Sciences et Lettres (PSL) University, Institut Curie, Paris, France
| | - Ana I. Lalanne
- Laboratoire d’Immunologie Clinique, Institut Curie, Paris, France
- Centre d’investigation Clinique en Biothérapie Gustave-Roussy Institut Curie (CIC-BT1428), Paris, France
| | - Anne-Laure Le Gac
- Department of Immunity and Cancer, Inserm U932, Paris Sciences et Lettres (PSL) University, Institut Curie, Paris, France
| | - Abdoulaye Soumare
- Department of Immunity and Cancer, Inserm U932, Paris Sciences et Lettres (PSL) University, Institut Curie, Paris, France
| | - Setareh Aflaki
- Department of Immunity and Cancer, Inserm U932, Paris Sciences et Lettres (PSL) University, Institut Curie, Paris, France
| | - Joana Cyrta
- Departments of Pathology, Institut Curie, Paris, France
| | - Lea Dubreuil
- Laboratoire d’Immunologie Clinique, Institut Curie, Paris, France
| | - Martin Mestdagh
- Department of Immunity and Cancer, Inserm U932, Paris Sciences et Lettres (PSL) University, Institut Curie, Paris, France
| | - Marion Salou
- Department of Immunity and Cancer, Inserm U932, Paris Sciences et Lettres (PSL) University, Institut Curie, Paris, France
| | - Alexandre Houy
- INSERM U830, DNA Repair and Uveal Melanoma (D.R.U.M.), Equipe Labellisée par la Ligue Nationale Contre le Cancer, PSL University, Institut Curie, Paris, France
| | - Christina Ekwegbara
- Laboratoire d’Immunologie Clinique, Institut Curie, Paris, France
- Centre d’investigation Clinique en Biothérapie Gustave-Roussy Institut Curie (CIC-BT1428), Paris, France
| | - Camille Jamet
- Department of Immunity and Cancer, Inserm U932, Paris Sciences et Lettres (PSL) University, Institut Curie, Paris, France
| | | | - Anais Le Ven
- INSERM U830, DNA Repair and Uveal Melanoma (D.R.U.M.), Equipe Labellisée par la Ligue Nationale Contre le Cancer, PSL University, Institut Curie, Paris, France
| | - Karine Bernardeau
- Centre Hospitalier Universitaire (CHU) Nantes, Centre National de la Recherche Scientifique, Inserm, BioCore, US16, Nantes Université, Nantes, France
| | - Nathalie Cassoux
- Department of Surgical Oncology, University of Paris, Institut Curie, Paris, France
| | - Alexandre Matet
- Department of Surgical Oncology, University of Paris, Institut Curie, Paris, France
| | - Denis Malaise
- Department of Surgical Oncology, University of Paris, Institut Curie, Paris, France
| | | | | | - Marc-Henri Stern
- INSERM U830, DNA Repair and Uveal Melanoma (D.R.U.M.), Equipe Labellisée par la Ligue Nationale Contre le Cancer, PSL University, Institut Curie, Paris, France
| | - Manuel Rodrigues
- INSERM U830, DNA Repair and Uveal Melanoma (D.R.U.M.), Equipe Labellisée par la Ligue Nationale Contre le Cancer, PSL University, Institut Curie, Paris, France
- Department of Medical Oncology, Institut Curie, Paris, France
| | - Olivier Lantz
- Department of Immunity and Cancer, Inserm U932, Paris Sciences et Lettres (PSL) University, Institut Curie, Paris, France
- Laboratoire d’Immunologie Clinique, Institut Curie, Paris, France
- Centre d’investigation Clinique en Biothérapie Gustave-Roussy Institut Curie (CIC-BT1428), Paris, France
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Rombaut D, Lefèvre C, Rached T, Bondu S, Letessier A, Mangione RM, Farhat B, Lesieur-Pasquier A, Castillo-Guzman D, Boussaid I, Friedrich C, Tourville A, De Carvalho M, Levavasseur F, Leduc M, Le Gall M, Battault S, Temple M, Houy A, Bouscary D, Willems L, Park S, Raynaud S, Cluzeau T, Clappier E, Fenaux P, Adès L, Margueron R, Wassef M, Alsafadi S, Chapuis N, Kosmider O, Solary E, Constantinou A, Stern MH, Droin N, Palancade B, Miotto B, Chédin F, Fontenay M. Accelerated DNA replication fork speed due to loss of R-loops in myelodysplastic syndromes with SF3B1 mutation. Nat Commun 2024; 15:3016. [PMID: 38589367 PMCID: PMC11001894 DOI: 10.1038/s41467-024-46547-7] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2022] [Accepted: 02/29/2024] [Indexed: 04/10/2024] Open
Abstract
Myelodysplastic syndromes (MDS) with mutated SF3B1 gene present features including a favourable outcome distinct from MDS with mutations in other splicing factor genes SRSF2 or U2AF1. Molecular bases of these divergences are poorly understood. Here we find that SF3B1-mutated MDS show reduced R-loop formation predominating in gene bodies associated with intron retention reduction, not found in U2AF1- or SRSF2-mutated MDS. Compared to erythroblasts from SRSF2- or U2AF1-mutated patients, SF3B1-mutated erythroblasts exhibit augmented DNA synthesis, accelerated replication forks, and single-stranded DNA exposure upon differentiation. Importantly, histone deacetylase inhibition using vorinostat restores R-loop formation, slows down DNA replication forks and improves SF3B1-mutated erythroblast differentiation. In conclusion, loss of R-loops with associated DNA replication stress represents a hallmark of SF3B1-mutated MDS ineffective erythropoiesis, which could be used as a therapeutic target.
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Affiliation(s)
- David Rombaut
- Université Paris Cité, Centre National de la Recherche Scientifique, Institut National de la Santé et de la Recherche Médicale, Institut Cochin, Paris, France
- Equipe labellisée par la Fondation pour la Recherche Médicale, Paris, France
- Laboratoire d'excellence du Globule Rouge GR-Ex, Université Paris Cité, Paris, France
- Assistance Publique-Hôpitaux de Paris.Centre-Université Paris Cité, Hôpital Cochin, Laboratory of Hematology, Paris, France
| | - Carine Lefèvre
- Université Paris Cité, Centre National de la Recherche Scientifique, Institut National de la Santé et de la Recherche Médicale, Institut Cochin, Paris, France
- Equipe labellisée par la Fondation pour la Recherche Médicale, Paris, France
- Laboratoire d'excellence du Globule Rouge GR-Ex, Université Paris Cité, Paris, France
| | - Tony Rached
- Université Paris Cité, Centre National de la Recherche Scientifique, Institut National de la Santé et de la Recherche Médicale, Institut Cochin, Paris, France
- Equipe labellisée par la Fondation pour la Recherche Médicale, Paris, France
| | - Sabrina Bondu
- Université Paris Cité, Centre National de la Recherche Scientifique, Institut National de la Santé et de la Recherche Médicale, Institut Cochin, Paris, France
- Equipe labellisée par la Fondation pour la Recherche Médicale, Paris, France
| | - Anne Letessier
- Université Paris Cité, Centre National de la Recherche Scientifique, Institut National de la Santé et de la Recherche Médicale, Institut Cochin, Paris, France
| | | | - Batoul Farhat
- Université Paris Cité, Centre National de la Recherche Scientifique, Institut National de la Santé et de la Recherche Médicale, Institut Cochin, Paris, France
- Equipe labellisée par la Fondation pour la Recherche Médicale, Paris, France
| | - Auriane Lesieur-Pasquier
- Université Paris Cité, Centre National de la Recherche Scientifique, Institut National de la Santé et de la Recherche Médicale, Institut Cochin, Paris, France
- Equipe labellisée par la Fondation pour la Recherche Médicale, Paris, France
| | - Daisy Castillo-Guzman
- Department of Molecular and Cellular Biology and Genome Center, University of California, Davis, CA, USA
| | - Ismael Boussaid
- Université Paris Cité, Centre National de la Recherche Scientifique, Institut National de la Santé et de la Recherche Médicale, Institut Cochin, Paris, France
- Equipe labellisée par la Fondation pour la Recherche Médicale, Paris, France
- Assistance Publique-Hôpitaux de Paris.Centre-Université Paris Cité, Hôpital Cochin, Laboratory of Hematology, Paris, France
| | - Chloé Friedrich
- Université Paris Cité, Centre National de la Recherche Scientifique, Institut National de la Santé et de la Recherche Médicale, Institut Cochin, Paris, France
- Equipe labellisée par la Fondation pour la Recherche Médicale, Paris, France
- Assistance Publique-Hôpitaux de Paris.Centre-Université Paris Cité, Hôpital Cochin, Laboratory of Hematology, Paris, France
| | - Aurore Tourville
- Université Paris Cité, Centre National de la Recherche Scientifique, Institut National de la Santé et de la Recherche Médicale, Institut Cochin, Paris, France
- Equipe labellisée par la Fondation pour la Recherche Médicale, Paris, France
| | - Magali De Carvalho
- Université Paris Cité, Centre National de la Recherche Scientifique, Institut National de la Santé et de la Recherche Médicale, Institut Cochin, Paris, France
- Equipe labellisée par la Fondation pour la Recherche Médicale, Paris, France
| | - Françoise Levavasseur
- Université Paris Cité, Centre National de la Recherche Scientifique, Institut National de la Santé et de la Recherche Médicale, Institut Cochin, Paris, France
- Equipe labellisée par la Fondation pour la Recherche Médicale, Paris, France
| | - Marjorie Leduc
- Université Paris Cité, Centre National de la Recherche Scientifique, Institut National de la Santé et de la Recherche Médicale, Institut Cochin, Paris, France
- Platform Proteom'IC, Université Paris Cité, Institut Cochin, Paris, France
| | - Morgane Le Gall
- Université Paris Cité, Centre National de la Recherche Scientifique, Institut National de la Santé et de la Recherche Médicale, Institut Cochin, Paris, France
- Platform Proteom'IC, Université Paris Cité, Institut Cochin, Paris, France
| | - Sarah Battault
- Université Paris Cité, Centre National de la Recherche Scientifique, Institut National de la Santé et de la Recherche Médicale, Institut Cochin, Paris, France
- Equipe labellisée par la Fondation pour la Recherche Médicale, Paris, France
| | - Marie Temple
- Assistance Publique-Hôpitaux de Paris.Centre-Université Paris Cité, Hôpital Cochin, Laboratory of Hematology, Paris, France
| | - Alexandre Houy
- Institut Curie, PSL Research University, Sorbonne University, INSERM U830, DNA repair and uveal melanoma, Equipe labellisée par la Ligue Nationale contre le Cancer, Paris, France
| | - Didier Bouscary
- Université Paris Cité, Centre National de la Recherche Scientifique, Institut National de la Santé et de la Recherche Médicale, Institut Cochin, Paris, France
- Assistance Publique-Hôpitaux de Paris.Centre-Université Paris Cité, Hôpital Cochin, Clinical Department of Hematology, Paris, France
| | - Lise Willems
- Université Paris Cité, Centre National de la Recherche Scientifique, Institut National de la Santé et de la Recherche Médicale, Institut Cochin, Paris, France
- Assistance Publique-Hôpitaux de Paris.Centre-Université Paris Cité, Hôpital Cochin, Clinical Department of Hematology, Paris, France
| | - Sophie Park
- Department of Hematology, Centre Hospitalier Universitaire, Université de Grenoble Alpes, Grenoble, France
| | - Sophie Raynaud
- Laboratory of Hematology, Université Côte d'Azur, Centre Hospitalier Universitaire, Nice, France
| | - Thomas Cluzeau
- Clinical Department of Hematology, Université Côte d'Azur, Centre Hospitalier Universitaire, Nice, France
| | - Emmanuelle Clappier
- Assistance Publique-Hôpitaux de Paris.Nord-Université Paris Cité, Saint-Louis Hospital, Laboratory of Hematology, Paris, France
| | - Pierre Fenaux
- Assistance Publique-Hôpitaux de Paris.Nord-Université Paris Cité, Saint-Louis Hospital, Service Hématologie Séniors, Paris, France
| | - Lionel Adès
- Assistance Publique-Hôpitaux de Paris.Nord-Université Paris Cité, Saint-Louis Hospital, Service Hématologie Séniors, Paris, France
| | - Raphael Margueron
- Institut Curie, Paris Sciences Lettres Research University, Sorbonne University, INSERM U934, UMR3215, Paris, France
| | - Michel Wassef
- Institut Curie, Paris Sciences Lettres Research University, Sorbonne University, INSERM U934, UMR3215, Paris, France
| | - Samar Alsafadi
- Institut Curie, PSL Research University, Sorbonne University, INSERM U830, DNA repair and uveal melanoma, Equipe labellisée par la Ligue Nationale contre le Cancer, Paris, France
| | - Nicolas Chapuis
- Université Paris Cité, Centre National de la Recherche Scientifique, Institut National de la Santé et de la Recherche Médicale, Institut Cochin, Paris, France
- Assistance Publique-Hôpitaux de Paris.Centre-Université Paris Cité, Hôpital Cochin, Laboratory of Hematology, Paris, France
| | - Olivier Kosmider
- Université Paris Cité, Centre National de la Recherche Scientifique, Institut National de la Santé et de la Recherche Médicale, Institut Cochin, Paris, France
- Equipe labellisée par la Fondation pour la Recherche Médicale, Paris, France
- Assistance Publique-Hôpitaux de Paris.Centre-Université Paris Cité, Hôpital Cochin, Laboratory of Hematology, Paris, France
| | - Eric Solary
- Institut Gustave Roussy, INSERM 1287, Université Paris Saclay, Villejuif, France
| | - Angelos Constantinou
- Institut de Génétique Humaine, Centre National de la Recherche Scientifique, Université de Montpellier, Montpellier, France
| | - Marc-Henri Stern
- Institut Curie, PSL Research University, Sorbonne University, INSERM U830, DNA repair and uveal melanoma, Equipe labellisée par la Ligue Nationale contre le Cancer, Paris, France
| | - Nathalie Droin
- Institut Gustave Roussy, INSERM 1287, Université Paris Saclay, Villejuif, France
| | - Benoit Palancade
- Université Paris Cité, CNRS, Institut Jacques Monod, Paris, France
| | - Benoit Miotto
- Université Paris Cité, Centre National de la Recherche Scientifique, Institut National de la Santé et de la Recherche Médicale, Institut Cochin, Paris, France
| | - Frédéric Chédin
- Department of Molecular and Cellular Biology and Genome Center, University of California, Davis, CA, USA
| | - Michaela Fontenay
- Université Paris Cité, Centre National de la Recherche Scientifique, Institut National de la Santé et de la Recherche Médicale, Institut Cochin, Paris, France.
- Equipe labellisée par la Fondation pour la Recherche Médicale, Paris, France.
- Laboratoire d'excellence du Globule Rouge GR-Ex, Université Paris Cité, Paris, France.
- Assistance Publique-Hôpitaux de Paris.Centre-Université Paris Cité, Hôpital Cochin, Laboratory of Hematology, Paris, France.
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Villy MC, Le Ven A, Le Mentec M, Masliah-Planchon J, Houy A, Bièche I, Vacher S, Vincent-Salomon A, Dubois d'Enghien C, Schwartz M, Piperno-Neumann S, Matet A, Malaise D, Bubien V, Lortholary A, Ait Omar A, Cavaillé M, Stoppa-Lyonnet D, Cassoux N, Stern MH, Rodrigues M, Golmard L, Colas C. Familial uveal melanoma and other tumors in 25 families with monoallelic germline MBD4 variants. J Natl Cancer Inst 2024; 116:580-587. [PMID: 38060262 DOI: 10.1093/jnci/djad248] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2023] [Revised: 11/02/2023] [Accepted: 11/18/2023] [Indexed: 12/08/2023] Open
Abstract
BACKGROUND Monoallelic germline MBD4 pathogenic variants were recently reported to cause a predisposition to uveal melanoma, associated with a specific tumor mutational signature and good response to immunotherapy. Monoallelic tumor pathogenic variants have also been described in brain tumors, breast cancers, and myxofibrosarcomas, whereas biallelic germline MBD4 pathogenic variants have been involved in a recessive hereditary adenomatous polyposis and a specific type of acute myeloid leukemia. METHODS We analyzed MBD4 for all patients with a diagnosis of uveal melanoma at Institut Curie since July 2021 and in the 3240 consecutive female probands explored at the Institut Curie for suspicion of predisposition to breast cancer between July 2021 and February 2023. RESULTS We describe 25 families whose probands carry a monoallelic germline pathogenic variant in MBD4. Eighteen of these families presented with uveal melanoma (including a case patient with multiple uveal melanoma), and 7 families presented with breast cancer. Family histories showed the first familial case of uveal melanoma in monoallelic MBD4 pathogenic variant carriers and other various types of cancers in relatives, especially breast, renal, and colorectal tumors. CONCLUSIONS Monoallelic MBD4 pathogenic variant may explain some cases of familial and multiple uveal melanoma as well as various cancer types, expanding the tumor spectrum of this predisposition. Further genetic testing in relatives combined with molecular tumor analyses will help define the tumor spectrum and estimate each tumor's risk.
