Michäel Duruisseaux1, Anna Martínez-Cardús2, Maria E Calleja-Cervantes2, Sebastian Moran2, Manuel Castro de Moura2, Veronica Davalos2, David Piñeyro2, Montse Sanchez-Cespedes2, Nicolas Girard3, Marie Brevet4, Etienne Giroux-Leprieur5, Coraline Dumenil6, Monica Pradotto7, Paolo Bironzo7, Enrica Capelletto7, Silvia Novello7, Alexis Cortot8, Marie-Christine Copin9, Niki Karachaliou10, Maria Gonzalez-Cao11, Sergio Peralta12, Luis M Montuenga13, Ignacio Gil-Bazo14, Iosune Baraibar15, Maria D Lozano16, Mar Varela17, Jose C Ruffinelli18, Ramon Palmero18, Ernest Nadal18, Teresa Moran19, Lidia Perez20, Immaculada Ramos21, Qingyang Xiao22, Agustin F Fernandez23, Mario F Fraga24, Marta Gut25, Ivo Gut25, Cristina Teixidó26, Noelia Vilariño27, Aleix Prat27, Noemi Reguart27, Amparo Benito28, Pilar Garrido29, Isabel Barragan30, Jean-François Emile31, Rafael Rosell32, Elisabeth Brambilla33, Manel Esteller34. 1. Cancer Epigenetics and Biology Program, Bellvitge Biomedical Research Institute, Barcelona, Spain; Department of Respiratory Medicine, Groupement Hospitalier Est, Hôpital Louis-Pradel, Hospices Civils de Lyon, Lyon, France. 2. Cancer Epigenetics and Biology Program, Bellvitge Biomedical Research Institute, Barcelona, Spain. 3. Department of Respiratory Medicine, Groupement Hospitalier Est, Hôpital Louis-Pradel, Hospices Civils de Lyon, Lyon, France. 4. Department of Pathology, Centre de biologie et pathologie Est, Institut de Cancérologie des Hospices Civils de Lyon, Université Lyon 1, Lyon, France. 5. Department of Respiratory Diseases and Thoracic Oncology, APHP-Hôpital Ambroise Pare, Boulogne-Billancourt, France; EA4340, UVSQ, University Paris-Saclay, Boulogne-Billancourt, France. 6. Department of Respiratory Diseases and Thoracic Oncology, APHP-Hôpital Ambroise Pare, Boulogne-Billancourt, France. 7. Department of Oncology, University of Turin, AOU San Luigi, Turin, Italy. 8. Thoracic Oncology Department, CHU Lille, University of Lille, Lille, France; UMR 8161-M3T-Mechanisms of Tumorigenesis and Targeted Therapies, CNRS, Institut Pasteur de Lille, University of Lille, Lille, France. 9. Department of Pathology, CHU Lille, University of Lille, Lille, France. 10. Medical Oncology Service, Institute of Oncology Rosell, University Hospital Sagrat Cor, QuironSalud Group, Barcelona, Spain. 11. Medical Oncology Service, Quirón Dexeus University Hospital, Barcelona, Catalonia, Spain. 12. Medical Oncology Service, University Hospital Sant Joan de Reus, Reus, Spain. 13. Program in Solid Tumors and Biomarkers, Center for Applied Medical Research, Pamplona, Spain; Navarra Health Research Institute, Pamplona, Spain; Centro de Investigación Biomédica en Red de Cancer, Madrid, Spain. 14. Department of Oncology, Clínica Universidad de Navarra, Pamplona, Spain; Navarra Health Research Institute, Pamplona, Spain; Centro de Investigación Biomédica en Red de Cancer, Madrid, Spain. 15. Department of Oncology, Clínica Universidad de Navarra, Pamplona, Spain; Navarra Health Research Institute, Pamplona, Spain. 16. Department of Pathology, Clínica Universidad de Navarra, Pamplona, Spain; Navarra Health Research Institute, Pamplona, Spain; Centro de Investigación Biomédica en Red de Cancer, Madrid, Spain. 17. Pathology Department, University Hospital Bellvitge, Barcelona, Spain. 18. Medical Oncology Department, Catalan Institute of Oncology, Hospital Duran I Reynals, Barcelona, Spain. 19. Medical Oncology Department, Catalan Institute of Oncology, Hospital Germans Trias i Pujol, Barcelona, Spain. 20. Department of Pathology, Hospitales Universitarios Regional y Virgen de la Victoria, Institute of Biomedical Research in Malaga, University of Málaga, Málaga, Spain. 21. Medical Oncology Service, Hospitales Universitarios Regional y Virgen de la Victoria, Institute of Biomedical Research in Malaga, University of Málaga, Málaga, Spain. 22. Pharmacoepigenetics Group, Department of Physiology and Pharmacology, Karolinska Institutet, Stockholm, Sweden. 23. Cancer Epigenetics Laboratory, Institute of Oncology of Asturias, Hospital Universitario Central de Asturias, Universidad de Oviedo, Oviedo, Spain; Fundación para la Investigación Biosanitaria de Asturias, Instituto de Investigación Sanitaria del Principado de Asturias, Oviedo, Spain. 24. Nanomaterials & Nanotechnology Research Center, Universidad de Oviedo, Oviedo, Spain. 25. CNAG-CRG, Centre for Genomic Regulation, Barcelona Institute of Science and Technology, Barcelona, Spain. 26. Pathology Department, Hospital Clinic, Institut d'Investigacions Biomédiques August Pi i Sunyer, Barcelona, Spain. 27. Medical Oncology Department, Hospital Clinic, Institut d'Investigacions Biomédiques August Pi i Sunyer, Barcelona, Spain. 