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Affiliation(s)
- Marie-Charlotte Villy
- Department of Genetics, Institut Curie, Paris, France
- Université Paris Cité, Paris, France
| | - Anaïs Le Ven
- Department of Genetics, Institut Curie, Paris, France
- Paris Sciences & Lettres Research University, Paris, France
- Inserm U830, DNA Repair and Uveal Melanoma (D.R.U.M.), Paris, France
| | - Marine Le Mentec
- Department of Genetics, Institut Curie, Paris, France
- Paris Sciences & Lettres Research University, Paris, France
| | - Julien Masliah-Planchon
- Department of Genetics, Institut Curie, Paris, France
- Paris Sciences & Lettres Research University, Paris, France
| | - Alexandre Houy
- Paris Sciences & Lettres Research University, Paris, France
- Inserm U830, DNA Repair and Uveal Melanoma (D.R.U.M.), Paris, France
| | - Ivan Bièche
- Department of Genetics, Institut Curie, Paris, France
- Université Paris Cité, Paris, France
| | - Sophie Vacher
- Department of Genetics, Institut Curie, Paris, France
- Paris Sciences & Lettres Research University, Paris, France
| | - Anne Vincent-Salomon
- Department of Genetics, Institut Curie, Paris, France
- Paris Sciences & Lettres Research University, Paris, France
| | - Catherine Dubois d'Enghien
- Department of Genetics, Institut Curie, Paris, France
- Paris Sciences & Lettres Research University, Paris, France
| | - Mathias Schwartz
- Department of Genetics, Institut Curie, Paris, France
- Paris Sciences & Lettres Research University, Paris, France
| | - Sophie Piperno-Neumann
- Paris Sciences & Lettres Research University, Paris, France
- Department of Medical Oncology, Institut Curie, Paris, France
| | - Alexandre Matet
- Université Paris Cité, Paris, France
- Department of Ocular Oncology, Institut Curie, Paris, France
| | - Denis Malaise
- Paris Sciences & Lettres Research University, Paris, France
- Department of Ocular Oncology, Institut Curie, Paris, France
| | | | - Alain Lortholary
- Department of Medical Oncology, GINECO-Hôpital Privé du Confluent, Nantes, France
| | - Amal Ait Omar
- Department of Gastroenterology, AP-HP, Hôpital Avicenne, Bobigny, France
| | - Mathias Cavaillé
- Department of Oncogenetics, Centre Jean Perrin, Université Clermont Auvergne, INSERM, U1240 Imagerie Moléculaire et Stratégies Théranostiques, AURAGEN, Clermont-Ferrand, France
| | - Dominique Stoppa-Lyonnet
- Department of Genetics, Institut Curie, Paris, France
- Université Paris Cité, Paris, France
- Inserm U830, DNA Repair and Uveal Melanoma (D.R.U.M.), Paris, France
| | - Nathalie Cassoux
- Université Paris Cité, Paris, France
- Department of Ocular Oncology, Institut Curie, Paris, France
| | - Marc-Henri Stern
- Department of Genetics, Institut Curie, Paris, France
- Paris Sciences & Lettres Research University, Paris, France
- Inserm U830, DNA Repair and Uveal Melanoma (D.R.U.M.), Paris, France
| | - Manuel Rodrigues
- Paris Sciences & Lettres Research University, Paris, France
- Inserm U830, DNA Repair and Uveal Melanoma (D.R.U.M.), Paris, France
- Department of Medical Oncology, Institut Curie, Paris, France
| | - Lisa Golmard
- Department of Genetics, Institut Curie, Paris, France
- Paris Sciences & Lettres Research University, Paris, France
| | - Chrystelle Colas
- Department of Genetics, Institut Curie, Paris, France
- Paris Sciences & Lettres Research University, Paris, France
- Inserm U830, DNA Repair and Uveal Melanoma (D.R.U.M.), Paris, France
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Mariani P, Bidard FC, Rampanou A, Houy A, Servois V, Ramtohul T, Pierron G, Chevrier M, Renouf B, Lantz O, Gardrat S, Vincent-Salomon A, Roman-Roman S, Rodrigues M, Piperno-Neumann S, Cassoux N, Stern MH, Renault S. Circulating Tumor DNA as a Prognostic Factor in Patients With Resectable Hepatic Metastases of Uveal Melanoma. Ann Surg 2023; 278:e827-e834. [PMID: 36847256 PMCID: PMC10481917 DOI: 10.1097/sla.0000000000005822] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/01/2023]
Abstract
OBJECTIVE We report here the results of a prospective study of circulating tumor DNA (ctDNA) detection in patients undergoing uveal melanoma (UM) liver metastases resection (NCT02849145). BACKGROUND In UM patients, the liver is the most common and often only site of metastases. Local treatments of liver metastases, such as surgical resection, have a likely benefit in selected patients. METHODS Upon enrollment, metastatic UM patients eligible for curative liver surgery had plasma samples collected before and after surgery. GNAQ / GNA11 mutations were identified in archived tumor tissue and used to quantify ctDNA by droplet digital polymerase chain reaction which was then associated with the patient's surgical outcomes. RESULTS Forty-seven patients were included. Liver surgery was associated with a major increase of cell-free circulating DNA levels, with a peak 2 days after surgery (∼20-fold). Among 40 evaluable patients, 14 (35%) had detectable ctDNA before surgery, with a median allelic frequency of 1.1%. These patients experienced statistically shorter relapse-free survival (RFS) versus patients with no detectable ctDNA before surgery (median RFS: 5.5 vs 12.2 months; hazard ratio=2.23, 95% CI: 1.06-4.69, P =0.04), and had a numerically shorter overall survival (OS) (median OS: 27.0 vs 42.3 months). ctDNA positivity at postsurgery time points was also associated with RFS and OS. CONCLUSIONS This study is the first to report ctDNA detection rate and prognostic impact in UM patients eligible for surgical resection of their liver metastases. If confirmed by further studies in this setting, this noninvasive biomarker could inform treatment decisions in UM patients with liver metastases.
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Affiliation(s)
- Pascale Mariani
- Department of Surgical Oncology, Institut Curie, Paris, PSL Research University, Paris, France
| | - François-Clément Bidard
- Circulating Tumor Biomarkers Laboratory, Inserm CIC-BT, Department of Translational Research, Institut Curie, Paris, France
- Department of Medical Oncology, Institut Curie, Paris and Saint-Cloud, France
- UVSQ, Paris-Saclay University, Saint Cloud, Paris, France
| | - Aurore Rampanou
- Circulating Tumor Biomarkers Laboratory, Inserm CIC-BT, Department of Translational Research, Institut Curie, Paris, France
| | - Alexandre Houy
- Inserm U830, DNA Repair and Uveal Melanoma (D.R.U.M.) Team, Institut Curie, PSL Research University, Paris, France
| | - Vincent Servois
- Department of Radiology, Institut Curie, PSL Research University, Paris, France
| | - Toulsie Ramtohul
- Department of Radiology, Institut Curie, PSL Research University, Paris, France
| | - Gaelle Pierron
- Somatic Genetic Unit, Department of Genetics, Institut Curie, PSL Research University, Paris, France
| | - Marion Chevrier
- Biometry Unit, Institut Curie, PSL Research University, Paris and Saint-Cloud, France
| | - Benjamin Renouf
- Direction of the Clinical Research, Institut Curie, Paris, France
| | - Olivier Lantz
- INSERM U932, Institut Curie, PSL University, Paris, France
- Clinical Immunology Laboratory, Institut Curie, Paris, France
- Inserm CIC-BT1428, Institut Curie, Paris, France
| | - Sophie Gardrat
- Department of Diagnostic and Theranostic Medicine, Institut Curie, PSL Research University, Paris, France
| | - Anne Vincent-Salomon
- Department of Diagnostic and Theranostic Medicine, Institut Curie, PSL Research University, Paris, France
| | - Sergio Roman-Roman
- Department of Translational Research, Institut Curie, PSL Research University, Paris, France
| | - Manuel Rodrigues
- Department of Medical Oncology, Institut Curie, Paris and Saint-Cloud, France
- Inserm U830, DNA Repair and Uveal Melanoma (D.R.U.M.) Team, Institut Curie, PSL Research University, Paris, France
| | | | - Nathalie Cassoux
- Department of Surgical Oncology, Institut Curie, Paris, PSL Research University, Paris, France
| | - Marc-Henri Stern
- Inserm U830, DNA Repair and Uveal Melanoma (D.R.U.M.) Team, Institut Curie, PSL Research University, Paris, France
| | - Shufang Renault
- Circulating Tumor Biomarkers Laboratory, Inserm CIC-BT, Department of Translational Research, Institut Curie, Paris, France
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Bland P, Saville H, Wai PT, Curnow L, Muirhead G, Nieminuszczy J, Ravindran N, John MB, Hedayat S, Barker HE, Wright J, Yu L, Mavrommati I, Read A, Peck B, Allen M, Gazinska P, Pemberton HN, Gulati A, Nash S, Noor F, Guppy N, Roxanis I, Pratt G, Oldreive C, Stankovic T, Barlow S, Kalirai H, Coupland SE, Broderick R, Alsafadi S, Houy A, Stern MH, Pettit S, Choudhary JS, Haider S, Niedzwiedz W, Lord CJ, Natrajan R. SF3B1 hotspot mutations confer sensitivity to PARP inhibition by eliciting a defective replication stress response. Nat Genet 2023; 55:1311-1323. [PMID: 37524790 PMCID: PMC10412459 DOI: 10.1038/s41588-023-01460-5] [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: 03/09/2023] [Accepted: 06/26/2023] [Indexed: 08/02/2023]
Abstract
SF3B1 hotspot mutations are associated with a poor prognosis in several tumor types and lead to global disruption of canonical splicing. Through synthetic lethal drug screens, we identify that SF3B1 mutant (SF3B1MUT) cells are selectively sensitive to poly (ADP-ribose) polymerase inhibitors (PARPi), independent of hotspot mutation and tumor site. SF3B1MUT cells display a defective response to PARPi-induced replication stress that occurs via downregulation of the cyclin-dependent kinase 2 interacting protein (CINP), leading to increased replication fork origin firing and loss of phosphorylated CHK1 (pCHK1; S317) induction. This results in subsequent failure to resolve DNA replication intermediates and G2/M cell cycle arrest. These defects are rescued through CINP overexpression, or further targeted by a combination of ataxia-telangiectasia mutated and PARP inhibition. In vivo, PARPi produce profound antitumor effects in multiple SF3B1MUT cancer models and eliminate distant metastases. These data provide the rationale for testing the clinical efficacy of PARPi in a biomarker-driven, homologous recombination proficient, patient population.
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Affiliation(s)
- Philip Bland
- The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, UK
| | - Harry Saville
- The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, UK
| | - Patty T Wai
- The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, UK
| | - Lucinda Curnow
- Division of Cancer Biology, The Institute of Cancer Research, London, UK
| | - Gareth Muirhead
- The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, UK
| | | | - Nivedita Ravindran
- The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, UK
| | - Marie Beatrix John
- The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, UK
| | - Somaieh Hedayat
- The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, UK
| | - Holly E Barker
- The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, UK
- Stem Cells and Cancer Division, The Walter and Eliza Hall Institute of Medical Research, Melbourne, Victoria, Australia
| | - James Wright
- Division of Cancer Biology, The Institute of Cancer Research, London, UK
| | - Lu Yu
- Division of Cancer Biology, The Institute of Cancer Research, London, UK
| | - Ioanna Mavrommati
- The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, UK
| | - Abigail Read
- The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, UK
| | - Barrie Peck
- The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, UK
- Translational Cancer Metabolism Team, Centre for Tumour Biology, Barts Cancer Institute, Cancer Research UK Centre of Excellence, Queen Mary University of London, Charterhouse Square, London, UK
| | - Mark Allen
- Biological Services Unit, The Institute of Cancer Research, London, UK
| | - Patrycja Gazinska
- The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, UK
| | - Helen N Pemberton
- The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, UK
- The Cancer Research UK Gene Function Laboratory, The Institute of Cancer Research, London, UK
| | - Aditi Gulati
- The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, UK
- The Cancer Research UK Gene Function Laboratory, The Institute of Cancer Research, London, UK
| | - Sarah Nash
- The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, UK
| | - Farzana Noor
- The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, UK
| | - Naomi Guppy
- The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, UK
| | - Ioannis Roxanis
- The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, UK
| | - Guy Pratt
- University Hospitals Birmingham NHS Foundation Trust, Birmingham, UK
| | - Ceri Oldreive
- Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham, UK
| | - Tatjana Stankovic
- Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham, UK
| | - Samantha Barlow
- Liverpool Ocular Oncology Research Group, Department of Molecular and Clinical Cancer Medicine, University of Liverpool, Liverpool, UK
| | - Helen Kalirai
- Liverpool Ocular Oncology Research Group, Department of Molecular and Clinical Cancer Medicine, University of Liverpool, Liverpool, UK
| | - Sarah E Coupland
- Liverpool Ocular Oncology Research Group, Department of Molecular and Clinical Cancer Medicine, University of Liverpool, Liverpool, UK
| | - Ronan Broderick
- Division of Cancer Biology, The Institute of Cancer Research, London, UK
| | - Samar Alsafadi
- Inserm U830, PSL University, Institut Curie, Paris, France
| | - Alexandre Houy
- Inserm U830, PSL University, Institut Curie, Paris, France
| | | | - Stephen Pettit
- The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, UK
- The Cancer Research UK Gene Function Laboratory, The Institute of Cancer Research, London, UK
| | - Jyoti S Choudhary
- Division of Cancer Biology, The Institute of Cancer Research, London, UK
| | - Syed Haider
- The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, UK
| | | | - Christopher J Lord
- The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, UK
- The Cancer Research UK Gene Function Laboratory, The Institute of Cancer Research, London, UK
| | - Rachael Natrajan
- The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, UK.
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Bland P, Saville H, Read A, Wai P, Muirhead G, Curnow L, Nieminuszczy J, Ravindran N, John M, Hedayat S, Barker H, Wright J, Yu L, Mavrommati I, Peck B, Allen M, Gazinska P, Pemberton H, Gulati A, Nash S, Noor F, Guppy N, Roxanis I, Barlow S, Kalirai H, Coupland S, Broderick R, Alsafadi S, Houy A, Stern MH, Pettit S, Choudhary J, Haider S, Niedzwiedz W, Lord C, Natrajan R. Abstract P6-10-05: Mutations in the RNA Splicing Factor SF3B1 drive endocrine therapy resistance and confer a targetable replication stress response defect through PARP inhibition. Cancer Res 2023. [DOI: 10.1158/1538-7445.sabcs22-p6-10-05] [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] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/06/2023]
Abstract
Abstract
Background: Heterozygous hotspot mutations in the RNA splicing factor SF3B1, occur in 3% of unselected breast cancers and are associated with oestrogen receptor (ER+) breast cancer (BC) where they are enriched in metastatic disease and are associated with a poor clinical outcome. SF3B1 mutations drive distinct signatures of alternative splicing through cryptic 3’ splice site selection leading to global transcriptomic and proteomic changes. The functional consequences of the mis-splicing events and resultant genetic vulnerabilities are poorly understood and precision medicine approaches that exploit these characteristics are not clinically available (Table 1).
Methods: To understand the role of SF3B1 mutations in ER+ BC, we generated a series of SF3B1 mutant (SF3B1MUT) isogenic cell lines which were characterised using RNA-sequencing and high content mass-spectrometry proteomic profiling. SF3B1 interactome analysis was also performed using immunoprecipitation of SF3B1 followed by mass-spectrometry. The molecular consequences of aberrant splicing were investigated using a targeted screening approach of 280 genes predicted to be alternatively spliced in SF3B1MUT BC, while high-throughput drug screens were used to identify novel therapeutic options for patients with SF3B1MUT breast cancer using isogenic cells. Hits were validated in vitro and in vivo using cell line and patient derived xenografts.
Results: Transcriptomic and proteomic profiling of SF3B1MUT cells identified global alternative 3’ splice site selection and subsequent proteomic changes induced by the mutations. Investigation of the SF3B1K700E interactome identified an enrichment of SF3B1K700E binding with ER, aberrant splicing of ER target genes, global rewiring of ER chromatin binding and resistance to endocrine therapy. Silencing of the aberrantly spliced candidate genes PPIH, TRIM37, HIGD1A, BRD9, and PHKG2 significantly enhanced the growth of the SF3B1 mutant cells, suggestive of a dose dependent tumour suppressive effect.
Through synthetic-lethal drug screens we found that SF3B1MUT cells are selectively sensitive to PARP inhibitors. SF3B1MUT cells display a defective response to PARPi induced replication stress. Mechanistically, this occurs via defective ATR signalling in SF3B1MUT cells, which upon PARPi exposure leads to increased replication origin firing and loss of pChk1 (S317) induction. The resultant replication stress leads to failure to resolve DNA replication intermediates via the endonuclease MUS81 and cell cycle stalling at the G2/M checkpoint. These defects can be further targeted by ATM, CDK7 or FACT inhibition, when used in combination with PARPi treatment. This SF3B1MUT selective PARPi sensitivity is preserved across multiple cell lines and patient derived tumour models. In vivo, PARPi produce profound anti-tumour effects in multiple SF3B1MUT cancer models and eliminate distant metastases.
Conclusions: Our integrative analysis reveals mechanistic insight into the role of SF3B1 mutations in endocrine therapy response in ER+ breast cancers, where altered SF3B1 induces ER-transcriptional re-programming. We further identified a robust synthetic-lethal relationship of mutant SF3B1 with PARP inhibition that is caused by a defective response to PARPi induced replication stress. Furthermore, we identified several potential selective combination strategies together with PARPi that are selective for SF3B1MUT cells. Together, these data provide the pre-clinical and mechanistic rationale for assessing already-approved PARPi in a biomarker-defined subset of advanced ER+ BC.
Table 1. Identified potential therapies for SF3B1 mutant cancers from this study and the literature
Citation Format: Phil Bland, Harry Saville, Abigail Read, Patty Wai, Gareth Muirhead, Lucinda Curnow, Jadwiga Nieminuszczy, Nivedita Ravindran, Marie John, Somaieh Hedayat, Holly Barker, James Wright, Lu Yu, Ioanna Mavrommati, Barrie Peck, Mark Allen, Patrycja Gazinska, Helen Pemberton, Aditi Gulati, Sarah Nash, Farzana Noor, Naomi Guppy, Ioannis Roxanis, Samantha Barlow, Helen Kalirai, Sarah Coupland, Ronan Broderick, Samar Alsafadi, Alexandre Houy, Marc-Henri Stern, Stephen Pettit, Jyoti Choudhary, Syed Haider, Wojciech Niedzwiedz, Christopher Lord, Rachael Natrajan. Mutations in the RNA Splicing Factor SF3B1 drive endocrine therapy resistance and confer a targetable replication stress response defect through PARP inhibition. [abstract]. In: Proceedings of the 2022 San Antonio Breast Cancer Symposium; 2022 Dec 6-10; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2023;83(5 Suppl):Abstract nr P6-10-05.
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Affiliation(s)
- Phil Bland
- 1The Institute of Cancer Research, London, United Kingdom
| | - Harry Saville
- 2The Institute of Cancer Research, London,, United Kingdom
| | - Abigail Read
- 3The Institute of Cancer Research, London, United Kingdom
| | - Patty Wai
- 4The Institute of Cancer Research, London, United Kingdom
| | | | - Lucinda Curnow
- 6The Institute of Cancer Research, London, United Kingdom
| | | | | | - Marie John
- 9The Institute of Cancer Research, United Kingdom
| | | | - Holly Barker
- 11The Institute of Cancer Research, London, Australia
| | - James Wright
- 12The Institute of Cancer Research, London, United Kingdom
| | - Lu Yu
- 13The Institute of Cancer Research, London, United Kingdom
| | | | - Barrie Peck
- 15Barts Cancer Institute, Queen Mary University of London, United Kingdom
| | - Mark Allen
- 16The Institute of Cancer Research, London, United Kingdom
| | | | | | - Aditi Gulati
- 19The Institute of Cancer Research, London, United Kingdom
| | - Sarah Nash
- 20The Institute of Cancer Research, London, United Kingdom
| | - Farzana Noor
- 21The Institute of Cancer Research, London, United Kingdom
| | - Naomi Guppy
- 22The Institute of Cancer Research, London, United Kingdom
| | - Ioannis Roxanis
- 23Breast Cancer Now Toby Robinsons Research Centre, The Institute of Cancer Research, London
| | - Samantha Barlow
- 24Department of Molecular and Clinical Cancer Medicine, University of Liverpool, United Kingdom
| | - Helen Kalirai
- 25Department of Molecular and Clinical Cancer Medicine, United Kingdom
| | - Sarah Coupland
- 26Department of Molecular and Clinical Cancer Medicine, United Kingdom
| | | | | | - Alexandre Houy
- 29Inserm U830, PSL University, Institut Curie, United Kingdom
| | | | - Stephen Pettit
- 31The Institute of Cancer Research, London, United Kingdom
| | | | - Syed Haider
- 33Breast Cancer Now Toby Robinsons Research Centre, The Institute of Cancer Research, London
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7
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Burbage M, Rocañín-Arjó A, Baudon B, Arribas YA, Merlotti A, Rookhuizen DC, Heurtebise-Chrétien S, Ye M, Houy A, Burgdorf N, Suarez G, Gros M, Sadacca B, Carrascal M, Garmilla A, Bohec M, Baulande S, Lombard B, Loew D, Waterfall JJ, Stern MH, Goudot C, Amigorena S. Epigenetically controlled tumor antigens derived from splice junctions between exons and transposable elements. Sci Immunol 2023; 8:eabm6360. [PMID: 36735776 DOI: 10.1126/sciimmunol.abm6360] [Citation(s) in RCA: 20] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Accepted: 01/12/2023] [Indexed: 02/05/2023]
Abstract
Oncogenesis often implicates epigenetic alterations, including derepression of transposable elements (TEs) and defects in alternative splicing. Here, we explore the possibility that noncanonical splice junctions between exons and TEs represent a source of tumor-specific antigens. We show that mouse normal tissues and tumor cell lines express wide but distinct ranges of mRNA junctions between exons and TEs, some of which are tumor specific. Immunopeptidome analyses in tumor cell lines identified peptides derived from exon-TE splicing junctions associated to MHC-I molecules. Exon-TE junction-derived peptides were immunogenic in tumor-bearing mice. Both prophylactic and therapeutic vaccinations with junction-derived peptides delayed tumor growth in vivo. Inactivation of the TE-silencing histone 3-lysine 9 methyltransferase Setdb1 caused overexpression of new immunogenic junctions in tumor cells. Our results identify exon-TE splicing junctions as epigenetically controlled, immunogenic, and protective tumor antigens in mice, opening possibilities for tumor targeting and vaccination in patients with cancer.
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Affiliation(s)
- Marianne Burbage
- Institut Curie, Université Paris Sciences et Lettres, 75005 Paris, France
| | - Ares Rocañín-Arjó
- Institut Curie, Université Paris Sciences et Lettres, 75005 Paris, France
| | - Blandine Baudon
- Institut Curie, Université Paris Sciences et Lettres, 75005 Paris, France
| | - Yago A Arribas
- Institut Curie, Université Paris Sciences et Lettres, 75005 Paris, France
| | - Antonela Merlotti
- Institut Curie, Université Paris Sciences et Lettres, 75005 Paris, France
| | - Derek C Rookhuizen
- Institut Curie, Université Paris Sciences et Lettres, 75005 Paris, France
| | | | - Mengliang Ye
- Institut Curie, Université Paris Sciences et Lettres, 75005 Paris, France
| | - Alexandre Houy
- Institut Curie, Université Paris Sciences et Lettres, INSERM U830, DNA Repair and Uveal Melanoma (D.R.U.M.), Equipe labellisée par la Ligue Nationale Contre le Cancer, 75005 Paris, France
| | - Nina Burgdorf
- Institut Curie, Université Paris Sciences et Lettres, 75005 Paris, France
| | - Guadalupe Suarez
- Institut Curie, Université Paris Sciences et Lettres, 75005 Paris, France
| | - Marine Gros
- Institut Curie, Université Paris Sciences et Lettres, 75005 Paris, France
| | - Benjamin Sadacca
- Institut Curie, Université Paris Sciences et Lettres, 75005 Paris, France
- INSERM U830, PSL Research University, Institute Curie Research Center, Paris, France
- Department of Translational Research, PSL Research University, Institut Curie Research Center, Paris, France
| | - Montserrat Carrascal
- Biological and Environmental Proteomics, Institut d'Investigacions Biomèdiques de Barcelona-CSIC, IDIBAPS, Roselló 161, 6a planta, 08036 Barcelona, Spain
| | - Andrea Garmilla
- Institut Curie, Université Paris Sciences et Lettres, 75005 Paris, France
| | - Mylène Bohec
- Institut Curie, Centre de Recherche, Genomics of Excellence Platform, PSL Research University, Paris cedex 05, France
| | - Sylvain Baulande
- Institut Curie, Centre de Recherche, Genomics of Excellence Platform, PSL Research University, Paris cedex 05, France
| | - Bérangère Lombard
- Institut Curie, Centre de Recherche, Laboratoire de Spectrométrie de Masse Protéomique, PSL Research University, Paris cedex 05, France
| | - Damarys Loew
- Institut Curie, Centre de Recherche, Laboratoire de Spectrométrie de Masse Protéomique, PSL Research University, Paris cedex 05, France
| | - Joshua J Waterfall
- INSERM U830, PSL Research University, Institute Curie Research Center, Paris, France
- Department of Translational Research, PSL Research University, Institut Curie Research Center, Paris, France
| | - Marc-Henri Stern
- Institut Curie, Université Paris Sciences et Lettres, INSERM U830, DNA Repair and Uveal Melanoma (D.R.U.M.), Equipe labellisée par la Ligue Nationale Contre le Cancer, 75005 Paris, France
| | - Christel Goudot
- Institut Curie, Université Paris Sciences et Lettres, 75005 Paris, France
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8
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Merlotti A, Sadacca B, Arribas YA, Ngoma M, Burbage M, Goudot C, Houy A, Rocañín-Arjó A, Lalanne A, Seguin-Givelet A, Lefevre M, Heurtebise-Chrétien S, Baudon B, Oliveira G, Loew D, Carrascal M, Wu CJ, Lantz O, Stern MH, Girard N, Waterfall JJ, Amigorena S. Noncanonical splicing junctions between exons and transposable elements represent a source of immunogenic recurrent neo-antigens in patients with lung cancer. Sci Immunol 2023; 8:eabm6359. [PMID: 36735774 DOI: 10.1126/sciimmunol.abm6359] [Citation(s) in RCA: 23] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Accepted: 01/12/2023] [Indexed: 02/05/2023]
Abstract
Although most characterized tumor antigens are encoded by canonical transcripts (such as differentiation or tumor-testis antigens) or mutations (both driver and passenger mutations), recent results have shown that noncanonical transcripts including long noncoding RNAs and transposable elements (TEs) can also encode tumor-specific neo-antigens. Here, we investigate the presentation and immunogenicity of tumor antigens derived from noncanonical mRNA splicing events between coding exons and TEs. Comparing human non-small cell lung cancer (NSCLC) and diverse healthy tissues, we identified a subset of splicing junctions that is both tumor specific and shared across patients. We used HLA-I peptidomics to identify peptides encoded by tumor-specific junctions in primary NSCLC samples and lung tumor cell lines. Recurrent junction-encoded peptides were immunogenic in vitro, and CD8+ T cells specific for junction-encoded epitopes were present in tumors and tumor-draining lymph nodes from patients with NSCLC. We conclude that noncanonical splicing junctions between exons and TEs represent a source of recurrent, immunogenic tumor-specific antigens in patients with NSCLC.
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Affiliation(s)
- Antonela Merlotti
- Institut Curie, Université Paris Sciences et Lettres, INSERM U932, 75005 Paris, France
| | - Benjamin Sadacca
- Institut Curie, Université Paris Sciences et Lettres, INSERM U932, 75005 Paris, France
- INSERM U830, PSL Research University, Institute Curie Research Center, Paris, France
- Department of Translational Research, PSL Research University, Institut Curie Research Center, Paris, France
| | - Yago A Arribas
- Institut Curie, Université Paris Sciences et Lettres, INSERM U932, 75005 Paris, France
| | - Mercia Ngoma
- Institut Curie, Université Paris Sciences et Lettres, INSERM U932, 75005 Paris, France
| | - Marianne Burbage
- Institut Curie, Université Paris Sciences et Lettres, INSERM U932, 75005 Paris, France
| | - Christel Goudot
- Institut Curie, Université Paris Sciences et Lettres, INSERM U932, 75005 Paris, France
| | - Alexandre Houy
- INSERM U830, PSL Research University, Institute Curie Research Center, Paris, France
| | - Ares Rocañín-Arjó
- Institut Curie, Université Paris Sciences et Lettres, INSERM U932, 75005 Paris, France
| | - Ana Lalanne
- Institut Curie, Laboratory of Clinical immunology, 75005 Paris, France
- Institut Curie, CIC-BT1428, 75005 Paris, France
| | - Agathe Seguin-Givelet
- Thoracic Surgery Department, Curie-Montsouris Thorax Institute - Institut Mutualiste Montsouris, Paris, France
- Paris 13 University, Sorbonne Paris Cité, Faculty of Medicine SMBH, Bobigny, France
| | - Marine Lefevre
- Department of Pathology, Institute Mutualiste Montsouris, Paris, France
| | | | - Blandine Baudon
- Institut Curie, Université Paris Sciences et Lettres, INSERM U932, 75005 Paris, France
| | - Giacomo Oliveira
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
| | - Damarys Loew
- Institut Curie, Centre de Recherche, Laboratoire de Spectrométrie de Masse Protéomique, PSL Research University, Paris cedex 05, France
| | - Montserrat Carrascal
- Biological and Environmental Proteomics, Institut d'Investigacions Biomèdiques de Barcelona-CSIC, IDIBAPS, Roselló 161, 6a planta, 08036 Barcelona, Spain
| | - Catherine J Wu
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
- Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | - Olivier Lantz
- Institut Curie, Université Paris Sciences et Lettres, INSERM U932, 75005 Paris, France
- Institut Curie, Laboratory of Clinical immunology, 75005 Paris, France
- Institut Curie, CIC-BT1428, 75005 Paris, France
| | - Marc-Henri Stern
- INSERM U830, PSL Research University, Institute Curie Research Center, Paris, France
| | - Nicolas Girard
- Thoracic Surgery Department, Curie-Montsouris Thorax Institute - Institut Mutualiste Montsouris, Paris, France
| | - Joshua J Waterfall
- INSERM U830, PSL Research University, Institute Curie Research Center, Paris, France
- Department of Translational Research, PSL Research University, Institut Curie Research Center, Paris, France
| | - Sebastian Amigorena
- Institut Curie, Université Paris Sciences et Lettres, INSERM U932, 75005 Paris, France
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9
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Saint-Ghislain M, Derrien AC, Geoffrois L, Gastaud L, Lesimple T, Negrier S, Penel N, Kurtz JE, Le Corre Y, Dutriaux C, Gardrat S, Barnhill R, Matet A, Cassoux N, Houy A, Ramtohul T, Servois V, Mariani P, Piperno-Neumann S, Stern MH, Rodrigues M. MBD4 deficiency is predictive of response to immune checkpoint inhibitors in metastatic uveal melanoma patients. Eur J Cancer 2022; 173:105-112. [PMID: 35863105 DOI: 10.1016/j.ejca.2022.06.033] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [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: 03/01/2022] [Revised: 05/24/2022] [Accepted: 06/17/2022] [Indexed: 12/12/2022]
Abstract
BACKGROUND MBD4 mutations have been reported in uveal melanomas, acute myeloid leukemias, colorectal adenocarcinomas, gliomas, and spiradenocarcinomas and cause a hypermutated phenotype. Although metastatic uveal melanomas (mUM) are usually resistant to immune checkpoint inhibitors (ICI), the first reported MBD4-mutated (MBD4m) patient responded to ICI, suggesting that MBD4 mutation may predict response to ICI. METHODS Retrospective cohort of mUM patients treated with ICI. MBD4 was sequenced in a subset of these patients. RESULTS Three hundred mUM patients were included. Median follow-up was 17.3 months. Ten patients with an objective response and 20 cases with stable disease for >12 months were observed, corresponding to an objective response rate of 3.3% and a clinical benefit (i.e., responder patients and stable disease) rate of 10%. Of the 131 tumors sequenced for MBD4, five (3.8%) were mutated. MBD4 mutation was associated with a better objective response rate as three out of five MBD4m versus 4% of MBD4 wild-type patients responded (p < 0.001). Of these five responders, three presented progressive disease at 2.8, 13.9, and 22.3 months. Median PFS was 4.0 months in MBD4 wild-type and 22.3 months in MBD4m patients (HR = 0.22; p = 0.01). Median OS in MBD4def patients was unreached as compared to 16.6 months in MBD4pro (HR = 0.11; 95% CI: 0.02-0.86; log-rank p-test = 0.04; Fig. 2e). CONCLUSIONS In mUM patients, MBD4 mutation is highly predictive for the response, PFS, and overall survival benefit to ICI. MBD4 could be a tissue-agnostic biomarker and should be sequenced in mUM, and other tumor types where MBD4 mutations are reported.