28. Pathology Department, University Hospital Ramon y Cajal, Madrid, Spain. 29. Medical Oncology Service, University Hospital Ramon y Cajal, Madrid, Spain; Centro de Investigación Biomédica en Red de Cancer, Madrid, Spain. 30. Medical Oncology Service, Hospitales Universitarios Regional y Virgen de la Victoria, Institute of Biomedical Research in Malaga, University of Málaga, Málaga, Spain; Pharmacoepigenetics Group, Department of Physiology and Pharmacology, Karolinska Institutet, Stockholm, Sweden. 31. Department of Pathology Department, APHP-Hôpital Ambroise Pare, Boulogne-Billancourt, France. 32. Catalan Institute of Oncology, Germans Trias i Pujol Health Sciences Institute and Hospital, Barcelona, Spain. 33. Centre Hospitalier Grenoble, INSERM U1219, University UGA, Grenoble, France. 34. Cancer Epigenetics and Biology Program, Bellvitge Biomedical Research Institute, Barcelona, Spain; Centro de Investigación Biomédica en Red de Cancer, Madrid, Spain; Physiological Sciences Department, School of Medicine and Health Sciences, University of Barcelona, Spain; Institucio Catalana de Recerca i Estudis Avançats, Barcelona, Spain. Electronic address: mesteller@idibell.cat.
Abstract
BACKGROUND: Anti-programmed death-1 (PD-1) treatment for advanced non-small-cell lung cancer (NSCLC) has improved the survival of patients. However, a substantial percentage of patients do not respond to this treatment. We examined the use of DNA methylation profiles to determine the efficacy of anti-PD-1 treatment in patients recruited with current stage IV NSCLC. METHODS: In this multicentre study, we recruited adult patients from 15 hospitals in France, Spain, and Italy who had histologically proven stage IV NSCLC and had been exposed to PD-1 blockade during the course of the disease. The study structure comprised a discovery cohort to assess the correlation between epigenetic features and clinical benefit with PD-1 blockade and two validation cohorts to assess the validity of our assumptions. We first established an epigenomic profile based on a microarray DNA methylation signature (EPIMMUNE) in a discovery set of tumour samples from patients treated with nivolumab or pembrolizumab. The EPIMMUNE signature was validated in an independent set of patients. A derived DNA methylation marker was validated by a single-methylation assay in a validation cohort of patients. The main study outcomes were progression-free survival and overall survival. We used the Kaplan-Meier method to estimate progression-free and overall survival, and calculated the differences between the groups with the log-rank test. We constructed a multivariate Cox model to identify the variables independently associated with progression-free and overall survival. FINDINGS: Between June 23, 2014, and May 18, 2017, we obtained samples from 142 patients: 34 in the discovery cohort, 47 in the EPIMMUNE validation cohort, and 61 in the derived methylation marker cohort (the T-cell differentiation factor forkhead box P1 [FOXP1]). The EPIMMUNE signature in patients with stage IV NSCLC treated with anti-PD-1 agents was associated with improved progression-free survival (hazard ratio [HR] 0·010, 95% CI 3·29 × 10-4-0·0282; p=0·0067) and overall survival (0·080, 0·017-0·373; p=0·0012). The EPIMMUNE-positive signature was not associated with PD-L1 expression, the presence of CD8+ cells, or mutational load. EPIMMUNE-negative tumours were enriched in tumour-associated macrophages and neutrophils, cancer-associated fibroblasts, and senescent endothelial cells. The EPIMMUNE-positive signature was associated with improved progression-free survival in the EPIMMUNE validation cohort (0·330, 0·149-0·727; p=0·0064). The unmethylated status of FOXP1 was associated with improved progression-free survival (0·415, 0·209-0·802; p=0·0063) and overall survival (0·409, 0·220-0·780; p=0·0094) in the FOXP1 validation cohort. The EPIMMUNE signature and unmethylated FOXP1 were not associated with clinical benefit in lung tumours that did not receive immunotherapy. INTERPRETATION: Our study shows that the epigenetic milieu of NSCLC tumours indicates which patients are most likely to benefit from nivolumab or pembrolizumab treatments. The methylation status of FOXP1 could be associated with validated predictive biomarkers such as PD-L1 staining and mutational load to better select patients who will experience clinical benefit with PD-1 blockade, and its predictive value should be evaluated in prospective studies. FUNDING: "Obra Social" La Caixa, Cellex Foundation, and the Health and Science Departments of the Generalitat de Catalunya.