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Affiliation(s)
- Mathilde Saint-Ghislain
- Department of Medical Oncology, Institut Curie, PSL Research University, Paris, France; INSERM U830, DNA Repair and Uveal Melanoma (D.R.U.M.), Equipe Labellisée Par La Ligue Nationale Contre le Cancer, Institut Curie, PSL Research University, Paris, France.
| | - Anne-Céline Derrien
- INSERM U830, DNA Repair and Uveal Melanoma (D.R.U.M.), Equipe Labellisée Par La Ligue Nationale Contre le Cancer, Institut Curie, PSL Research University, Paris, France.
| | - Lionnel Geoffrois
- Department of Medical Oncology, Institut de Cancérologie de Lorraine - Alexis Vautrin Cancer, Nancy, France.
| | - Lauris Gastaud
- Department of Medical Oncology, Antoine Lacassagne Cancer Centre, 06000 Nice, France.
| | - Thierry Lesimple
- Department of Medical Oncology, Centre Eugène Marquis, Rennes, France.
| | | | - Nicolas Penel
- Department of Medical Oncology, Centre Oscar Lambret, Lille University, Lille, France.
| | - Jean-Emmanuel Kurtz
- Department of Medical Oncology, Strasbourg University Hospital, Strasbourg, France.
| | - Yannick Le Corre
- Department of Dermatology, Angers University Hospital, UNAM, France.
| | - Caroline Dutriaux
- Dermatology Department, CHU de Bordeaux, Hôpital Saint André, Bordeaux, France.
| | - Sophie Gardrat
- Department of Biopathology, Institut Curie, PSL Research University, Paris, France.
| | - Raymond Barnhill
- Department of Biopathology, Institut Curie, PSL Research University, Paris, France; Faculty of Medicine, Université de Paris, Paris, France.
| | - Alexandre Matet
- Department of Ocular Oncology, Institut Curie, PSL Research University, Paris, France; Université de Paris, Paris, France.
| | - Nathalie Cassoux
- Department of Ocular Oncology, Institut Curie, PSL Research University, Paris, France; Université de Paris, Paris, France.
| | - Alexandre Houy
- INSERM U830, DNA Repair and Uveal Melanoma (D.R.U.M.), Equipe Labellisée Par La Ligue Nationale Contre le Cancer, Institut Curie, PSL Research University, Paris, France.
| | - Toulsie Ramtohul
- Department of Radiology, Institut Curie, PSL Research University, Paris, France.
| | - Vincent Servois
- Department of Radiology, Institut Curie, PSL Research University, Paris, France.
| | - Pascale Mariani
- Department of Surgical Oncology, Institut Curie, PSL Research University, Paris, France.
| | | | - Marc-Henri Stern
- INSERM U830, DNA Repair and Uveal Melanoma (D.R.U.M.), Equipe Labellisée Par La Ligue Nationale Contre le Cancer, Institut Curie, PSL Research University, Paris, France; Department of Genetics, Institut Curie, PSL Research University, Paris, France.
| | - Manuel Rodrigues
- Department of Medical Oncology, Institut Curie, PSL Research University, Paris, France; INSERM U830, DNA Repair and Uveal Melanoma (D.R.U.M.), Equipe Labellisée Par La Ligue Nationale Contre le Cancer, Institut Curie, PSL Research University, Paris, France.
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10
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Mobuchon L, Derrien AC, Houy A, Verrier T, Pierron G, Cassoux N, Milder M, Deleuze JF, Boland A, Scelo G, Cancel-Tassin G, Cussenot O, Rodrigues M, Noirel J, Machiela MJ, Stern MH. Different Pigmentation Risk Loci for High-Risk Monosomy 3 and Low-Risk Disomy 3 Uveal Melanomas. J Natl Cancer Inst 2022; 114:302-309. [PMID: 34424336 PMCID: PMC8826635 DOI: 10.1093/jnci/djab167] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2021] [Revised: 07/06/2021] [Accepted: 08/19/2021] [Indexed: 11/12/2022] Open
Abstract
BACKGROUND Uveal melanoma (UM), a rare malignant tumor of the eye, is predominantly observed in populations of European ancestry. UMs carrying a monosomy 3 (M3) frequently relapse mainly in the liver, whereas UMs with disomy 3 (D3) are associated with more favorable outcome. Here, we explored the UM genetic predisposition factors in a large genome-wide association study (GWAS) of 1142 European UM patients and 882 healthy controls . METHODS We combined 2 independent datasets (Global Screening Array) with the dataset described in a previously published GWAS in UM (Omni5 array), which were imputed separately and subsequently merged. Patients were stratified according to their chromosome 3 status, and identified UM risk loci were tested for differential association with M3 or D3 subgroups. All statistical tests were 2-sided. RESULTS We recapitulated the previously identified risk locus on chromosome 5 on CLPTM1L (rs421284: odds ratio [OR] =1.58, 95% confidence interval [CI] = 1.35 to 1.86; P = 1.98 × 10-8) and identified 2 additional risk loci involved in eye pigmentation: IRF4 locus on chromosome 6 (rs12203592: OR = 1.76, 95% CI = 1.44 to 2.16; P = 3.55 × 10-8) and HERC2 locus on chromosome 15 (rs12913832: OR= 0.57, 95% CI = 0.48 to 0.67; P = 1.88 × 10-11). The IRF4 rs12203592 single-nucleotide polymorphism was found to be exclusively associated with risk for the D3 UM subtype (ORD3 = 2.73, 95% CI = 1.87 to 3.97; P = 1.78 × 10-7), and the HERC2 rs12913832 single-nucleotide polymorphism was exclusively associated with risk for the M3 UM subtype (ORM3 = 2.43, 95% CI = 1.79 to 3.29; P = 1.13 × 10-8). However, the CLPTM1L risk locus was equally statistically significant in both subgroups. CONCLUSIONS This work identified 2 additional UM risk loci known for their role in pigmentation. Importantly, we demonstrate that UM tumor biology and metastatic potential are influenced by patients' genetic backgrounds.
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Affiliation(s)
- Lenha Mobuchon
- Inserm U830, DNA Repair and Uveal Melanoma (D.R.U.M), Equipe Labellisée par la Ligue Nationale Contre le Cancer, Institut Curie, PSL Research University, Paris, France
| | - Anne-Céline Derrien
- Inserm U830, DNA Repair and Uveal Melanoma (D.R.U.M), Equipe Labellisée par la Ligue Nationale Contre le Cancer, Institut Curie, PSL Research University, Paris, France
| | - Alexandre Houy
- Inserm U830, DNA Repair and Uveal Melanoma (D.R.U.M), Equipe Labellisée par la Ligue Nationale Contre le Cancer, Institut Curie, PSL Research University, Paris, France
| | - Thibault Verrier
- Inserm U830, DNA Repair and Uveal Melanoma (D.R.U.M), Equipe Labellisée par la Ligue Nationale Contre le Cancer, Institut Curie, PSL Research University, Paris, France
| | - Gaëlle Pierron
- Somatic Genetic Unit, Department of Genetics, Institut Curie, PSL Research University, Paris, France
| | - Nathalie Cassoux
- Department of Ocular Oncology, Institut Curie, Paris, France
- Faculty of Medicine, University of Paris Descartes, Paris, France
| | - Maud Milder
- Inserm CIC BT 1418, Institut Curie, PSL Research University, Paris, France
| | - Jean-François Deleuze
- Université Paris-Saclay, CEA, Centre National de Recherche en Génomique Humaine, Evry, France
| | - Anne Boland
- Université Paris-Saclay, CEA, Centre National de Recherche en Génomique Humaine, Evry, France
| | - Ghislaine Scelo
- International Agency for Research on Cancer (IARC), Lyon, France
- Cancer Epidemiology Unit, Department of Medical Sciences, University of Turin, Turin, Italy
| | - Géraldine Cancel-Tassin
- CeRePP, Tenon Hospital, Paris, France
- Sorbonne University, GRC n°5 Predictive Onco-Urology, AP-HP, Tenon Hospital, Paris, France
| | - Olivier Cussenot
- CeRePP, Tenon Hospital, Paris, France
- Sorbonne University, GRC n°5 Predictive Onco-Urology, AP-HP, Tenon Hospital, Paris, France
| | - Manuel Rodrigues
- Inserm U830, DNA Repair and Uveal Melanoma (D.R.U.M), Equipe Labellisée par la Ligue Nationale Contre le Cancer, Institut Curie, PSL Research University, Paris, France
- Department of Medical Oncology, Institut Curie, PSL Research University, Paris, France
| | - Josselin Noirel
- Laboratoire GBCM (EA7528), CNAM, HESAM Université, Paris, France
| | - Mitchell J Machiela
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD 20892, USA
| | - Marc-Henri Stern
- Inserm U830, DNA Repair and Uveal Melanoma (D.R.U.M), Equipe Labellisée par la Ligue Nationale Contre le Cancer, Institut Curie, PSL Research University, Paris, France
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11
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Gardrat S, Houy A, Brooks K, Cassoux N, Barnhill R, Dayot S, Bièche I, Raynal V, Baulande S, Marais R, Roman-Roman S, Stern MH, Rodrigues M. Definition of Biologically Distinct Groups of Conjunctival Melanomas According to Etiological Factors and Implications for Precision Medicine. Cancers (Basel) 2021; 13:3836. [PMID: 34359736 PMCID: PMC8345091 DOI: 10.3390/cancers13153836] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2021] [Revised: 07/19/2021] [Accepted: 07/26/2021] [Indexed: 02/06/2023] Open
Abstract
Conjunctival melanoma (ConjMel) is a potentially deadly ocular melanoma, originating from partially sunlight-exposed mucosa. We explored the mutational landscape of ConjMel and studied the correlation with etiological factors. We collected 47 primary ConjMel samples and performed next-generation sequencing of 400 genes. Hotspot mutations in BRAF, NRAS, HRAS, and KIT were observed in 16 (34%), 5 (11%), 2, and 2 cases, respectively. Patients with BRAF and CDKN2A-mutated ConjMel tended to be younger while the NF1-mutated one tended to be older. The eight tumors arising from nevi were enriched in CTNNB1 mutations (63% vs. 8%; Fisher's exact p-test = 0.001) compared to non-nevi ConjMel and five were devoid of BRAF, RAS, NF1, or KIT mutations, suggesting a specific oncogenic process in these tumors. The two KIT-mutated cases carried SF3B1 mutations and were located on sun-protected mucosa, a genotype shared with genital and anorectal mucosal melanomas. Targetable mutations were observed in ERBB2, IDH1, MET, and MAP2K1 (one occurrence each). Mutational landscape of ConjMel characterizes distinct molecular subtypes with oncogenic drivers common with mucosal and skin melanomas. CTNNB1 mutations were associated with nevus-derived ConjMel. Concomitant KIT/SF3B1 mutations in sun-protected cases suggest a common tumorigenic process with genital and anorectal mucosal melanomas.
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Affiliation(s)
- Sophie Gardrat
- INSERM U830, DNA Repair and Uveal Melanoma (D.R.U.M.), Equipe Labellisée par la Ligue Nationale Contre le Cancer and PSL Research University, Department of Biopathology, Institut Curie, PSL Research University, F-75005 Paris, France;
| | - Alexandre Houy
- INSERM U830, DNA Repair and Uveal Melanoma (D.R.U.M.), Equipe Labellisée par la Ligue Nationale Contre le Cancer, Department of Genetics, Institut Curie, PSL Research University, F-75005 Paris, France; (A.H.); (S.D.); (M.-H.S.)
| | - Kelly Brooks
- Molecular Oncology Group, CRUK Manchester Institute, The University of Manchester, Alderley Park, Manchester M13 9PL, UK; (K.B.); (R.M.)
- QIMR Berghofer Medical Research Institute, Brisbane, QLD 4006, Australia
| | - Nathalie Cassoux
- Department of Ocular Oncology, Faculty of Medicine, Institut Curie, Université de Paris Descartes, F-75005 Paris, France;
| | - Raymond Barnhill
- Department of Biopathology, Institut Curie, PSL Research University, F-75005 Paris, France;
| | - Stéphane Dayot
- INSERM U830, DNA Repair and Uveal Melanoma (D.R.U.M.), Equipe Labellisée par la Ligue Nationale Contre le Cancer, Department of Genetics, Institut Curie, PSL Research University, F-75005 Paris, France; (A.H.); (S.D.); (M.-H.S.)
| | - Ivan Bièche
- INSERM U1016, Institut Curie, Department of Genetics, Faculty of Pharmaceutical and Biological Sciences, Université de Paris, F-75005 Paris, France;
| | - Virginie Raynal
- Institut Curie Genomics of Excellence (ICGex) Platform, Institut Curie, PSL Research University, F-75005 Paris, France; (V.R.); (S.B.)
| | - Sylvain Baulande
- Institut Curie Genomics of Excellence (ICGex) Platform, Institut Curie, PSL Research University, F-75005 Paris, France; (V.R.); (S.B.)
| | - Richard Marais
- Molecular Oncology Group, CRUK Manchester Institute, The University of Manchester, Alderley Park, Manchester M13 9PL, UK; (K.B.); (R.M.)
| | - Sergio Roman-Roman
- Translational Research Department, Institut Curie, PSL Research University, F-75005 Paris, France;
| | - Marc-Henri Stern
- INSERM U830, DNA Repair and Uveal Melanoma (D.R.U.M.), Equipe Labellisée par la Ligue Nationale Contre le Cancer, Department of Genetics, Institut Curie, PSL Research University, F-75005 Paris, France; (A.H.); (S.D.); (M.-H.S.)
| | - Manuel Rodrigues
- INSERM U830, DNA Repair and Uveal Melanoma (D.R.U.M.), Equipe Labellisée par la Ligue Nationale Contre le Cancer, Department of Genetics, Institut Curie, PSL Research University, F-75005 Paris, France; (A.H.); (S.D.); (M.-H.S.)
- Department of Medical Oncology, Institut Curie, PSL Research University, F-75005, Paris, France
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12
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Derrien AC, Rodrigues M, Eeckhoutte A, Dayot S, Houy A, Mobuchon L, Gardrat S, Lequin D, Ballet S, Pierron G, Alsafadi S, Mariani O, El-Marjou A, Matet A, Colas C, Cassoux N, Stern MH. Germline MBD4 Mutations and Predisposition to Uveal Melanoma. J Natl Cancer Inst 2021; 113:80-87. [PMID: 32239153 PMCID: PMC7781447 DOI: 10.1093/jnci/djaa047] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [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: 12/20/2019] [Revised: 03/19/2020] [Accepted: 03/26/2020] [Indexed: 12/11/2022] Open
Abstract
Background Uveal melanoma (UM) arises from malignant transformation of melanocytes in the uveal tract of the eye. This rare tumor has a poor outcome with frequent chemo-resistant liver metastases. BAP1 is the only known predisposing gene for UM. UMs are generally characterized by low tumor mutation burden, but some UMs display a high level of CpG>TpG mutations associated with MBD4 inactivation. Here, we explored the incidence of germline MBD4 variants in a consecutive series of 1093 primary UM case patients and a series of 192 UM tumors with monosomy 3 (M3). Methods We performed MBD4 targeted sequencing on pooled germline (n = 1093) and tumor (n = 192) DNA samples of UM patients. MBD4 variants (n = 28) were validated by Sanger sequencing. We performed whole-exome sequencing on available tumor samples harboring MBD4 variants (n = 9). Variants of unknown pathogenicity were further functionally assessed. Results We identified 8 deleterious MBD4 mutations in the consecutive UM series, a 9.15-fold (95% confidence interval = 4.24-fold to 19.73-fold) increased incidence compared with the general population (Fisher exact test, P = 2.00 × 10–5, 2-sided), and 4 additional deleterious MBD4 mutations in the M3 cohort, including 3 germline and 1 somatic mutations. Tumors carrying deleterious MBD4 mutations were all associated with high tumor mutation burden and a CpG>TpG hypermutator phenotype. Conclusions We demonstrate that MBD4 is a new predisposing gene for UM associated with hypermutated M3 tumors. The tumor spectrum of this predisposing condition will likely expand with the addition of MBD4 to diagnostic panels. Tumors arising in such a context should be recognized because they may respond to immunotherapy.
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Affiliation(s)
- Anne-Céline Derrien
- Inserm U830, DNA Repair and Uveal Melanoma (D.R.U.M.), Equipe Labellisée Par la Ligue Nationale Contre le Cancer, Paris, France
| | - Manuel Rodrigues
- Inserm U830, DNA Repair and Uveal Melanoma (D.R.U.M.), Equipe Labellisée Par la Ligue Nationale Contre le Cancer, Paris, France.,Department of Medical Oncology, Institut Curie, PSL Research University, Paris, France
| | - Alexandre Eeckhoutte
- Inserm U830, DNA Repair and Uveal Melanoma (D.R.U.M.), Equipe Labellisée Par la Ligue Nationale Contre le Cancer, Paris, France
| | - Stéphane Dayot
- Inserm U830, DNA Repair and Uveal Melanoma (D.R.U.M.), Equipe Labellisée Par la Ligue Nationale Contre le Cancer, Paris, France
| | - Alexandre Houy
- Inserm U830, DNA Repair and Uveal Melanoma (D.R.U.M.), Equipe Labellisée Par la Ligue Nationale Contre le Cancer, Paris, France
| | - Lenha Mobuchon
- Inserm U830, DNA Repair and Uveal Melanoma (D.R.U.M.), Equipe Labellisée Par la Ligue Nationale Contre le Cancer, Paris, France
| | - Sophie Gardrat
- Inserm U830, DNA Repair and Uveal Melanoma (D.R.U.M.), Equipe Labellisée Par la Ligue Nationale Contre le Cancer, Paris, France.,Department of Biopathology, Institut Curie, PSL Research University, Paris, France
| | - Delphine Lequin
- Department of Biopathology, Institut Curie, PSL Research University, Paris, France
| | - Stelly Ballet
- Department of Biopathology, Institut Curie, PSL Research University, Paris, France
| | - Gaëlle Pierron
- Department of Biopathology, Institut Curie, PSL Research University, Paris, France
| | - Samar Alsafadi
- Inserm U830, DNA Repair and Uveal Melanoma (D.R.U.M.), Equipe Labellisée Par la Ligue Nationale Contre le Cancer, Paris, France.,Translational Research Department, Institut Curie, PSL Research University, Paris, France
| | - Odette Mariani
- Biological Resource Center, Institut Curie, PSL Research University, Paris, France
| | - Ahmed El-Marjou
- Institut Curie, PSL Research University, UMR144, Recombinant Protein Facility, Paris, France
| | - Alexandre Matet
- Department of Ocular Oncology, Institut Curie, Paris, France.,Faculty of Medicine, University of Paris Descartes, Paris, France
| | | | - Nathalie Cassoux
- Department of Ocular Oncology, Institut Curie, Paris, France.,Faculty of Medicine, University of Paris Descartes, Paris, France
| | - Marc-Henri Stern
- Inserm U830, DNA Repair and Uveal Melanoma (D.R.U.M.), Equipe Labellisée Par la Ligue Nationale Contre le Cancer, Paris, France.,Department of Genetics, Institut Curie, Paris, France
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13
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Bigot J, Lalanne AI, Lucibello F, Gueguen P, Houy A, Dayot S, Ganier O, Gilet J, Tosello J, Nemati F, Pierron G, Waterfall JJ, Barnhill R, Gardrat S, Piperno-Neumann S, Popova T, Masson V, Loew D, Mariani P, Cassoux N, Amigorena S, Rodrigues M, Alsafadi S, Stern MH, Lantz O. Splicing Patterns in SF3B1-Mutated Uveal Melanoma Generate Shared Immunogenic Tumor-Specific Neoepitopes. Cancer Discov 2021; 11:1938-1951. [PMID: 33811047 DOI: 10.1158/2159-8290.cd-20-0555] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2020] [Revised: 01/29/2021] [Accepted: 03/31/2021] [Indexed: 11/16/2022]
Abstract
Disruption of splicing patterns due to mutations of genes coding splicing factors in tumors represents a potential source of tumor neoantigens, which would be both public (shared between patients) and tumor-specific (not expressed in normal tissues). In this study, we show that mutations of the splicing factor SF3B1 in uveal melanoma generate such immunogenic neoantigens. Memory CD8+ T cells specific for these neoantigens are preferentially found in 20% of patients with uveal melanoma bearing SF3B1-mutated tumors. Single-cell analyses of neoepitope-specific T cells from the blood identified large clonal T-cell expansions, with distinct effector transcription patterns. Some of these expanded T-cell receptors are also present in the corresponding tumors. CD8+ T-cell clones specific for the neoepitopes specifically recognize and kill SF3B1-mutated tumor cells, supporting the use of this new family of neoantigens as therapeutic targets. SIGNIFICANCE: Mutations of the splicing factor SF3B1 in uveal melanoma generate shared neoantigens that are uniquely expressed by tumor cells, leading to recognition and killing by specific CD8 T cells. Mutations in splicing factors can be sources of new therapeutic strategies applicable to diverse tumors.This article is highlighted in the In This Issue feature, p. 1861.
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Affiliation(s)
- Jeremy Bigot
- INSERM U932, PSL University, Institut Curie, Paris, France
| | - Ana I Lalanne
- Laboratoire d'immunologie clinique, Institut Curie, Paris, France.,Centre d'investigation Clinique en Biothérapie, Institut Curie (CIC-BT1428), Paris, France
| | | | - Paul Gueguen
- INSERM U932, PSL University, Institut Curie, Paris, France
| | - Alexandre Houy
- INSERM U830, DNA Repair and Uveal Melanoma (D.R.U.M.), Equipe labellisée par la Ligue Nationale Contre le Cancer, PSL University, Institut Curie, Paris, France
| | - Stephane Dayot
- INSERM U830, DNA Repair and Uveal Melanoma (D.R.U.M.), Equipe labellisée par la Ligue Nationale Contre le Cancer, PSL University, Institut Curie, Paris, France
| | - Olivier Ganier
- INSERM U830, DNA Repair and Uveal Melanoma (D.R.U.M.), Equipe labellisée par la Ligue Nationale Contre le Cancer, PSL University, Institut Curie, Paris, France
| | - Jules Gilet
- INSERM U932, PSL University, Institut Curie, Paris, France
| | - Jimena Tosello
- INSERM U932, PSL University, Institut Curie, Paris, France
| | - Fariba Nemati
- Centre d'investigation Clinique en Biothérapie, Institut Curie (CIC-BT1428), Paris, France.,Laboratory of Preclinical Investigation, Translational Research Department, PSL Research University, Institut Curie, Paris, France
| | | | - Joshua J Waterfall
- INSERM U830, PSL University, Institut Curie, Paris, France, and Department of Translational Research, PSL University, Institut Curie, Paris, France
| | - Raymond Barnhill
- Departments of Pathology and Translational Research, Institut Curie, Paris, France
| | - Sophie Gardrat
- INSERM U830, DNA Repair and Uveal Melanoma (D.R.U.M.), Equipe labellisée par la Ligue Nationale Contre le Cancer, PSL University, Institut Curie, Paris, France.,Departments of Pathology and Translational Research, Institut Curie, Paris, France
| | | | - Tatiana Popova
- INSERM U830, DNA Repair and Uveal Melanoma (D.R.U.M.), Equipe labellisée par la Ligue Nationale Contre le Cancer, PSL University, Institut Curie, Paris, France
| | - Vanessa Masson
- Laboratoire de Spectrométrie de Masse Protéomique, PSL University, Institut Curie, Paris, France
| | - Damarys Loew
- Laboratoire de Spectrométrie de Masse Protéomique, PSL University, Institut Curie, Paris, France
| | - Pascale Mariani
- Department of Surgical Oncology, University of Paris, Institut Curie, Paris, France
| | - Nathalie Cassoux
- Department of Surgical Oncology, University of Paris, Institut Curie, Paris, France
| | | | - Manuel Rodrigues
- INSERM U830, DNA Repair and Uveal Melanoma (D.R.U.M.), Equipe labellisée par la Ligue Nationale Contre le Cancer, PSL University, Institut Curie, Paris, France.,Department of Medical Oncology, Institut Curie, Paris, France
| | - Samar Alsafadi
- INSERM U830, DNA Repair and Uveal Melanoma (D.R.U.M.), Equipe labellisée par la Ligue Nationale Contre le Cancer, PSL University, Institut Curie, Paris, France.,Laboratory of Uveal Biology, Translational Research Department, Institut Curie, Paris, France
| | - Marc-Henri Stern
- INSERM U830, DNA Repair and Uveal Melanoma (D.R.U.M.), Equipe labellisée par la Ligue Nationale Contre le Cancer, PSL University, Institut Curie, Paris, France
| | - Olivier Lantz
- INSERM U932, PSL University, Institut Curie, Paris, France. .,Laboratoire d'immunologie clinique, Institut Curie, Paris, France.,Centre d'investigation Clinique en Biothérapie, Institut Curie (CIC-BT1428), Paris, France
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14
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Canbezdi C, Tarin M, Houy A, Bellanger D, Popova T, Stern MH, Roman-Roman S, Alsafadi S. Functional and conformational impact of cancer-associated SF3B1 mutations depends on the position and the charge of amino acid substitution. Comput Struct Biotechnol J 2021; 19:1361-1370. [PMID: 33777335 PMCID: PMC7960499 DOI: 10.1016/j.csbj.2021.02.012] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [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: 12/03/2020] [Revised: 02/13/2021] [Accepted: 02/16/2021] [Indexed: 11/18/2022] Open
Abstract
Aberrant splicing patterns are key markers of the impact of splicing gene mutations. SF3B1 Mut-induced aberrant splicing is due to the protein conformational change. SF3B1 conformational change depends on the position and charge of AA substitution. SF3B1 mutations present unequal pathogenic and prognostic potentials.
The hotspot mutations of SF3B1, the most frequently mutated splicing gene in cancers, contribute to oncogenesis by corrupting the mRNA splicing. Further SF3B1 mutations have been reported in cancers but their consequences remain unclear. Here, we screened for SF3B1 mutations in the vicinity of the hotspot region in tumors. We then performed in-silico prediction of the functional outcome followed by in-cellulo modelling of different SF3B1 mutants. We show that cancer-associated SF3B1 mutations present varying functional consequences that are loosely predicted by the in-silico algorithms. Analysis of the tertiary structure of SF3B1 mutants revealed that the resulting splicing errors may be due to a conformational change in SF3B1 N-terminal region, which mediates binding with other splicing factors. Our study demonstrates a varying functional impact of SF3B1 mutations according to the mutated codon and the amino acid substitution, implying unequal pathogenic and prognostic potentials of SF3B1 mutations in cancers.
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Affiliation(s)
- Christine Canbezdi
- Institut Curie, PSL Research University, Uveal Melanoma Group, Translational Research Department, Paris, France
| | - Malcy Tarin
- Institut Curie, PSL Research University, Uveal Melanoma Group, Translational Research Department, Paris, France
| | - Alexandre Houy
- Institut Curie, PSL Research University, INSERM U830, DNA Repair and Uveal Melanoma (D.R.U.M.), Paris, France
| | - Dorine Bellanger
- Institut Curie, PSL Research University, INSERM U830, DNA Repair and Uveal Melanoma (D.R.U.M.), Paris, France
- University of Tours, INSERM UMR1069, Tours, France
| | - Tatiana Popova
- Institut Curie, PSL Research University, INSERM U830, DNA Repair and Uveal Melanoma (D.R.U.M.), Paris, France
| | - Marc-Henri Stern
- Institut Curie, PSL Research University, INSERM U830, DNA Repair and Uveal Melanoma (D.R.U.M.), Paris, France
| | - Sergio Roman-Roman
- Institut Curie, PSL Research University, Uveal Melanoma Group, Translational Research Department, Paris, France
| | - Samar Alsafadi
- Institut Curie, PSL Research University, Uveal Melanoma Group, Translational Research Department, Paris, France
- Corresponding author at: Uveal Melanoma Group, Translational Research Department, Institut Curie, PSL Research University, 26 rue d’Ulm, 75248 Paris, Cedex 05, France.