BACKGROUND: Anti-programmed death-1 (PD-1) treatment for advanced non-small-cell lung cancer (NSCLC) has improved the survival of patients. However, a substantial percentage of patients do not respond to this treatment. We examined the use of DNA methylation profiles to determine the efficacy of anti-PD-1 treatment in patients recruited with current stage IV NSCLC. METHODS: In this multicentre study, we recruited adult patients from 15 hospitals in France, Spain, and Italy who had histologically proven stage IV NSCLC and had been exposed to PD-1 blockade during the course of the disease. The study structure comprised a discovery cohort to assess the correlation between epigenetic features and clinical benefit with PD-1 blockade and two validation cohorts to assess the validity of our assumptions. We first established an epigenomic profile based on a microarray DNA methylation signature (EPIMMUNE) in a discovery set of tumour samples from patients treated with nivolumab or pembrolizumab. The EPIMMUNE signature was validated in an independent set of patients. A derived DNA methylation marker was validated by a single-methylation assay in a validation cohort of patients. The main study outcomes were progression-free survival and overall survival. We used the Kaplan-Meier method to estimate progression-free and overall survival, and calculated the differences between the groups with the log-rank test. We constructed a multivariate Cox model to identify the variables independently associated with progression-free and overall survival. FINDINGS: Between June 23, 2014, and May 18, 2017, we obtained samples from 142 patients: 34 in the discovery cohort, 47 in the EPIMMUNE validation cohort, and 61 in the derived methylation marker cohort (the T-cell differentiation factor forkhead box P1 [FOXP1]). The EPIMMUNE signature in patients with stage IV NSCLC treated with anti-PD-1 agents was associated with improved progression-free survival (hazard ratio [HR] 0·010, 95% CI 3·29 × 10-4-0·0282; p=0·0067) and overall survival (0·080, 0·017-0·373; p=0·0012). The EPIMMUNE-positive signature was not associated with PD-L1 expression, the presence of CD8+ cells, or mutational load. EPIMMUNE-negative tumours were enriched in tumour-associated macrophages and neutrophils, cancer-associated fibroblasts, and senescent endothelial cells. The EPIMMUNE-positive signature was associated with improved progression-free survival in the EPIMMUNE validation cohort (0·330, 0·149-0·727; p=0·0064). The unmethylated status of FOXP1 was associated with improved progression-free survival (0·415, 0·209-0·802; p=0·0063) and overall survival (0·409, 0·220-0·780; p=0·0094) in the FOXP1 validation cohort. The EPIMMUNE signature and unmethylated FOXP1 were not associated with clinical benefit in lung tumours that did not receive immunotherapy. INTERPRETATION: Our study shows that the epigenetic milieu of NSCLC tumours indicates which patients are most likely to benefit from nivolumab or pembrolizumab treatments. The methylation status of FOXP1 could be associated with validated predictive biomarkers such as PD-L1 staining and mutational load to better select patients who will experience clinical benefit with PD-1 blockade, and its predictive value should be evaluated in prospective studies. FUNDING: "Obra Social" La Caixa, Cellex Foundation, and the Health and Science Departments of the Generalitat de Catalunya.
Authors: Siwen Hu-Lieskovan; Srabani Bhaumik; Kavita Dhodapkar; Jean-Charles J B Grivel; Sumati Gupta; Brent A Hanks; Sylvia Janetzki; Thomas O Kleen; Yoshinobu Koguchi; Amanda W Lund; Cristina Maccalli; Yolanda D Mahnke; Ruslan D Novosiadly; Senthamil R Selvan; Tasha Sims; Yingdong Zhao; Holden T Maecker Journal: J Immunother Cancer Date: 2020-12 Impact factor: 13.751
Authors: Maria Gonzalez-Cao; Santiago Viteri; Niki Karachaliou; Andres Aguilar; Juan Jose García-Mosquera; Rafael Rosell Journal: Transl Lung Cancer Res Date: 2018-12
Authors: Aimee Merino; Bin Zhang; Philip Dougherty; Xianghua Luo; Jinhua Wang; Bruce R Blazar; Jeffrey S Miller; Frank Cichocki Journal: J Clin Invest Date: 2019-06-18 Impact factor: 14.808