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15
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Eeckhoutte A, Houy A, Manié E, Reverdy M, Bièche I, Marangoni E, Goundiam O, Vincent-Salomon A, Stoppa-Lyonnet D, Bidard FC, Stern MH, Popova T. ShallowHRD: detection of homologous recombination deficiency from shallow whole genome sequencing. Bioinformatics 2020; 36:3888-3889. [PMID: 32315385 PMCID: PMC7320600 DOI: 10.1093/bioinformatics/btaa261] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [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: 01/03/2020] [Revised: 03/25/2020] [Accepted: 04/14/2020] [Indexed: 11/23/2022] Open
Abstract
Summary We introduce shallowHRD, a software tool to evaluate tumor homologous recombination deficiency (HRD) based on whole genome sequencing (WGS) at low coverage (shallow WGS or sWGS; ∼1X coverage). The tool, based on mining copy number alterations profile, implements a fast and straightforward procedure that shows 87.5% sensitivity and 90.5% specificity for HRD detection. shallowHRD could be instrumental in predicting response to poly(ADP-ribose) polymerase inhibitors, to which HRD tumors are selectively sensitive. shallowHRD displays efficiency comparable to most state-of-art approaches, is cost-effective, generates low-storable outputs and is also suitable for fixed-formalin paraffin embedded tissues. Availability and implementation shallowHRD R script and documentation are available at https://github.com/aeeckhou/shallowHRD. Supplementary information Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Alexandre Eeckhoutte
- DNA Repair and Uveal Melanoma (D.R.U.M.), Inserm U830, Institut Curie, Paris 75248, France.,Institut Curie, PSL Research University, Paris 75005, France
| | - Alexandre Houy
- DNA Repair and Uveal Melanoma (D.R.U.M.), Inserm U830, Institut Curie, Paris 75248, France.,Institut Curie, PSL Research University, Paris 75005, France
| | - Elodie Manié
- DNA Repair and Uveal Melanoma (D.R.U.M.), Inserm U830, Institut Curie, Paris 75248, France.,Institut Curie, PSL Research University, Paris 75005, France
| | - Manon Reverdy
- DNA Repair and Uveal Melanoma (D.R.U.M.), Inserm U830, Institut Curie, Paris 75248, France.,Institut Curie, PSL Research University, Paris 75005, France
| | - Ivan Bièche
- Department of Genetics, Institut Curie, Paris 75248, France
| | - Elisabetta Marangoni
- Institut Curie, PSL Research University, Paris 75005, France.,Department of Translational Research, Institut Curie PSL Research University, Paris 75248, France
| | - Oumou Goundiam
- Institut Curie, PSL Research University, Paris 75005, France.,Department of Translational Research, Institut Curie PSL Research University, Paris 75248, France
| | - Anne Vincent-Salomon
- Department of Biopathology, Institut Curie PSL Research University, Paris 75005, France
| | - Dominique Stoppa-Lyonnet
- DNA Repair and Uveal Melanoma (D.R.U.M.), Inserm U830, Institut Curie, Paris 75248, France.,Faculty of Medicine, University of Paris, Paris, France
| | - François-Clément Bidard
- Department of Medical Oncology, Institut Curie PSL Research University, Paris 75248, France.,Versailles Saint Quentin en Yvelines University, Paris Saclay University, Versailles 78035, France
| | - Marc-Henri Stern
- DNA Repair and Uveal Melanoma (D.R.U.M.), Inserm U830, Institut Curie, Paris 75248, France.,Institut Curie, PSL Research University, Paris 75005, France.,Department of Genetics, Institut Curie, Paris 75248, France
| | - Tatiana Popova
- DNA Repair and Uveal Melanoma (D.R.U.M.), Inserm U830, Institut Curie, Paris 75248, France.,Institut Curie, PSL Research University, Paris 75005, France
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16
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Alsafadi S, Dayot S, Tarin M, Houy A, Bellanger D, Cornella M, Wassef M, Waterfall JJ, Lehnert E, Roman-Roman S, Stern MH, Popova T. Genetic alterations of SUGP1 mimic mutant-SF3B1 splice pattern in lung adenocarcinoma and other cancers. Oncogene 2020; 40:85-96. [PMID: 33057152 PMCID: PMC7790757 DOI: 10.1038/s41388-020-01507-5] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2020] [Revised: 09/30/2020] [Accepted: 10/01/2020] [Indexed: 12/31/2022]
Abstract
Genes involved in 3′-splice site recognition during mRNA splicing constitute an emerging class of oncogenes. SF3B1 is the most frequently mutated splicing factor in cancer, and SF3B1 mutants corrupt branchpoint recognition leading to usage of cryptic 3′-splice sites and subsequent aberrant junctions. For a comprehensive determination of alterations leading to this splicing pattern, we performed a pan-TCGA screening for SF3B1-specific aberrant acceptor usage. While the most of aberrant 3′-splice patterns were explained by SF3B1 mutations, we also detected nine SF3B1 wild-type tumors (including five lung adenocarcinomas). Genomic profile analysis of these tumors identified somatic mutations combined with loss-of-heterozygosity in the splicing factor SUGP1 in five of these cases. Modeling of SUGP1 loss and mutations in cell lines showed that both alterations induced mutant-SF3B1-like aberrant splicing. Our study provides definitive evidence that genetic alterations of SUGP1 genocopy SF3B1 mutations in lung adenocarcinoma and other cancers.
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Affiliation(s)
- Samar Alsafadi
- Institut Curie, Translational Research Department, PSL Research University, Paris, France.,Institut Curie, INSERM U830, DNA Repair and Uveal Melanoma (D.R.U.M.), Equipe labellisée par la Ligue Nationale Contre le Cancer, PSL Research University, Paris, France
| | - Stephane Dayot
- Institut Curie, INSERM U830, DNA Repair and Uveal Melanoma (D.R.U.M.), Equipe labellisée par la Ligue Nationale Contre le Cancer, PSL Research University, Paris, France
| | - Malcy Tarin
- Institut Curie, Translational Research Department, PSL Research University, Paris, France
| | - Alexandre Houy
- Institut Curie, INSERM U830, DNA Repair and Uveal Melanoma (D.R.U.M.), Equipe labellisée par la Ligue Nationale Contre le Cancer, PSL Research University, Paris, France
| | - Dorine Bellanger
- Institut Curie, INSERM U830, DNA Repair and Uveal Melanoma (D.R.U.M.), Equipe labellisée par la Ligue Nationale Contre le Cancer, PSL Research University, Paris, France
| | - Michele Cornella
- Institut Curie, INSERM U830, DNA Repair and Uveal Melanoma (D.R.U.M.), Equipe labellisée par la Ligue Nationale Contre le Cancer, PSL Research University, Paris, France
| | - Michel Wassef
- Institut Curie, PSL Research University, Sorbonne University, Paris, France.,U934 INSERM, UMR3215 CNRS, Paris, France
| | - Joshua J Waterfall
- Institut Curie, Translational Research Department, PSL Research University, Paris, France.,Institut Curie, INSERM U830, DNA Repair and Uveal Melanoma (D.R.U.M.), Equipe labellisée par la Ligue Nationale Contre le Cancer, PSL Research University, Paris, France
| | | | - Sergio Roman-Roman
- Institut Curie, Translational Research Department, PSL Research University, Paris, France
| | - Marc-Henri Stern
- Institut Curie, INSERM U830, DNA Repair and Uveal Melanoma (D.R.U.M.), Equipe labellisée par la Ligue Nationale Contre le Cancer, PSL Research University, Paris, France.
| | - Tatiana Popova
- Institut Curie, INSERM U830, DNA Repair and Uveal Melanoma (D.R.U.M.), Equipe labellisée par la Ligue Nationale Contre le Cancer, PSL Research University, Paris, France
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17
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Bondu S, Alary AS, Lefèvre C, Houy A, Jung G, Lefebvre T, Rombaut D, Boussaid I, Bousta A, Guillonneau F, Perrier P, Alsafadi S, Wassef M, Margueron R, Rousseau A, Droin N, Cagnard N, Kaltenbach S, Winter S, Kubasch AS, Bouscary D, Santini V, Toma A, Hunault M, Stamatoullas A, Gyan E, Cluzeau T, Platzbecker U, Adès L, Puy H, Stern MH, Karim Z, Mayeux P, Nemeth E, Park S, Ganz T, Kautz L, Kosmider O, Fontenay M. A variant erythroferrone disrupts iron homeostasis in SF3B1-mutated myelodysplastic syndrome. Sci Transl Med 2020; 11:11/500/eaav5467. [PMID: 31292266 DOI: 10.1126/scitranslmed.aav5467] [Citation(s) in RCA: 52] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2018] [Revised: 03/19/2019] [Accepted: 06/12/2019] [Indexed: 12/21/2022]
Abstract
Myelodysplastic syndromes (MDS) with ring sideroblasts are hematopoietic stem cell disorders with erythroid dysplasia and mutations in the SF3B1 splicing factor gene. Patients with MDS with SF3B1 mutations often accumulate excessive tissue iron, even in the absence of transfusions, but the mechanisms that are responsible for their parenchymal iron overload are unknown. Body iron content, tissue distribution, and the supply of iron for erythropoiesis are controlled by the hormone hepcidin, which is regulated by erythroblasts through secretion of the erythroid hormone erythroferrone (ERFE). Here, we identified an alternative ERFE transcript in patients with MDS with the SF3B1 mutation. Induction of this ERFE transcript in primary SF3B1-mutated bone marrow erythroblasts generated a variant protein that maintained the capacity to suppress hepcidin transcription. Plasma concentrations of ERFE were higher in patients with MDS with an SF3B1 gene mutation than in patients with SF3B1 wild-type MDS. Thus, hepcidin suppression by a variant ERFE is likely responsible for the increased iron loading in patients with SF3B1-mutated MDS, suggesting that ERFE could be targeted to prevent iron-mediated toxicity. The expression of the variant ERFE transcript that was restricted to SF3B1-mutated erythroblasts decreased in lenalidomide-responsive anemic patients, identifying variant ERFE as a specific biomarker of clonal erythropoiesis.
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Affiliation(s)
- Sabrina Bondu
- Université de Paris, Paris 75006, France.,Institut Cochin, Département Développement, Reproduction, Cancer, Paris 75014, France.,Institut National de la Santé et de la Recherche médicale (INSERM) U1016, Paris 75014, France.,Centre National de la Recherche Scientifique (CNRS) Unité Mixte de recherche (UMR) 8104, Paris 75014, France
| | - Anne-Sophie Alary
- Université de Paris, Paris 75006, France.,Institut Cochin, Département Développement, Reproduction, Cancer, Paris 75014, France.,Institut National de la Santé et de la Recherche médicale (INSERM) U1016, Paris 75014, France.,Centre National de la Recherche Scientifique (CNRS) Unité Mixte de recherche (UMR) 8104, Paris 75014, France.,Service d'hématologie biologique, Assistance Publique-Hôpitaux de Paris (AP-HP), Hôpitaux Universitaires Paris Centre-Cochin, Paris 75014, France
| | - Carine Lefèvre
- Université de Paris, Paris 75006, France.,Institut Cochin, Département Développement, Reproduction, Cancer, Paris 75014, France.,Institut National de la Santé et de la Recherche médicale (INSERM) U1016, Paris 75014, France.,Centre National de la Recherche Scientifique (CNRS) Unité Mixte de recherche (UMR) 8104, Paris 75014, France.,Laboratoire d'excellence du Globule Rouge GR-Ex, Paris 75015, France
| | - Alexandre Houy
- Institut Curie, PSL Research University, Human Genetics and Oncogenesis, Paris 75005, France
| | - Grace Jung
- Department of Medicine, David Geffen School of Medicine, University of California, Los Angeles, CA 90095, USA
| | - Thibaud Lefebvre
- Université de Paris, Paris 75006, France.,Laboratoire d'excellence du Globule Rouge GR-Ex, Paris 75015, France.,INSERM, UMR 1149/ERL CNRS 8252, Centre de Recherches sur l'inflammation, Université de Paris, Paris 75018, France
| | - David Rombaut
- Université de Paris, Paris 75006, France.,Institut Cochin, Département Développement, Reproduction, Cancer, Paris 75014, France.,Institut National de la Santé et de la Recherche médicale (INSERM) U1016, Paris 75014, France.,Centre National de la Recherche Scientifique (CNRS) Unité Mixte de recherche (UMR) 8104, Paris 75014, France
| | - Ismael Boussaid
- Université de Paris, Paris 75006, France.,Institut Cochin, Département Développement, Reproduction, Cancer, Paris 75014, France.,Institut National de la Santé et de la Recherche médicale (INSERM) U1016, Paris 75014, France.,Centre National de la Recherche Scientifique (CNRS) Unité Mixte de recherche (UMR) 8104, Paris 75014, France
| | - Abderrahmane Bousta
- Université de Paris, Paris 75006, France.,Institut Cochin, Département Développement, Reproduction, Cancer, Paris 75014, France.,Institut National de la Santé et de la Recherche médicale (INSERM) U1016, Paris 75014, France.,Centre National de la Recherche Scientifique (CNRS) Unité Mixte de recherche (UMR) 8104, Paris 75014, France
| | - François Guillonneau
- Université de Paris, Paris 75006, France.,Institut Cochin, Département Développement, Reproduction, Cancer, Paris 75014, France.,Institut National de la Santé et de la Recherche médicale (INSERM) U1016, Paris 75014, France.,Centre National de la Recherche Scientifique (CNRS) Unité Mixte de recherche (UMR) 8104, Paris 75014, France.,Proteomic platform 3P5, Université de Paris, Paris 75014, France
| | - Prunelle Perrier
- Institut de Recherche en Santé Digestive (IRSD), Université de Toulouse, INSERM U1220, Institut National de la Recherche Agronomique U1416, Ecole Nationale Vétérinaire de Toulouse, Université Paul Sabatier, Toulouse 31024, France
| | - Samar Alsafadi
- Institut Curie, PSL Research University, Department of Translational Research, Paris 75005, France
| | - Michel Wassef
- Institut Curie, PSL Research University, INSERM 934/UMR 3215, Genetics and biology of Development, Paris 75005 France
| | - Raphaël Margueron
- Institut Curie, PSL Research University, INSERM 934/UMR 3215, Genetics and biology of Development, Paris 75005 France
| | - Alice Rousseau
- Université de Paris, Paris 75006, France.,Institut Cochin, Département Développement, Reproduction, Cancer, Paris 75014, France.,Institut National de la Santé et de la Recherche médicale (INSERM) U1016, Paris 75014, France.,Centre National de la Recherche Scientifique (CNRS) Unité Mixte de recherche (UMR) 8104, Paris 75014, France
| | - Nathalie Droin
- Institut Gustave Roussy, Genomic platform, Villejuif 94805, France
| | - Nicolas Cagnard
- Université de Paris, Paris 75006, France.,Platform Bioinformatics, Université de Paris, Paris 75015, France
| | - Sophie Kaltenbach
- Université de Paris, Paris 75006, France.,Laboratoire de Génétique, AP-HP, Hôpital Necker, Paris 75015, France
| | - Susann Winter
- Medical Clinic und Policlinic 1, Technische Universität Dresden, Dresden 01307, Germany
| | - Anne-Sophie Kubasch
- Medical Clinic und Policlinic 1, Hematology and Cellular Therapy, University Hospital, Leipzig 04103, Germany
| | - Didier Bouscary
- Université de Paris, Paris 75006, France.,Institut Cochin, Département Développement, Reproduction, Cancer, Paris 75014, France.,Institut National de la Santé et de la Recherche médicale (INSERM) U1016, Paris 75014, France.,Centre National de la Recherche Scientifique (CNRS) Unité Mixte de recherche (UMR) 8104, Paris 75014, France.,Service d'Hématologie clinique, AP-HP, Hôpitaux Universitaires Paris Centre-Cochin, Paris 75014, France
| | - Valeria Santini
- MDS unit, Hematology, AOU Careggi, University of Florence, Florence 50134, Italy
| | - Andrea Toma
- Département d'Hématologie, AP-HP, Hôpital Henri-Mondor, Université Paris 12, Créteil 94000, France
| | - Mathilde Hunault
- Service des Maladies du Sang, Centre hospitalo-universitaire, Angers 49100, France
| | | | - Emmanuel Gyan
- Service d'hématologie et thérapie cellulaire, Centre hospitalo-universitaire, CNRS ERL 7001 LNOx, Université de Tours, Tours 37044, France
| | - Thomas Cluzeau
- Côte d'Azur University, CHU of Nice, Hematology department and INSERM U1065, Mediterranean Center of Molecular Medecine, Nice 06204, France
| | - Uwe Platzbecker
- Medical Clinic und Policlinic 1, Hematology and Cellular Therapy, University Hospital, Leipzig 04103, Germany
| | - Lionel Adès
- Université de Paris, Paris 75006, France.,Service d'Hématologie Senior, AP-HP, Hôpital Saint-Louis, Paris 75010, France
| | - Hervé Puy
- Université de Paris, Paris 75006, France.,Laboratoire d'excellence du Globule Rouge GR-Ex, Paris 75015, France.,INSERM, UMR 1149/ERL CNRS 8252, Centre de Recherches sur l'inflammation, Université de Paris, Paris 75018, France
| | - Marc-Henri Stern
- Institut Curie, PSL Research University, INSERM U830, Genetics and biology of cancers, DNA repair and uveal melanoma (D.R.U.M.), Équipe labellisée par la Ligue nationale contre le cancer, Paris 75005, France
| | - Zoubida Karim
- Université de Paris, Paris 75006, France.,Laboratoire d'excellence du Globule Rouge GR-Ex, Paris 75015, France.,INSERM, UMR 1149/ERL CNRS 8252, Centre de Recherches sur l'inflammation, Université de Paris, Paris 75018, France
| | - Patrick Mayeux
- Université de Paris, Paris 75006, France.,Institut Cochin, Département Développement, Reproduction, Cancer, Paris 75014, France.,Institut National de la Santé et de la Recherche médicale (INSERM) U1016, Paris 75014, France.,Centre National de la Recherche Scientifique (CNRS) Unité Mixte de recherche (UMR) 8104, Paris 75014, France.,Laboratoire d'excellence du Globule Rouge GR-Ex, Paris 75015, France.,Proteomic platform 3P5, Université de Paris, Paris 75014, France
| | - Elizabeta Nemeth
- Department of Medicine, David Geffen School of Medicine, University of California, Los Angeles, CA 90095, USA
| | - Sophie Park
- Département d'Hématologie, Centre Hospitalier Universitaire, Université de Grenoble Alpes, La Tronche 38700, France
| | - Tomas Ganz
- Department of Medicine, David Geffen School of Medicine, University of California, Los Angeles, CA 90095, USA
| | - Léon Kautz
- Institut de Recherche en Santé Digestive (IRSD), Université de Toulouse, INSERM U1220, Institut National de la Recherche Agronomique U1416, Ecole Nationale Vétérinaire de Toulouse, Université Paul Sabatier, Toulouse 31024, France
| | - Olivier Kosmider
- Université de Paris, Paris 75006, France. .,Institut Cochin, Département Développement, Reproduction, Cancer, Paris 75014, France.,Institut National de la Santé et de la Recherche médicale (INSERM) U1016, Paris 75014, France.,Centre National de la Recherche Scientifique (CNRS) Unité Mixte de recherche (UMR) 8104, Paris 75014, France.,Service d'hématologie biologique, Assistance Publique-Hôpitaux de Paris (AP-HP), Hôpitaux Universitaires Paris Centre-Cochin, Paris 75014, France.,Laboratoire d'excellence du Globule Rouge GR-Ex, Paris 75015, France
| | - Michaëla Fontenay
- Université de Paris, Paris 75006, France. .,Institut Cochin, Département Développement, Reproduction, Cancer, Paris 75014, France.,Institut National de la Santé et de la Recherche médicale (INSERM) U1016, Paris 75014, France.,Centre National de la Recherche Scientifique (CNRS) Unité Mixte de recherche (UMR) 8104, Paris 75014, France.,Service d'hématologie biologique, Assistance Publique-Hôpitaux de Paris (AP-HP), Hôpitaux Universitaires Paris Centre-Cochin, Paris 75014, France.,Laboratoire d'excellence du Globule Rouge GR-Ex, Paris 75015, France
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Tsantoulis P, Delorenzi M, Bièche I, Vacher S, Mariani P, Cassoux N, Houy A, Stern MH, Roman-Roman S, Dietrich PY, Roth A, Cacheux W. Prospective validation in epithelial tumors of a gene expression predictor of liver metastasis derived from uveal melanoma. Sci Rep 2019; 9:17178. [PMID: 31748560 PMCID: PMC6868129 DOI: 10.1038/s41598-019-52841-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [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: 03/19/2019] [Accepted: 10/18/2019] [Indexed: 12/13/2022] Open
Abstract
Predicting the risk of liver metastasis can have important prognostic and therapeutic implications, given the availability of liver-directed therapy. Uveal melanoma has a striking predisposition for liver metastasis despite the absence of anatomical proximity. Understanding its biology may uncover factors promoting liver metastasis in other malignancies. We quantified gene expression by RNAseq in 76 uveal melanomas and combined with public data in a meta-analysis of 196 patients. The meta-analysis of uveal melanoma gene expression identified 63 genes which remained prognostic after adjustment for chromosome 3 status. Two genes, PTP4A3 and JPH1, were selected by L1-penalized regression and combined in a prognostic score. The score predicted liver-specific relapse in a public pan-cancer dataset and in two public colorectal cancer datasets. The score varied between colorectal consensus molecular subtypes (CMS), as did the risk of liver relapse, which was lowest in CMS1. Additional prospective validation was done by real-time PCR in 463 breast cancer patients. The score was significantly correlated with liver relapse in hormone receptor positive tumors. In conclusion, the expression of PTP4A3 and JPH1 correlates with risk of liver metastasis in colorectal cancer and breast cancer. The underlying biological mechanism is an interesting area for further research.
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Affiliation(s)
- Petros Tsantoulis
- Hôpitaux Universitaires de Genève, Service d'Oncologie, Geneva, Switzerland. .,University of Geneva, Geneva, Switzerland. .,SIB Swiss Institute of Bioinformatics, Bioinformatics Core Facility, Lausanne, Switzerland.
| | - Mauro Delorenzi
- SIB Swiss Institute of Bioinformatics, Bioinformatics Core Facility, Lausanne, Switzerland.,University Lausanne, Department of Fundamental Oncology, Lausanne, Switzerland.,Ludwig Institute for Cancer Research, Epalinges, Switzerland
| | - Ivan Bièche
- Institut Curie, Département de génétique, Paris, France
| | - Sophie Vacher
- Institut Curie, Département de génétique, Paris, France
| | | | | | - Alexandre Houy
- Institut Curie, Département de génétique, Paris, France.,Institut Curie, PSL Research University, INSERM U830, Paris, France
| | - Marc-Henri Stern
- Institut Curie, Département de génétique, Paris, France.,Institut Curie, PSL Research University, INSERM U830, Paris, France
| | - Sergio Roman-Roman
- Institut Curie, PSL Research University, Translational Research Department, Paris, France
| | - Pierre-Yves Dietrich
- Hôpitaux Universitaires de Genève, Service d'Oncologie, Geneva, Switzerland.,University of Geneva, Geneva, Switzerland
| | - Arnaud Roth
- Hôpitaux Universitaires de Genève, Service d'Oncologie, Geneva, Switzerland.,University of Geneva, Geneva, Switzerland
| | - Wulfran Cacheux
- Hôpitaux Universitaires de Genève, Service d'Oncologie, Geneva, Switzerland.,Institut Curie, Département de génétique, Paris, France.,Hôpital Privé - Pays de Savoie, Oncology department, Annemasse, France
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Rodrigues M, Mobuchon L, Houy A, Alsafadi S, Gardrat S, Piperno-Neumann S, Cassoux N, Pierron G, Roman-Roman S, Mariani P, Stern MH. Abstract 2895: MBD4 inactivation results in an alternative evolutionary route in uveal melanoma. Cancer Res 2019. [DOI: 10.1158/1538-7445.am2019-2895] [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] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Introduction
Uveal melanomas (UM) are chemoresistant tumors that carry few copy number variations (CNV) and a low mutation burden. Genomics of UM metastases have been scarcely described. We assessed genetic heterogeneity in UM at primary and metastatic stages, in order to evaluate if tumor heterogeneity may explain this chemoresistance.
Methods
Whole-exome sequencing of primary and metastatic UM tumors.
Results
We obtained 97 tumor samples from 26 patients (16 samples from 15 primary tumors and 81 samples from 50 metastases). MBD4 was inactivated in two cases (MBD4-deficient; MBD4def). All samples presented high variant allelic frequencies of UM driver mutations (Gαq pathway mutations, BAP1, SF3B1 and EIF1AX). Indeed, mutational statuses of these genes were identical between primary tumors and metastases, except for one MBD4def case that carried both SF3B1 and BAP1 mutations in the primary tumor, while the metastasis only carried a different BAP1 mutation. MBD4-proficient (MBD4pro) primary tumors presented a median of 11.5 single nucleotide variants (SNV; range 5-22); while MBD4pro metastases carried a median of 14 SNV (range 6-23) with a very high genetic homogeneity between samples. No mutation was recurrently acquired during the metastatic process. Metastases presented a higher number of copy number variations (CNV; median = 11; range 2-25) than matched primary (median = 5; range 2-18). Metastases-associated CNV were similar to that usually associated with UM primary tumors, including 8q gain, 1p loss, 1q gain, 6q loss and isodisomy 3. MBD4def samples were hypermutated with at least 266 mutations/sample (>20-fold increase compared to MBD4pro) with >70% of CpG>TpG. MBD4def cases presented a higher heterogeneity with less than 60% of common SNV concordance between tumors in a given patient. No major difference in CNV profiles was observed between MBD4def and MBD4pro samples.
Conclusion
MBD4pro are homogeneous diseases that evolve as metastases with few non-recurrent SNV and recurrent UM-typical CNV. These characteristics lead to simple evolutionary trees with a limited number of short clades and branches, supporting a punctuated evolutionary process. Genetic heterogeneity thus cannot explain the resistance to chemotherapy. In contrast, MBD4 inactivation in UM results in genetic heterogeneity, subclonality and risk of secondary resistance to anticancer drugs.
Citation Format: Manuel Rodrigues, Lenha Mobuchon, Alexandre Houy, Samar Alsafadi, Sophie Gardrat, Sophie Piperno-Neumann, Nathalie Cassoux, Gaelle Pierron, Sergio Roman-Roman, Pascale Mariani, Marc-Henri Stern. MBD4 inactivation results in an alternative evolutionary route in uveal melanoma [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 2895.
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Rodrigues M, Mobuchon L, Houy A, Alsafadi S, Baulande S, Mariani O, Marande B, Ait Rais K, Van der Kooij MK, Kapiteijn E, Gassama S, Gardrat S, Barnhill RL, Servois V, Dendale R, Putterman M, Tick S, Piperno-Neumann S, Cassoux N, Pierron G, Waterfall JJ, Roman-Roman S, Mariani P, Stern MH. Evolutionary Routes in Metastatic Uveal Melanomas Depend on MBD4 Alterations. Clin Cancer Res 2019; 25:5513-5524. [DOI: 10.1158/1078-0432.ccr-19-1215] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2019] [Revised: 05/29/2019] [Accepted: 06/18/2019] [Indexed: 11/16/2022]
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Rodrigues M, Mobuchon L, Houy A, Derrien AC, Fiévet A, Stern MH. [Role of MBD4 in hypermutator phenotype and malignant transformation]. Med Sci (Paris) 2018; 34:925-927. [PMID: 30526825 DOI: 10.1051/medsci/2018226] [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: 11/14/2022] Open
Affiliation(s)
- Manuel Rodrigues
- Institut Curie, Université de recherche PSL, Inserm U830, DNA repair and uveal melanoma (D.R.U.M.), Équipe labellisée par la Ligue nationale contre le cancer, Paris, 75248, France - Département d'oncologie médicale, Institut Curie, Université de recherche PSL, Paris, 75248, France
| | - Lenha Mobuchon
- Institut Curie, Université de recherche PSL, Inserm U830, DNA repair and uveal melanoma (D.R.U.M.), Équipe labellisée par la Ligue nationale contre le cancer, Paris, 75248, France
| | - Alexandre Houy
- Institut Curie, Université de recherche PSL, Inserm U830, DNA repair and uveal melanoma (D.R.U.M.), Équipe labellisée par la Ligue nationale contre le cancer, Paris, 75248, France
| | - Anne-Céline Derrien
- Institut Curie, Université de recherche PSL, Inserm U830, DNA repair and uveal melanoma (D.R.U.M.), Équipe labellisée par la Ligue nationale contre le cancer, Paris, 75248, France
| | - Alice Fiévet
- Département de génétique, Institut Curie, Université de recherche PSL, Paris, 75248, France
| | - Marc-Henri Stern
- Institut Curie, Université de recherche PSL, Inserm U830, DNA repair and uveal melanoma (D.R.U.M.), Équipe labellisée par la Ligue nationale contre le cancer, Paris, 75248, France - Département de génétique, Institut Curie, Université de recherche PSL, Paris, 75248, France
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Rodrigues M, Mobuchon L, Houy A, Derrien AC, Stern MH. L’inactivation de MBD4, un nouveau phénotype hypermutateur en oncologie. Bull Cancer 2018; 105:736-737. [DOI: 10.1016/j.bulcan.2018.06.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2018] [Accepted: 06/20/2018] [Indexed: 10/28/2022]
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Decraene C, Silveira AB, Bidard FC, Vallée A, Michel M, Melaabi S, Vincent-Salomon A, Saliou A, Houy A, Milder M, Lantz O, Ychou M, Denis MG, Pierga JY, Stern MH, Proudhon C. Multiple Hotspot Mutations Scanning by Single Droplet Digital PCR. Clin Chem 2018; 64:317-328. [DOI: 10.1373/clinchem.2017.272518] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2017] [Accepted: 10/10/2017] [Indexed: 11/06/2022]
Abstract
Abstract
BACKGROUND
Progress in the liquid biopsy field, combined with the development of droplet digital PCR (ddPCR), has enabled noninvasive monitoring of mutations with high detection accuracy. However, current assays detect a restricted number of mutations per reaction. ddPCR is a recognized method for detecting alterations previously characterized in tumor tissues, but its use as a discovery tool when the mutation is unknown a priori remains limited.
METHODS
We established 2 ddPCR assays detecting all genomic alterations within KRAS exon 2 and EGFR exon 19 mutation hotspots, which are of clinical importance in colorectal and lung cancer, with use of a unique pair of TaqMan® oligoprobes. The KRAS assay scanned for the 7 most common mutations in codons 12/13 but also all other mutations found in that region. The EGFR assay screened for all in-frame deletions of exon 19, which are frequent EGFR-activating events.
RESULTS
The KRAS and EGFR assays were highly specific and both reached a limit of detection of <0.1% in mutant allele frequency. We further validated their performance on multiple plasma and formalin-fixed and paraffin-embedded tumor samples harboring a panel of different KRAS or EGFR mutations.
CONCLUSIONS
This method presents the advantage of detecting a higher number of mutations with single-reaction ddPCRs while consuming a minimum of patient sample. This is particularly useful in the context of liquid biopsy because the amount of circulating tumor DNA is often low. This method should be useful as a discovery tool when the tumor tissue is unavailable or to monitor disease during therapy.
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Affiliation(s)
- Charles Decraene
- Circulating Tumor Biomarkers Laboratory, SiRIC, Translational Research Department, Institut Curie, PSL Research University, Paris, France
- CNRS UMR144, Institut Curie, PSL Research University, Paris, France
| | - Amanda B Silveira
- Circulating Tumor Biomarkers Laboratory, SiRIC, Translational Research Department, Institut Curie, PSL Research University, Paris, France
| | - François-Clément Bidard
- Circulating Tumor Biomarkers Laboratory, SiRIC, Translational Research Department, Institut Curie, PSL Research University, Paris, France
- Department of Medical Oncology, Institut Curie, PSL Research University, Paris, France
| | - Audrey Vallée
- Department of Biochemistry and INSERM U1232, Nantes University Hospital, Nantes, France
| | - Marc Michel
- Circulating Tumor Biomarkers Laboratory, SiRIC, Translational Research Department, Institut Curie, PSL Research University, Paris, France
| | - Samia Melaabi
- Department of Biopathology, Institut Curie, PSL Research University, Paris, France
| | - Anne Vincent-Salomon
- Department of Biopathology, Institut Curie, PSL Research University, Paris, France
- Inserm U934, Institut Curie, PSL Research University, Paris, France
| | - Adrien Saliou
- Circulating Tumor Biomarkers Laboratory, SiRIC, Translational Research Department, Institut Curie, PSL Research University, Paris, France
| | - Alexandre Houy
- Circulating Tumor Biomarkers Laboratory, SiRIC, Translational Research Department, Institut Curie, PSL Research University, Paris, France
- Inserm U830, Institut Curie, PSL Research University, Paris, France
| | - Maud Milder
- Circulating Tumor Biomarkers Laboratory, SiRIC, Translational Research Department, Institut Curie, PSL Research University, Paris, France
- Inserm CIC BT 1418, Institut Curie, PSL Research University, Paris, France
| | - Olivier Lantz
- Circulating Tumor Biomarkers Laboratory, SiRIC, Translational Research Department, Institut Curie, PSL Research University, Paris, France
- Inserm CIC BT 1418, Institut Curie, PSL Research University, Paris, France
- Inserm U932, Institut Curie, PSL Research University, Paris, France
| | - Marc Ychou
- Department of Medical Oncology, Montpellier Cancer Institute, Montpellier, France
| | - Marc G Denis
- Department of Biochemistry and INSERM U1232, Nantes University Hospital, Nantes, France
| | - Jean-Yves Pierga
- Circulating Tumor Biomarkers Laboratory, SiRIC, Translational Research Department, Institut Curie, PSL Research University, Paris, France
- Department of Medical Oncology, Institut Curie, PSL Research University, Paris, France
- University Paris Descartes, Paris, France
| | - Marc-Henri Stern
- Circulating Tumor Biomarkers Laboratory, SiRIC, Translational Research Department, Institut Curie, PSL Research University, Paris, France
- Inserm U830, Institut Curie, PSL Research University, Paris, France
| | - Charlotte Proudhon
- Circulating Tumor Biomarkers Laboratory, SiRIC, Translational Research Department, Institut Curie, PSL Research University, Paris, France
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Mobuchon L, Battistella A, Bardel C, Scelo G, Renoud A, Houy A, Cassoux N, Milder M, Cancel-Tassin G, Cussenot O, Delattre O, Besse C, Boland A, Deleuze JF, Cox DG, Stern MH. A GWAS in uveal melanoma identifies risk polymorphisms in the CLPTM1L locus. NPJ Genom Med 2017; 2:5. [PMID: 28781888 PMCID: PMC5542017 DOI: 10.1038/s41525-017-0008-5] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2016] [Revised: 01/31/2017] [Accepted: 02/01/2017] [Indexed: 02/03/2023] Open
Abstract
Uveal melanoma, a rare malignant tumor of the eye, is predominantly observed in populations of European ancestry. A genome-wide association study of 259 uveal melanoma patients compared to 401 controls all of European ancestry revealed a candidate locus at chromosome 5p15.33 (region rs421284: OR = 1.7, CI 1.43-2.05). This locus was replicated in an independent set of 276 cases and 184 controls. In addition, risk variants from this region were positively associated with higher expression of CLPTM1L. In conclusion, the CLPTM1L region contains risk alleles for uveal melanoma susceptibility, suggesting that CLPTM1L could play a role in uveal melanoma oncogenesis.
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Affiliation(s)
- Lenha Mobuchon
- Inserm U830 and Ensemble Hospitalier, PSL Research University, Institut Curie, Paris, France
| | - Aude Battistella
- Inserm U830 and Ensemble Hospitalier, PSL Research University, Institut Curie, Paris, France
| | - Claire Bardel
- UMR5558, Laboratoire de Biométrie et Biologie Evolutive, Equipe Biostatistique-Santé, Université Claude Bernard-Lyon 1, Lyon, France
- Service de Biostatistique-bioinformatique, Hospices Civils de Lyon, Lyon, France
| | - Ghislaine Scelo
- International Agency for Research on Cancer (IARC), Lyon, France
| | - Alexia Renoud
- INSERM U1052, CNRS UMR5286, Université Lyon 1, Centre de Recherche en Cancérologie de Lyon, Lyon, France
| | - Alexandre Houy
- Inserm U830 and Ensemble Hospitalier, PSL Research University, Institut Curie, Paris, France
| | - Nathalie Cassoux
- Inserm U830 and Ensemble Hospitalier, PSL Research University, Institut Curie, Paris, France
| | - Maud Milder
- Inserm U830 and Ensemble Hospitalier, PSL Research University, Institut Curie, Paris, France
| | | | - Olivier Cussenot
- UPMC University Paris 06 GRC n°5, CeRePP, Hôpital Tenon, Paris, France
| | - Olivier Delattre
- Inserm U830 and Ensemble Hospitalier, PSL Research University, Institut Curie, Paris, France
| | - Céline Besse
- Centre National de Génotypage, Institut de Génomique, CEA, Evry, France
| | - Anne Boland
- Centre National de Génotypage, Institut de Génomique, CEA, Evry, France
| | | | - David G. Cox
- INSERM U1052, CNRS UMR5286, Université Lyon 1, Centre de Recherche en Cancérologie de Lyon, Lyon, France
| | - Marc-Henri Stern
- Inserm U830 and Ensemble Hospitalier, PSL Research University, Institut Curie, Paris, France
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Riva F, Bidard FC, Houy A, Saliou A, Madic J, Rampanou A, Hego C, Milder M, Cottu P, Sablin MP, Vincent-Salomon A, Lantz O, Stern MH, Proudhon C, Pierga JY. Patient-Specific Circulating Tumor DNA Detection during Neoadjuvant Chemotherapy in Triple-Negative Breast Cancer. Clin Chem 2017; 63:691-699. [DOI: 10.1373/clinchem.2016.262337] [Citation(s) in RCA: 111] [Impact Index Per Article: 15.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2016] [Accepted: 10/20/2016] [Indexed: 12/29/2022]
Abstract
Abstract
BACKGROUND
In nonmetastatic triple-negative breast cancer (TNBC) patients, we investigated whether circulating tumor DNA (ctDNA) detection can reflect the tumor response to neoadjuvant chemotherapy (NCT) and detect minimal residual disease after surgery.
METHODS
Ten milliliters of plasma were collected at 4 time points: before NCT; after 1 cycle; before surgery; after surgery. Customized droplet digital PCR (ddPCR) assays were used to track tumor protein p53 (TP53) mutations previously characterized in tumor tissue by massively parallel sequencing (MPS).
RESULTS
Forty-six patients with nonmetastatic TNBC were enrolled. TP53 mutations were identified in 40 of them. Customized ddPCR probes were validated for 38 patients, with excellent correlation with MPS (r = 0.99), specificity (≥2 droplets/assay), and sensitivity (at least 0.1%). At baseline, ctDNA was detected in 27/36 patients (75%). Its detection was associated with mitotic index (P = 0.003), tumor grade (P = 0.003), and stage (P = 0.03). During treatment, we observed a drop of ctDNA levels in all patients but 1. No patient had detectable ctDNA after surgery. The patient with rising ctDNA levels experienced tumor progression during NCT. Pathological complete response (16/38 patients) was not correlated with ctDNA detection at any time point. ctDNA positivity after 1 cycle of NCT was correlated with shorter disease-free (P < 0.001) and overall (P = 0.006) survival.
CONCLUSIONS
Customized ctDNA detection by ddPCR achieved a 75% detection rate at baseline. During NCT, ctDNA levels decreased quickly and minimal residual disease was not detected after surgery. However, a slow decrease of ctDNA level during NCT was strongly associated with shorter survival.
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Affiliation(s)
- Francesca Riva
- Laboratory of Circulating Tumor Biomarkers, Institut Curie, PSL Research University, SiRIC, Paris, France
- Department of Medical Oncology, San Gerardo Hospital, Monza, Italy
| | - Francois-Clement Bidard
- Laboratory of Circulating Tumor Biomarkers, Institut Curie, PSL Research University, SiRIC, Paris, France
- Department of Medical Oncology, Institut Curie, PSL Research University, Paris, France
| | - Alexandre Houy
- INSERM U830, Institut Curie, PSL Research University, Paris, France
| | - Adrien Saliou
- Laboratory of Circulating Tumor Biomarkers, Institut Curie, PSL Research University, SiRIC, Paris, France
| | - Jordan Madic
- Laboratory of Circulating Tumor Biomarkers, Institut Curie, PSL Research University, SiRIC, Paris, France
| | - Aurore Rampanou
- Laboratory of Circulating Tumor Biomarkers, Institut Curie, PSL Research University, SiRIC, Paris, France
- INSERM CIC-BT 1428, Institut Curie, PSL Research University, Paris, France
| | - Caroline Hego
- Laboratory of Circulating Tumor Biomarkers, Institut Curie, PSL Research University, SiRIC, Paris, France
| | - Maud Milder
- Laboratory of Circulating Tumor Biomarkers, Institut Curie, PSL Research University, SiRIC, Paris, France
- INSERM CIC-BT 1428, Institut Curie, PSL Research University, Paris, France
| | - Paul Cottu
- Department of Medical Oncology, Institut Curie, PSL Research University, Paris, France
| | - Marie-Paule Sablin
- Department of Medical Oncology, Institut Curie, PSL Research University, Paris, France
| | - Anne Vincent-Salomon
- Department of Biopathology, Institut Curie, PSL Research University, Paris, France
| | - Olivier Lantz
- INSERM CIC-BT 1428, Institut Curie, PSL Research University, Paris, France
- Department of Biopathology, Institut Curie, PSL Research University, Paris, France
- Department of Tumor Biology, Institut Curie, PSL Research University, Paris, France
- INSERM U932, Institut Curie, PSL Research University, Paris, France
| | - Marc-Henri Stern
- INSERM U830, Institut Curie, PSL Research University, Paris, France
| | - Charlotte Proudhon
- Laboratory of Circulating Tumor Biomarkers, Institut Curie, PSL Research University, SiRIC, Paris, France
| | - Jean-Yves Pierga
- Laboratory of Circulating Tumor Biomarkers, Institut Curie, PSL Research University, SiRIC, Paris, France
- Department of Medical Oncology, Institut Curie, PSL Research University, Paris, France
- Université Paris Descartes, Sorbonne Paris Cité, Paris, France
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Pierga JY, Riva F, Houy A, Saliou A, Madic J, Rampanou A, Hego C, Milder M, Cottu P, Sablin MP, Vincent-Salomon A, Lantz O, Stern MH, Proudhon C, Bidard FC. Patient-specific circulating tumor DNA detection during neoadjuvant chemotherapy in triple negative breast cancer. Ann Oncol 2016. [DOI: 10.1093/annonc/mdw365.34] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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Decraene C, Bidard FC, Belaabi S, Rouleau E, Saliou A, Houy A, Milder M, Lantz O, Ychou M, Pierga JY, Stern MH, Proudhon C. Abstract 410: Exhaustive scanning of mutation hotspot regions using a new tool: The MHS-ddPCR. Cancer Res 2016. [DOI: 10.1158/1538-7445.am2016-410] [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] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Background: Recent progress in the ‘liquid biopsy’ field in combination with the development of the droplet digital PCR (ddPCR) technology now enables non-invasive monitoring of cancer-related genomic alterations with high detection accuracy. Current ddPCR techniques represent the gold standard for the detection of point mutations that have been previously characterized on tumor tissues. However, ddPCR screen for only one mutation (or a few mutations, with multicolor ddPCR) per reaction. This is a clear limitation to use it as a discovery tool, to detect resistance-associated mutations that may appear during therapy (e.g. ESR1 activating mutations in breast cancer) or when tumor tissue is not available (e.g. EGFR activating mutations in lung cancers).
Methods:
We developed the Multiple Hotspot mutations detection by Single droplet digital PCR (MHS-ddPCR) method, a variant of the conventional ddPCR technique, which detects all genomic alterations within a hotspot region, using a unique couple of Taqman oligo-probes. We first established two specific assays covering KRAS and EGFR mutation hotspot regions, which are of clinical importance in the context of colorectal cancer. The assay for KRAS scans for the 7 most common mutations in codons 12 and 13 of the gene as well as all other mutations with lower frequency (<1%). The EGFR assay screens for all in-frame deletions of exon 19, which are frequent activating events in EGFR.
Results:
Sensitivity and specificity of MHS-ddPCR were assessed on decreasing fractions of tumor DNA mutated for KRAS. The KRAS assay reaches a sensitivity of 0.02% and was validated on plasma and tumor samples harboring a panel of different KRAS mutations. Similarly, the EGFR assay can detect numerous exon 19 deletions from patient samples and with limited amounts of tumor DNA.
Conclusions:
The MHS-ddPCR is extremely sensitive, works for numerous hotspot regions with different types of alterations (SNV, deletion) and is cost-effective as it combines multiple assays in one reaction.
Citation Format: Charles Decraene, Francois-Clement Bidard, Samia Belaabi, Etienne Rouleau, Adrien Saliou, Alexandre Houy, Maud Milder, Olivier Lantz, Marc Ychou, Jean-Yves Pierga, Marc-Henri Stern, Charlotte Proudhon. Exhaustive scanning of mutation hotspot regions using a new tool: The MHS-ddPCR. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 410.
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Affiliation(s)
| | | | | | | | | | | | | | | | - Marc Ychou
- 2Institut de Cancerologie de Montpellier, Montpellier, France
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Alsafadi S, Houy A, Battistella A, Popova T, Wassef M, Henry E, Tirode F, Constantinou A, Piperno-Neumann S, Roman-Roman S, Dutertre M, Stern M. Cancer-associated SF3B1 mutations affect alternative splicing by promoting alternative branchpoint usage. Eur J Cancer 2016. [DOI: 10.1016/s0959-8049(16)61332-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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Alsafadi S, Houy A, Battistella A, Popova T, Wassef M, Henry E, Tirode F, Constantinou A, Piperno-Neumann S, Roman-Roman S, Dutertre M, Stern MH. Cancer-associated SF3B1 mutations affect alternative splicing by promoting alternative branchpoint usage. Nat Commun 2016; 7:10615. [PMID: 26842708 DOI: 10.1038/ncomms10615] [Citation(s) in RCA: 266] [Impact Index Per Article: 33.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2015] [Accepted: 01/05/2016] [Indexed: 12/20/2022] Open
Abstract
Hotspot mutations in the spliceosome gene SF3B1 are reported in ∼20% of uveal melanomas. SF3B1 is involved in 3'-splice site (3'ss) recognition during RNA splicing; however, the molecular mechanisms of its mutation have remained unclear. Here we show, using RNA-Seq analyses of uveal melanoma, that the SF3B1(R625/K666) mutation results in deregulated splicing at a subset of junctions, mostly by the use of alternative 3'ss. Modelling the differential junctions in SF3B1(WT) and SF3B1(R625/K666) cell lines demonstrates that the deregulated splice pattern strictly depends on SF3B1 status and on the 3'ss-sequence context. SF3B1(WT) knockdown or overexpression do not reproduce the SF3B1(R625/K666) splice pattern, qualifying SF3B1(R625/K666) as change-of-function mutants. Mutagenesis of predicted branchpoints reveals that the SF3B1(R625/K666)-promoted splice pattern is a direct result of alternative branchpoint usage. Altogether, this study provides a better understanding of the mechanisms underlying splicing alterations induced by mutant SF3B1 in cancer, and reveals a role for alternative branchpoints in disease.
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Affiliation(s)
- Samar Alsafadi
- Department of Genetics and Biology of Cancers, INSERM U830, Institut Curie, PSL Research University, Paris 75248, France
| | - Alexandre Houy
- Department of Genetics and Biology of Cancers, INSERM U830, Institut Curie, PSL Research University, Paris 75248, France
| | - Aude Battistella
- Department of Genetics and Biology of Cancers, INSERM U830, Institut Curie, PSL Research University, Paris 75248, France
| | - Tatiana Popova
- Department of Genetics and Biology of Cancers, INSERM U830, Institut Curie, PSL Research University, Paris 75248, France
| | - Michel Wassef
- Depatment of Developmental Biology and Genetics, CNRS UMR 3215/INSERM U934, Institut Curie, PSL Research University, Paris 75248, France
| | - Emilie Henry
- Translational Research Department, Institut Curie, PSL Research University, Paris 75248, France
| | - Franck Tirode
- Department of Genetics and Biology of Cancers, INSERM U830, Institut Curie, PSL Research University, Paris 75248, France
| | - Angelos Constantinou
- Department of Molecular Bases of Human Diseases, CNRS UPR 1142, IGH-Institute of Human Genetics, Montpellier 34090, France
| | | | - Sergio Roman-Roman
- Translational Research Department, Institut Curie, PSL Research University, Paris 75248, France
| | - Martin Dutertre
- Department of Genotoxic stress and Cancer, CNRS UMR 3348, Institut Curie, PSL Research University, Orsay 91400, France
| | - Marc-Henri Stern
- Department of Genetics and Biology of Cancers, INSERM U830, Institut Curie, PSL Research University, Paris 75248, France
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